On the distribution of interspecies correlation for Markov models of character evolution on Yule trees.

PubMed

Mulder, Willem H; Crawford, Forrest W

2015-01-07

Efforts to reconstruct phylogenetic trees and understand evolutionary processes depend fundamentally on stochastic models of speciation and mutation. The simplest continuous-time model for speciation in phylogenetic trees is the Yule process, in which new species are "born" from existing lineages at a constant rate. Recent work has illuminated some of the structural properties of Yule trees, but it remains mostly unknown how these properties affect sequence and trait patterns observed at the tips of the phylogenetic tree. Understanding the interplay between speciation and mutation under simple models of evolution is essential for deriving valid phylogenetic inference methods and gives insight into the optimal design of phylogenetic studies. In this work, we derive the probability distribution of interspecies covariance under Brownian motion and Ornstein-Uhlenbeck models of phenotypic change on a Yule tree. We compute the probability distribution of the number of mutations shared between two randomly chosen taxa in a Yule tree under discrete Markov mutation models. Our results suggest summary measures of phylogenetic information content, illuminate the correlation between site patterns in sequences or traits of related organisms, and provide heuristics for experimental design and reconstruction of phylogenetic trees. Copyright © 2014 Elsevier Ltd. All rights reserved.

TreeWatch.net: A Water and Carbon Monitoring and Modeling Network to Assess Instant Tree Hydraulics and Carbon Status.

PubMed

Steppe, Kathy; von der Crone, Jonas S; De Pauw, Dirk J W

2016-01-01

TreeWatch.net is an initiative that has been developed to watch trees grow and function in real-time. It is a water- and carbon-monitoring and modeling network, in which high-quality measurements of sap flow and stem diameter variation are collected on individual trees. Automated data processing using a cloud service enables instant visualization of water movement and radial stem growth. This can be used to demonstrate the sensitivity of trees to changing weather conditions, such as drought, heat waves, or heavy rain showers. But TreeWatch.net's true innovation lies in its use of these high-precision harmonized data to also parameterize process-based tree models in real-time, which makes displaying the much-needed mechanisms underlying tree responses to climate change possible. Continuous simulation of turgor to describe growth processes and long-term time series of hydraulic resistance to assess drought-vulnerability in real-time are only a few of the opportunities our approach offers. TreeWatch.net has been developed with the view to be complementary to existing forest monitoring networks and with the aim to contribute to existing dynamic global vegetation models. It provides high-quality data and real-time simulations in order to advance research on the impact of climate change on the biological response of trees and forests. Besides its application in natural forests to answer climate-change related scientific and political questions, we also envision a broader societal application of TreeWatch.net by selecting trees in nature reserves, public areas, cities, university areas, schoolyards, and parks to teach youngsters and create public awareness on the effects of changing weather conditions on trees and forests in this era of climate change.

Growth-Mortality Relationships in Piñon Pine (Pinus edulis) during Severe Droughts of the Past Century: Shifting Processes in Space and Time

PubMed Central

Macalady, Alison K.; Bugmann, Harald

2014-01-01

The processes leading to drought-associated tree mortality are poorly understood, particularly long-term predisposing factors, memory effects, and variability in mortality processes and thresholds in space and time. We use tree rings from four sites to investigate Pinus edulis mortality during two drought periods in the southwestern USA. We draw on recent sampling and archived collections to (1) analyze P. edulis growth patterns and mortality during the 1950s and 2000s droughts; (2) determine the influence of climate and competition on growth in trees that died and survived; and (3) derive regression models of growth-mortality risk and evaluate their performance across space and time. Recent growth was 53% higher in surviving vs. dying trees, with some sites exhibiting decades-long growth divergences associated with previous drought. Differential growth response to climate partly explained growth differences between live and dead trees, with responses wet/cool conditions most influencing eventual tree status. Competition constrained tree growth, and reduced trees’ ability to respond to favorable climate. The best predictors in growth-mortality models included long-term (15–30 year) average growth rate combined with a metric of growth variability and the number of abrupt growth increases over 15 and 10 years, respectively. The most parsimonious models had high discriminatory power (ROC>0.84) and correctly classified ∼70% of trees, suggesting that aspects of tree growth, especially over decades, can be powerful predictors of widespread drought-associated die-off. However, model discrimination varied across sites and drought events. Weaker growth-mortality relationships and higher growth at lower survival probabilities for some sites during the 2000s event suggest a shift in mortality processes from longer-term growth-related constraints to shorter-term processes, such as rapid metabolic decline even in vigorous trees due to acute drought stress, and/or increases in the attack rate of both chronically stressed and more vigorous trees by bark beetles. PMID:24786646

Hierarchical Multinomial Processing Tree Models: A Latent-Trait Approach

ERIC Educational Resources Information Center

Klauer, Karl Christoph

2010-01-01

Multinomial processing tree models are widely used in many areas of psychology. A hierarchical extension of the model class is proposed, using a multivariate normal distribution of person-level parameters with the mean and covariance matrix to be estimated from the data. The hierarchical model allows one to take variability between persons into…

Birth-death models and coalescent point processes: the shape and probability of reconstructed phylogenies.

PubMed

Lambert, Amaury; Stadler, Tanja

2013-12-01

Forward-in-time models of diversification (i.e., speciation and extinction) produce phylogenetic trees that grow "vertically" as time goes by. Pruning the extinct lineages out of such trees leads to natural models for reconstructed trees (i.e., phylogenies of extant species). Alternatively, reconstructed trees can be modelled by coalescent point processes (CPPs), where trees grow "horizontally" by the sequential addition of vertical edges. Each new edge starts at some random speciation time and ends at the present time; speciation times are drawn from the same distribution independently. CPPs lead to extremely fast computation of tree likelihoods and simulation of reconstructed trees. Their topology always follows the uniform distribution on ranked tree shapes (URT). We characterize which forward-in-time models lead to URT reconstructed trees and among these, which lead to CPP reconstructed trees. We show that for any "asymmetric" diversification model in which speciation rates only depend on time and extinction rates only depend on time and on a non-heritable trait (e.g., age), the reconstructed tree is CPP, even if extant species are incompletely sampled. If rates additionally depend on the number of species, the reconstructed tree is (only) URT (but not CPP). We characterize the common distribution of speciation times in the CPP description, and discuss incomplete species sampling as well as three special model cases in detail: (1) the extinction rate does not depend on a trait; (2) rates do not depend on time; (3) mass extinctions may happen additionally at certain points in the past. Copyright © 2013 Elsevier Inc. All rights reserved.

iTREE: Long-term variability of tree growth in a changing environment - identifying physiological mechanisms using stable C and O isotopes in tree rings.

NASA Astrophysics Data System (ADS)

Siegwolf, R. T. W.; Buchmann, N.; Frank, D.; Joos, F.; Kahmen, A.; Treydte, K.; Leuenberger, M.; Saurer, M.

2012-04-01

Trees play are a critical role in the carbon cycle - their photosynthetic assimilation is one of the largest terrestrial carbon fluxes and their standing biomass represents the largest carbon pool of the terrestrial biosphere. Understanding how tree physiology and growth respond to long-term environmental change is pivotal to predict the magnitude and direction of the terrestrial carbon sink. iTREE is an interdisciplinary research framework to capitalize on synergies among leading dendroclimatologists, plant physiologists, isotope specialists, and global carbon cycle modelers with the objectives of reducing uncertainties related to tree/forest growth in the context of changing natural environments. Cross-cutting themes in our project are tree rings, stable isotopes, and mechanistic modelling. We will (i) establish a European network of tree-ring based isotope time-series to retrodict interannual to long-term tree physiological changes, (ii) conduct laboratory and field experiments to adapt a mechanistic isotope model to derive plant physiological variables from tree-ring isotopes, (iii) implement this model into a dynamic global vegetation model, and perform subsequent model-data validation exercises to refine model representation of plant physiological processes and (iv) attribute long-term variation in tree growth to plant physiological and environmental drivers, and identify how our refined knowledge revises predictions of the coupled carbon-cycle climate system. We will contribute to i) advanced quantifications of long-term variation in tree growth across Central Europe, ii) novel long-term information on key physiological processes that underlie variations in tree growth, and iii) improved carbon cycle models that can be employed to revise predictions of the coupled carbon-cycle climate system. Hence iTREE will significantly contribute towards a seamless understanding of the responses of terrestrial ecosystems to long-term environmental change, and ultimately help reduce uncertainties of the magnitude and direction of the past and future terrestrial carbon sink.

Simulation of Plant Physiological Process Using Fuzzy Variables

Treesearch

Daniel L. Schmoldt

1991-01-01

Qualitative modelling can help us understand and project effects of multiple stresses on trees. It is not practical to collect and correlate empirical data for all combinations of plant/environments and human/climate stresses, especially for mature trees in natural settings. Therefore, a mechanistic model was developed to describe ecophysiological processes. This model...

TreePOD: Sensitivity-Aware Selection of Pareto-Optimal Decision Trees.

PubMed

Muhlbacher, Thomas; Linhardt, Lorenz; Moller, Torsten; Piringer, Harald

2018-01-01

Balancing accuracy gains with other objectives such as interpretability is a key challenge when building decision trees. However, this process is difficult to automate because it involves know-how about the domain as well as the purpose of the model. This paper presents TreePOD, a new approach for sensitivity-aware model selection along trade-offs. TreePOD is based on exploring a large set of candidate trees generated by sampling the parameters of tree construction algorithms. Based on this set, visualizations of quantitative and qualitative tree aspects provide a comprehensive overview of possible tree characteristics. Along trade-offs between two objectives, TreePOD provides efficient selection guidance by focusing on Pareto-optimal tree candidates. TreePOD also conveys the sensitivities of tree characteristics on variations of selected parameters by extending the tree generation process with a full-factorial sampling. We demonstrate how TreePOD supports a variety of tasks involved in decision tree selection and describe its integration in a holistic workflow for building and selecting decision trees. For evaluation, we illustrate a case study for predicting critical power grid states, and we report qualitative feedback from domain experts in the energy sector. This feedback suggests that TreePOD enables users with and without statistical background a confident and efficient identification of suitable decision trees.

A way forward for fire-caused tree mortality prediction: Modeling a physiological consequence of fire

Treesearch

Kathleen L. Kavanaugh; Matthew B. Dickinson; Anthony S. Bova

2010-01-01

Current operational methods for predicting tree mortality from fire injury are regression-based models that only indirectly consider underlying causes and, thus, have limited generality. A better understanding of the physiological consequences of tree heating and injury are needed to develop biophysical process models that can make predictions under changing or novel...

Climate change impacts on tree ranges: model intercomparison facilitates understanding and quantification of uncertainty.

PubMed

Cheaib, Alissar; Badeau, Vincent; Boe, Julien; Chuine, Isabelle; Delire, Christine; Dufrêne, Eric; François, Christophe; Gritti, Emmanuel S; Legay, Myriam; Pagé, Christian; Thuiller, Wilfried; Viovy, Nicolas; Leadley, Paul

2012-06-01

Model-based projections of shifts in tree species range due to climate change are becoming an important decision support tool for forest management. However, poorly evaluated sources of uncertainty require more scrutiny before relying heavily on models for decision-making. We evaluated uncertainty arising from differences in model formulations of tree response to climate change based on a rigorous intercomparison of projections of tree distributions in France. We compared eight models ranging from niche-based to process-based models. On average, models project large range contractions of temperate tree species in lowlands due to climate change. There was substantial disagreement between models for temperate broadleaf deciduous tree species, but differences in the capacity of models to account for rising CO(2) impacts explained much of the disagreement. There was good quantitative agreement among models concerning the range contractions for Scots pine. For the dominant Mediterranean tree species, Holm oak, all models foresee substantial range expansion. © 2012 Blackwell Publishing Ltd/CNRS.

How to make a tree ring: Coupling stem water flow and cambial activity in mature Alpine conifers

NASA Astrophysics Data System (ADS)

Peters, Richard L.; Frank, David C.; Treydte, Kerstin; Steppe, Kathy; Kahmen, Ansgar; Fonti, Patrick

2017-04-01

Inter-annual tree-ring measurements are used to understand tree-growth responses to climatic variability and reconstruct past climate conditions. In parallel, mechanistic models use experimentally defined plant-atmosphere interactions to explain past growth responses and predict future environmental impact on forest productivity. Yet, substantial inconsistencies within mechanistic model ensembles and mismatches with empirical data indicate that significant progress is still needed to understand the processes occurring at an intra-annual resolution that drive annual growth. However, challenges arise due to i) few datasets describing climatic responses of high-resolution physiological processes over longer time-scales, ii) uncertainties on the main mechanistic process limiting radial stem growth and iii) complex interactions between multiple environmental factors which obscure detection of the main stem growth driver, generating a gap between our understanding of intra- and inter-annual growth mechanisms. We attempt to bridge the gap between inter-annual tree-ring width and sub-daily radial stem-growth and provide a mechanistic perspective on how environmental conditions affect physiological processes that shape tree rings in conifers. We combine sub-hourly sap flow and point dendrometer measurements performed on mature Alpine conifers (Larix decidua) into an individual-based mechanistic tree-growth model to simulate sub-hourly cambial activity. The monitored trees are located along a high elevational transect in the Swiss Alps (Lötschental) to analyse the effect of increasing temperature. The model quantifies internal tree hydraulic pathways that regulate the turgidity within the cambial zone and induce cell enlargement for radial growth. The simulations are validated against intra-annual growth patterns derived from xylogenesis data and anatomical analyses. Our efforts advance the process-based understanding of how climate shapes the annual tree-ring structures and could potentially improve our ability to reconstruct the climate of the past and predict future growth under changing climate.

Comparison of a species distribution model and a process model from a hierarchical perspective to quantify effects of projected climate change on tree species

Treesearch

Jeffrey E. Schneiderman; Hong S. He; Frank R. Thompson; William D. Dijak; Jacob S. Fraser

2015-01-01

Tree species distribution and abundance are affected by forces operating across a hierarchy of ecological scales. Process and species distribution models have been developed emphasizing forces at different scales. Understanding model agreement across hierarchical scales provides perspective on prediction uncertainty and ultimately enables policy makers and managers to...

Simulating effects of fire on northern Rocky Mountain landscapes with the ecological process model FIRE-BGC.

PubMed

Keane, R E; Ryan, K C; Running, S W

1996-03-01

A mechanistic, biogeochemical succession model, FIRE-BGC, was used to investigate the role of fire on long-term landscape dynamics in northern Rocky Mountain coniferous forests of Glacier National Park, Montana, USA. FIRE-BGC is an individual-tree model-created by merging the gap-phase process-based model FIRESUM with the mechanistic ecosystem biogeochemical model FOREST-BGC-that has mixed spatial and temporal resolution in its simulation architecture. Ecological processes that act at a landscape level, such as fire and seed dispersal, are simulated annually from stand and topographic information. Stand-level processes, such as tree establishment, growth and mortality, organic matter accumulation and decomposition, and undergrowth plant dynamics are simulated both daily and annually. Tree growth is mechanistically modeled based on the ecosystem process approach of FOREST-BGC where carbon is fixed daily by forest canopy photosynthesis at the stand level. Carbon allocated to the tree stem at the end of the year generates the corresponding diameter and height growth. The model also explicitly simulates fire behavior and effects on landscape characteristics. We simulated the effects of fire on ecosystem characteristics of net primary productivity, evapotranspiration, standing crop biomass, nitrogen cycling and leaf area index over 200 years for the 50,000-ha McDonald Drainage in Glacier National Park. Results show increases in net primary productivity and available nitrogen when fires are included in the simulation. Standing crop biomass and evapotranspiration decrease under a fire regime. Shade-intolerant species dominate the landscape when fires are excluded. Model tree increment predictions compared well with field data.

A diameter growth model for the SRS FIA

Treesearch

David Gartner

2015-01-01

Changes in the national Forest Inventory and Analysis (FIA) processing system required the Southern Research Station’s FIA unit to create a diameter growth model to estimate the growth of trees that could not be measured at both ends of a measurement interval. Examples of such trees are trees that have died or been harvested, and trees that grow over the minimum...

Disentangling the Effects of Water Stress on Carbon Acquisition, Vegetative Growth, and Fruit Quality of Peach Trees by Means of the QualiTree Model.

PubMed

Rahmati, Mitra; Mirás-Avalos, José M; Valsesia, Pierre; Lescourret, Françoise; Génard, Michel; Davarynejad, Gholam H; Bannayan, Mohammad; Azizi, Majid; Vercambre, Gilles

2018-01-01

Climate change projections predict warmer and drier conditions. In general, moderate to severe water stress reduce plant vegetative growth and leaf photosynthesis. However, vegetative and reproductive growths show different sensitivities to water deficit. In fruit trees, water restrictions may have serious implications not only on tree growth and yield, but also on fruit quality, which might be improved. Therefore, it is of paramount importance to understand the complex interrelations among the physiological processes involved in within-tree carbon acquisition and allocation, water uptake and transpiration, organ growth, and fruit composition when affected by water stress. This can be studied using process-based models of plant functioning, which allow assessing the sensitivity of various physiological processes to water deficit and their relative impact on vegetative growth and fruit quality. In the current study, an existing fruit-tree model (QualiTree) was adapted for describing the water stress effects on peach ( Prunus persica L. Batsch) vegetative growth, fruit size and composition. First, an energy balance calculation at the fruit-bearing shoot level and a water transfer formalization within the plant were integrated into the model. Next, a reduction function of vegetative growth according to tree water status was added to QualiTree. Then, the model was parameterized and calibrated for a late-maturing peach cultivar ("Elberta") under semi-arid conditions, and for three different irrigation practices. Simulated vegetative and fruit growth variability over time was consistent with observed data. Sugar concentrations in fruit flesh were well simulated. Finally, QualiTree allowed for determining the relative importance of photosynthesis and vegetative growth reduction on carbon acquisition, plant growth and fruit quality under water constrains. According to simulations, water deficit impacted vegetative growth first through a direct effect on its sink strength, and; secondly, through an indirect reducing effect on photosynthesis. Fruit composition was moderately affected by water stress. The enhancements performed in the model broadened its predictive capabilities and proved that QualiTree allows for a better understanding of the water stress effects on fruit-tree functioning and might be useful for designing innovative horticultural practices in a changing climate scenario.

Biophysical modelling of intra-ring variations in tracheid features and wood density of Pinus pinaster trees exposed to seasonal droughts

Treesearch

Sarah Wilkinson; Jerome Ogee; Jean-Christophe Domec; Mark Rayment; Lisa Wingate

2015-01-01

Process-based models that link seasonally varying environmental signals to morphological features within tree rings are essential tools to predict tree growth response and commercially important wood quality traits under future climate scenarios. This study evaluated model portrayal of radial growth and wood anatomy observations within a mature maritime pine (Pinus...

Modeling potential future individual tree-species distributions in the eastern United States under a climate change scenario: a case study with Pinus virginiana

Treesearch

Louis R. Iverson; Anantha Prasad; Mark W. Schwartz; Mark W. Schwartz

1999-01-01

We are using a deterministic regression tree analysis model (DISTRIB) and a stochastic migration model (SHIFT) to examine potential distributions of ~66 individual species of eastern US trees under a 2 x CO2 climate change scenario. This process is demonstrated for Virginia pine (Pinus virginiana).

Does Gene Tree Discordance Explain the Mismatch between Macroevolutionary Models and Empirical Patterns of Tree Shape and Branching Times?

PubMed Central

Stadler, Tanja; Degnan, James H.; Rosenberg, Noah A.

2016-01-01

Classic null models for speciation and extinction give rise to phylogenies that differ in distribution from empirical phylogenies. In particular, empirical phylogenies are less balanced and have branching times closer to the root compared to phylogenies predicted by common null models. This difference might be due to null models of the speciation and extinction process being too simplistic, or due to the empirical datasets not being representative of random phylogenies. A third possibility arises because phylogenetic reconstruction methods often infer gene trees rather than species trees, producing an incongruity between models that predict species tree patterns and empirical analyses that consider gene trees. We investigate the extent to which the difference between gene trees and species trees under a combined birth–death and multispecies coalescent model can explain the difference in empirical trees and birth–death species trees. We simulate gene trees embedded in simulated species trees and investigate their difference with respect to tree balance and branching times. We observe that the gene trees are less balanced and typically have branching times closer to the root than the species trees. Empirical trees from TreeBase are also less balanced than our simulated species trees, and model gene trees can explain an imbalance increase of up to 8% compared to species trees. However, we see a much larger imbalance increase in empirical trees, about 100%, meaning that additional features must also be causing imbalance in empirical trees. This simulation study highlights the necessity of revisiting the assumptions made in phylogenetic analyses, as these assumptions, such as equating the gene tree with the species tree, might lead to a biased conclusion. PMID:26968785

A Linked Model for Simulating Stand Development and Growth Processes of Loblolly Pine

Treesearch

V. Clark Baldwin; Phillip M. Dougherty; Harold E. Burkhart

1998-01-01

Linking models of different scales (e.g., process, tree-stand-ecosystem) is essential for furthering our understanding of stand, climatic, and edaphic effects on tree growth and forest productivity. Moreover, linking existing models that differ in scale and levels of resolution quickly identifies knowledge gaps in information required to scale from one level to another...

Monte Carlo Simulation of Markov, Semi-Markov, and Generalized Semi- Markov Processes in Probabilistic Risk Assessment

NASA Technical Reports Server (NTRS)

English, Thomas

2005-01-01

A standard tool of reliability analysis used at NASA-JSC is the event tree. An event tree is simply a probability tree, with the probabilities determining the next step through the tree specified at each node. The nodal probabilities are determined by a reliability study of the physical system at work for a particular node. The reliability study performed at a node is typically referred to as a fault tree analysis, with the potential of a fault tree existing.for each node on the event tree. When examining an event tree it is obvious why the event tree/fault tree approach has been adopted. Typical event trees are quite complex in nature, and the event tree/fault tree approach provides a systematic and organized approach to reliability analysis. The purpose of this study was two fold. Firstly, we wanted to explore the possibility that a semi-Markov process can create dependencies between sojourn times (the times it takes to transition from one state to the next) that can decrease the uncertainty when estimating time to failures. Using a generalized semi-Markov model, we studied a four element reliability model and were able to demonstrate such sojourn time dependencies. Secondly, we wanted to study the use of semi-Markov processes to introduce a time variable into the event tree diagrams that are commonly developed in PRA (Probabilistic Risk Assessment) analyses. Event tree end states which change with time are more representative of failure scenarios than are the usual static probability-derived end states.

Reconstruction of late Holocene climate based on tree growth and mechanistic hierarchical models

USGS Publications Warehouse

Tipton, John; Hooten, Mevin B.; Pederson, Neil; Tingley, Martin; Bishop, Daniel

2016-01-01

Reconstruction of pre-instrumental, late Holocene climate is important for understanding how climate has changed in the past and how climate might change in the future. Statistical prediction of paleoclimate from tree ring widths is challenging because tree ring widths are a one-dimensional summary of annual growth that represents a multi-dimensional set of climatic and biotic influences. We develop a Bayesian hierarchical framework using a nonlinear, biologically motivated tree ring growth model to jointly reconstruct temperature and precipitation in the Hudson Valley, New York. Using a common growth function to describe the response of a tree to climate, we allow for species-specific parameterizations of the growth response. To enable predictive backcasts, we model the climate variables with a vector autoregressive process on an annual timescale coupled with a multivariate conditional autoregressive process that accounts for temporal correlation and cross-correlation between temperature and precipitation on a monthly scale. Our multi-scale temporal model allows for flexibility in the climate response through time at different temporal scales and predicts reasonable climate scenarios given tree ring width data.

Inferring duplications, losses, transfers and incomplete lineage sorting with nonbinary species trees.

PubMed

Stolzer, Maureen; Lai, Han; Xu, Minli; Sathaye, Deepa; Vernot, Benjamin; Durand, Dannie

2012-09-15

Gene duplication (D), transfer (T), loss (L) and incomplete lineage sorting (I) are crucial to the evolution of gene families and the emergence of novel functions. The history of these events can be inferred via comparison of gene and species trees, a process called reconciliation, yet current reconciliation algorithms model only a subset of these evolutionary processes. We present an algorithm to reconcile a binary gene tree with a nonbinary species tree under a DTLI parsimony criterion. This is the first reconciliation algorithm to capture all four evolutionary processes driving tree incongruence and the first to reconcile non-binary species trees with a transfer model. Our algorithm infers all optimal solutions and reports complete, temporally feasible event histories, giving the gene and species lineages in which each event occurred. It is fixed-parameter tractable, with polytime complexity when the maximum species outdegree is fixed. Application of our algorithms to prokaryotic and eukaryotic data show that use of an incomplete event model has substantial impact on the events inferred and resulting biological conclusions. Our algorithms have been implemented in Notung, a freely available phylogenetic reconciliation software package, available at http://www.cs.cmu.edu/~durand/Notung. mstolzer@andrew.cmu.edu.

iTree-Hydro: Snow hydrology update for the urban forest hydrology model

Treesearch

Yang Yang; Theodore A. Endreny; David J. Nowak

2011-01-01

This article presents snow hydrology updates made to iTree-Hydro, previously called the Urban Forest Effects—Hydrology model. iTree-Hydro Version 1 was a warm climate model developed by the USDA Forest Service to provide a process-based planning tool with robust water quantity and quality predictions given data limitations common to most urban areas. Cold climate...

Process model simulations of the divergence effect

NASA Astrophysics Data System (ADS)

Anchukaitis, K. J.; Evans, M. N.; D'Arrigo, R. D.; Smerdon, J. E.; Hughes, M. K.; Kaplan, A.; Vaganov, E. A.

2007-12-01

We explore the extent to which the Vaganov-Shashkin (VS) model of conifer tree-ring formation can explain evidence for changing relationships between climate and tree growth over recent decades. The VS model is driven by daily environmental forcing (temperature, soil moisture, and solar radiation), and simulates tree-ring growth cell-by-cell as a function of the most limiting environmental control. This simplified representation of tree physiology allows us to examine using a selection of case studies whether instances of divergence may be explained in terms of changes in limiting environmental dependencies or transient climate change. Identification of model-data differences permits further exploration of the effects of tree-ring standardization, atmospheric composition, and additional non-climatic factors.

Assessing the Dynamic Effects of Climate on Individual Tree Growth Across Time and Space

NASA Astrophysics Data System (ADS)

Itter, M.; Finley, A. O.; D'Amato, A. W.; Foster, J. R.; Bradford, J. B.

2015-12-01

The relationship between climate variability and an ecosystem process, such as forest growth, is frequently not fixed over time, but changes due to complex interactions between unobserved ecological factors and the process of interest. Climate data and forecasts are frequently spatially and temporally misaligned with ecological observations making inference regarding the effects of climate on ecosystem processes particularly challenging. Here we develop a Bayesian dynamic hierarchical model for annual tree growth increment that allows the effects of climate to evolve over time, applies climate data at a spatial-temporal scale consistent with observations, and controls for individual-level variability commonly encountered in ecological datasets. The model is applied to individual tree data from northern Minnesota using a modified Thornthwaite-type water balance model to transform PRISM temperature and precipitation estimates to physiologically relevant values of actual and potential evapotranspiration (AET, PET), and climatic water deficit. Model results indicate that mean tree growth is most sensitive to AET during the growing season and PET and minimum temperature in the spring prior to growth. The effects of these variables on tree growth, however, are not stationary with significant effects observed in only a subset of years during the 111-year study period. Importantly, significant effects of climate do not result from anomalous climate observations, but follow from large growth deviations unexplained by tree age and size, and time since forest disturbance. Results differ markedly from alternative models that assume the effects of climate are stationary over time or apply climate estimates at the individual scale. Forecasts of future tree growth as a function of climate follow directly from the dynamic hierarchical model allowing for assessment of forest change. Current work is focused on extending the model framework to include regional climate and ecosystem effects for application to a larger tree growth dataset spanning a latitudinal gradient within the US from Maine to Florida.

Effects of species biological traits and environmental heterogeneity on simulated tree species distribution shifts under climate change

Treesearch

Wen J. Wang; Hong S. He; Frank R. Thompson; Martin A. Spetich; Jacob S. Fraser

2018-01-01

Demographic processes (fecundity, dispersal, colonization, growth, and mortality) and their interactions with environmental changes are notwell represented in current climate-distribution models (e.g., niche and biophysical process models) and constitute a large uncertainty in projections of future tree species distribution shifts.We investigate how species biological...

Stochastic modelling of tree architecture and biomass allocation: application to teak (Tectona grandis L. f.), a tree species with polycyclic growth and leaf neoformation.

PubMed

Tondjo, Kodjo; Brancheriau, Loïc; Sabatier, Sylvie; Kokutse, Adzo Dzifa; Kokou, Kouami; Jaeger, Marc; de Reffye, Philippe; Fourcaud, Thierry

2018-06-08

For a given genotype, the observed variability of tree forms results from the stochasticity of meristem functioning and from changing and heterogeneous environmental factors affecting biomass formation and allocation. In response to climate change, trees adapt their architecture by adjusting growth processes such as pre- and neoformation, as well as polycyclic growth. This is the case for the teak tree. The aim of this work was to adapt the plant model, GreenLab, in order to take into consideration both these processes using existing data on this tree species. This work adopted GreenLab formalism based on source-sink relationships at organ level that drive biomass production and partitioning within the whole plant over time. The stochastic aspect of phytomer production can be modelled by a Bernoulli process. The teak model was designed, parameterized and analysed using the architectural data from 2- to 5-year-old teak trees in open field stands. Growth and development parameters were identified, fitting the observed compound organic series with the theoretical series, using generalized least squares methods. Phytomer distributions of growth units and branching pattern varied depending on their axis category, i.e. their physiological age. These emerging properties were in accordance with the observed growth patterns and biomass allocation dynamics during a growing season marked by a short dry season. Annual growth patterns observed on teak, including shoot pre- and neoformation and polycyclism, were reproduced by the new version of the GreenLab model. However, further updating is discussed in order to ensure better consideration of radial variation in basic specific gravity of wood. Such upgrading of the model will enable teak ideotypes to be defined for improving wood production in terms of both volume and quality.

The Inference of Gene Trees with Species Trees

PubMed Central

Szöllősi, Gergely J.; Tannier, Eric; Daubin, Vincent; Boussau, Bastien

2015-01-01

This article reviews the various models that have been used to describe the relationships between gene trees and species trees. Molecular phylogeny has focused mainly on improving models for the reconstruction of gene trees based on sequence alignments. Yet, most phylogeneticists seek to reveal the history of species. Although the histories of genes and species are tightly linked, they are seldom identical, because genes duplicate, are lost or horizontally transferred, and because alleles can coexist in populations for periods that may span several speciation events. Building models describing the relationship between gene and species trees can thus improve the reconstruction of gene trees when a species tree is known, and vice versa. Several approaches have been proposed to solve the problem in one direction or the other, but in general neither gene trees nor species trees are known. Only a few studies have attempted to jointly infer gene trees and species trees. These models account for gene duplication and loss, transfer or incomplete lineage sorting. Some of them consider several types of events together, but none exists currently that considers the full repertoire of processes that generate gene trees along the species tree. Simulations as well as empirical studies on genomic data show that combining gene tree–species tree models with models of sequence evolution improves gene tree reconstruction. In turn, these better gene trees provide a more reliable basis for studying genome evolution or reconstructing ancestral chromosomes and ancestral gene sequences. We predict that gene tree–species tree methods that can deal with genomic data sets will be instrumental to advancing our understanding of genomic evolution. PMID:25070970

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...

Bayesian Ensemble Trees (BET) for Clustering and Prediction in Heterogeneous Data

PubMed Central

Duan, Leo L.; Clancy, John P.; Szczesniak, Rhonda D.

2016-01-01

We propose a novel “tree-averaging” model that utilizes the ensemble of classification and regression trees (CART). Each constituent tree is estimated with a subset of similar data. We treat this grouping of subsets as Bayesian Ensemble Trees (BET) and model them as a Dirichlet process. We show that BET determines the optimal number of trees by adapting to the data heterogeneity. Compared with the other ensemble methods, BET requires much fewer trees and shows equivalent prediction accuracy using weighted averaging. Moreover, each tree in BET provides variable selection criterion and interpretation for each subset. We developed an efficient estimating procedure with improved estimation strategies in both CART and mixture models. We demonstrate these advantages of BET with simulations and illustrate the approach with a real-world data example involving regression of lung function measurements obtained from patients with cystic fibrosis. Supplemental materials are available online. PMID:27524872

Decision tree modeling using R.

PubMed

Zhang, Zhongheng

2016-08-01

In machine learning field, decision tree learner is powerful and easy to interpret. It employs recursive binary partitioning algorithm that splits the sample in partitioning variable with the strongest association with the response variable. The process continues until some stopping criteria are met. In the example I focus on conditional inference tree, which incorporates tree-structured regression models into conditional inference procedures. While growing a single tree is subject to small changes in the training data, random forests procedure is introduced to address this problem. The sources of diversity for random forests come from the random sampling and restricted set of input variables to be selected. Finally, I introduce R functions to perform model based recursive partitioning. This method incorporates recursive partitioning into conventional parametric model building.

Stem mortality in surface fires: Part II, experimental methods for characterizing the thermal response of tree stems to heating by fires

Treesearch

D. M. Jimenez; B. W. Butler; J. Reardon

2003-01-01

Current methods for predicting fire-induced plant mortality in shrubs and trees are largely empirical. These methods are not readily linked to duff burning, soil heating, and surface fire behavior models. In response to the need for a physics-based model of this process, a detailed model for predicting the temperature distribution through a tree stem as a function of...

Modeling Tree Growth Taking into Account Carbon Source and Sink Limitations.

PubMed

Hayat, Amaury; Hacket-Pain, Andrew J; Pretzsch, Hans; Rademacher, Tim T; Friend, Andrew D

2017-01-01

Increasing CO 2 concentrations are strongly controlled by the behavior of established forests, which are believed to be a major current sink of atmospheric CO 2 . There are many models which predict forest responses to environmental changes but they are almost exclusively carbon source (i.e., photosynthesis) driven. Here we present a model for an individual tree that takes into account the intrinsic limits of meristems and cellular growth rates, as well as control mechanisms within the tree that influence its diameter and height growth over time. This new framework is built on process-based understanding combined with differential equations solved by numerical method. Our aim is to construct a model framework of tree growth for replacing current formulations in Dynamic Global Vegetation Models, and so address the issue of the terrestrial carbon sink. Our approach was successfully tested for stands of beech trees in two different sites representing part of a long-term forest yield experiment in Germany. This model provides new insights into tree growth and limits to tree height, and addresses limitations of previous models with respect to sink-limited growth.

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

The efficacy of using inventory data to develop optimal diameter increment models

Treesearch

Don C. Bragg

2002-01-01

Most optimal tree diameter growth models have arisen through either the conceptualization of physiological processes or the adaptation of empirical increment models. However, surprisingly little effort has been invested in the melding of these approaches even though it is possible to develop theoretically sound, computationally efficient optimal tree growth models...

The contribution of competition to tree mortality in old-growth coniferous forests

USGS Publications Warehouse

Das, A.; Battles, J.; Stephenson, N.L.; van Mantgem, P.J.

2011-01-01

Competition is a well-documented contributor to tree mortality in temperate forests, with numerous studies documenting a relationship between tree death and the competitive environment. Models frequently rely on competition as the only non-random mechanism affecting tree mortality. However, for mature forests, competition may cease to be the primary driver of mortality.We use a large, long-term dataset to study the importance of competition in determining tree mortality in old-growth forests on the western slope of the Sierra Nevada of California, U.S.A. We make use of the comparative spatial configuration of dead and live trees, changes in tree spatial pattern through time, and field assessments of contributors to an individual tree's death to quantify competitive effects.Competition was apparently a significant contributor to tree mortality in these forests. Trees that died tended to be in more competitive environments than trees that survived, and suppression frequently appeared as a factor contributing to mortality. On the other hand, based on spatial pattern analyses, only three of 14 plots demonstrated compelling evidence that competition was dominating mortality. Most of the rest of the plots fell within the expectation for random mortality, and three fit neither the random nor the competition model. These results suggest that while competition is often playing a significant role in tree mortality processes in these forests it only infrequently governs those processes. In addition, the field assessments indicated a substantial presence of biotic mortality agents in trees that died.While competition is almost certainly important, demographics in these forests cannot accurately be characterized without a better grasp of other mortality processes. In particular, we likely need a better understanding of biotic agents and their interactions with one another and with competition. ?? 2011.

Interplay between field observations and numerical modeling to understand temporal pulsing of tree root throw processes, Canadian Rockies, Canada

NASA Astrophysics Data System (ADS)

Martin, Y. E.; Johnson, E. A.; Chaikina, O.

2013-10-01

During the cycle of forest disturbance, regeneration, and maturity, tree mortality leading to topple is a regular occurrence. When tree topple occurs relatively soon after mortality and if the tree has attained some threshold diameter at breast height (dbh) at the time of death, then notable amounts of soil may be upheaved along with the root wad. This upheaval may result in sediment transfers and soil production. A combination of field evidence and numerical modeling is used herein to gain insights regarding the temporal dynamics of tree topple, associated root throw processes, and pit-mound microtopography. Results from our model of tree population dynamics demonstrate temporal patterns in root throw processes in subalpine forests of the Canadian Rockies, a region in which forests are affected largely by wildfire disturbance. As the forest regenerates after disturbance, the new cohort of trees has to reach a critical dbh before significant root plate upheaval can occur; in the subalpine forests of the Canadian Rockies, this may take up to ~ 102 years. Once trees begin to reach this critical dbh for root plate upheaval, a period of sporadic root throw arises that is caused by mortality of trees during competition. In due course, another wildfire will occur on the landscape and a period of much increased root throw activity then takes place for the next several decades; tree sizes and, therefore, the amount of sediment disturbance will be greater the longer the time period since the previous fire. Results of previous root throw studies covering a number of regional settings are used to guide an exercise in diffusion modeling with the aim of defining a range of reasonable diffusion coefficients for pit-mound degradation; the most appropriate values to fit the field data ranged from 0.01 m2 y- 1 to 0.1 m2 y- 1. A similar exercise is then undertaken that is guided by our field observations in subalpine forests of the Canadian Rockies. For these forests, the most appropriate range of diffusion coefficients is in the range 0.001 m2 y- 1 to 0.01 m2 y- 1. Finally, the model of tree population dynamics is combined with the model of pit-mound degradation to demonstrate the integration of these combined processes on the appearance of pit-mound microtopography and soil bioturbation in subalpine forests of the Canadian Rockies. We conclude that the appearance of notable pit-mound microtopography is limited to very specific time periods and is not visible for much of the time. Most of the hillslope plot is affected by root throw during the 1000-year model run time.

Modelling of information diffusion on social networks with applications to WeChat

NASA Astrophysics Data System (ADS)

Liu, Liang; Qu, Bo; Chen, Bin; Hanjalic, Alan; Wang, Huijuan

2018-04-01

Traces of user activities recorded in online social networks open new possibilities to systematically understand the information diffusion process on social networks. From the online social network WeChat, we collected a large number of information cascade trees, each of which tells the spreading trajectory of a message/information such as which user creates the information and which users view or forward the information shared by which neighbours. In this work, we propose two heterogeneous non-linear models, one for the topologies of the information cascade trees and the other for the stochastic process of information diffusion on a social network. Both models are validated by the WeChat data in reproducing and explaining key features of cascade trees. Specifically, we apply the Random Recursive Tree (RRT) to model the growth of cascade trees. The RRT model could capture key features, i.e. the average path length and degree variance of a cascade tree in relation to the number of nodes (size) of the tree. Its single identified parameter quantifies the relative depth or broadness of the cascade trees and indicates that information propagates via a star-like broadcasting or viral-like hop by hop spreading. The RRT model explains the appearance of hubs, thus a possibly smaller average path length as the cascade size increases, as observed in WeChat. We further propose the stochastic Susceptible View Forward Removed (SVFR) model to depict the dynamic user behaviour including creating, viewing, forwarding and ignoring a message on a given social network. Beside the average path length and degree variance of the cascade trees in relation to their sizes, the SVFR model could further explain the power-law cascade size distribution in WeChat and unravel that a user with a large number of friends may actually have a smaller probability to read a message (s)he receives due to limited attention.

Random forests and stochastic gradient boosting for predicting tree canopy cover: Comparing tuning processes and model performance

Treesearch

E. Freeman; G. Moisen; J. Coulston; B. Wilson

2014-01-01

Random forests (RF) and stochastic gradient boosting (SGB), both involving an ensemble of classification and regression trees, are compared for modeling tree canopy cover for the 2011 National Land Cover Database (NLCD). The objectives of this study were twofold. First, sensitivity of RF and SGB to choices in tuning parameters was explored. Second, performance of the...

Random forests and stochastic gradient boosting for predicting tree canopy cover: Comparing tuning processes and model performance

Treesearch

Elizabeth A. Freeman; Gretchen G. Moisen; John W. Coulston; Barry T. (Ty) Wilson

2015-01-01

As part of the development of the 2011 National Land Cover Database (NLCD) tree canopy cover layer, a pilot project was launched to test the use of high-resolution photography coupled with extensive ancillary data to map the distribution of tree canopy cover over four study regions in the conterminous US. Two stochastic modeling techniques, random forests (RF...

Climate insensitivity of treeline in the Canadian Rocky Mountains

NASA Astrophysics Data System (ADS)

Johnson, E. A.; Macias Fauria, M.

2011-12-01

Successful modelling efforts demonstrate that tree presence over a ~ 200 km2 alpine/subalpine area in the Front Ranges of the Canadian Rocky Mountains results from a multi-scale spatiotemporal process competition involving not only growing season temperatures but also topographical shelter, water availability, and substrate stability and availability. The study area was selected to represent the diversity of substrates and geomorphologic processes found in the Canadian Rockies, and ranges in elevation from 1400 to > 2800 meters above sea level. Tree presence was mapped at 10m resolution using a combination of remote sensing imagery (taken in 2008) and intensive ground truthing, and modelled with an ensemble of state-of-the-art environmental envelope models. Explanatory variables chosen represented not only temperature and moisture availability (computed over 1971-2000 climate normals), but also substrate diversity, slope angle and type, geomorphologic features, modelled regolith depth, and concavity/convexity of the terrain. Such variables were meant to serve as proxies for known convergent and divergent processes that occur on steep landscapes and that have profound influence on tree establishment and survival. Model performance was very high and revealed substrate and geomorphology to be the most important explanatory variables for tree presence in the area. Available high-resolution imagery for 1954 enabled the mapping of tree presence over most of the study area and the identification of changes in the distribution of trees over the last nearly six decades. Overall, the only major observed changes were related to post-fire stand recovery, and areas with treeline advance were insignificant at the landscape scale. Tree suitable sites were projected onto high resolution grids of late 21st century climatic conditions predicted by regional climate models driven by atmosphere-ocean general circulation models. Emissions scenario was A2 (as defined in the Special Report on Emissions Scenarios used by the Intergovernmental Panel on Climate Change), at the higher end of emissions scenarios, and thus at the higher end of forecasted temperature increases. Projected changes in tree site availability were minimal at the landscape scale, as the presence of trees in the uppermost part of these forests largely depends on the existence of suitable sites largely linked to topography. Such places are the result of geomorphologic processes acting on a framework set by the structural geology of the region, and thus the appearance of new sites suitable for tree growth does not depend on short (i.e. yearly to decadal) time scales but on longer ones (i.e. centuries to millennia). This work has the strength of studying treeline over a whole area, thus avoiding potential biases in the regional representativity of local study sites, and warns against careless upscaling of site-based studies. Moreover, we suggest that the term 'treeline' is weak at a high-resolution landscape scale in our study area (i.e. young glaciated terrain) because the distribution of trees over the landscape is spatially irregular and most of the processes enabling or preventing tree presence occur over its whole elevational range.

Effects of species biological traits and environmental heterogeneity on simulated tree species distribution shifts under climate change.

PubMed

Wang, Wen J; He, Hong S; Thompson, Frank R; Spetich, Martin A; Fraser, Jacob S

2018-09-01

Demographic processes (fecundity, dispersal, colonization, growth, and mortality) and their interactions with environmental changes are not well represented in current climate-distribution models (e.g., niche and biophysical process models) and constitute a large uncertainty in projections of future tree species distribution shifts. We investigate how species biological traits and environmental heterogeneity affect species distribution shifts. We used a species-specific, spatially explicit forest dynamic model LANDIS PRO, which incorporates site-scale tree species demography and competition, landscape-scale dispersal and disturbances, and regional-scale abiotic controls, to simulate the distribution shifts of four representative tree species with distinct biological traits in the central hardwood forest region of United States. Our results suggested that biological traits (e.g., dispersal capacity, maturation age) were important for determining tree species distribution shifts. Environmental heterogeneity, on average, reduced shift rates by 8% compared to perfect environmental conditions. The average distribution shift rates ranged from 24 to 200myear -1 under climate change scenarios, implying that many tree species may not able to keep up with climate change because of limited dispersal capacity, long generation time, and environmental heterogeneity. We suggest that climate-distribution models should include species demographic processes (e.g., fecundity, dispersal, colonization), biological traits (e.g., dispersal capacity, maturation age), and environmental heterogeneity (e.g., habitat fragmentation) to improve future predictions of species distribution shifts in response to changing climates. Copyright © 2018 Elsevier B.V. All rights reserved.

Breakage or uprooting: How tree death type affects hillslope processes in old-growth temperate forests

NASA Astrophysics Data System (ADS)

Šamonil, Pavel; Daněk, Pavel; Adam, Dušan; Phillips, Jonathan D.

2017-12-01

Tree breakage and uprooting are two possible scenarios of tree death that have differing effects on hillslope processes. In this study we aimed to (i) reveal the long-term structure of the biomechanical effects of trees (BETs) in relation to their radial growth and tree death types in four old-growth temperate forests in four different elevation settings with an altitudinal gradient of 152-1105 m a.s.l., (ii) quantify affected areas and soil volumes associated with the studied BETs in reserves, and (iii) derive a general model of the role of BETs in hillslope processes in central European temperate forests. We analyzed the individual dynamics of circa 55,000 trees in an area of 161 ha within four old-growth forests over 3-4 decades. Basal tree censuses established in all sites in the 1970s and repeated tree censuses in the 1990s and 2000s provided detailed information about the radial growth of each tree of DBH ≥ 10 cm as well as about types of tree death. We focused on the quantification of: (i) surviving still-living trees, (ii) new recruits, (iii) standing dead trees, (iv) uprooted trees, and (v) broken trees. Frequencies of phenomena were related to affected areas and volumes of soil using individual statistical models. The elevation contrasts were a significant factor in the structure of BETs. Differences between sites increased from frequencies of events through affected areas to volumes of soil associated with BETs. An average 2.7 m3 ha-1 year-1 was associated with all BETs of the living and dying trees in lowlands, while there was an average of 7.8 m3 ha-1 year-1 in the highest mountain site. Differences were caused mainly by the effects of dying trees. BETs associated with dead trees were 7-8 times larger in the mountains. Effects of dying trees and particularly treethrows represented about 70% of all BETs at both mountain sites, while it was 58% at the highland site and only 32% at the lowland site. Our results show a more significant role of BETs in hillslope processes including slope denudation in the mountains. We would expect a significant decrease of the biogeomorphic effect of trees in managed forests, but with a greater relative effect in mountains.

An enhanced Oct-tree data structure and operations for solid modeling

NASA Technical Reports Server (NTRS)

Fujimura, K.; Toriya, H.; Yamaguchi, K.; Kunii, T. L.

1984-01-01

Oct-trees are enhanced to increase the processing efficiency of geometric operations for interactive CAD use. Further enhancement is made to combine them with surface models for more precise boundary specification as needed by tool path generation in CAM applications.

An object-oriented forest landscape model and its representation of tree species

Treesearch

Hong S. He; David J. Mladenoff; Joel Boeder

1999-01-01

LANDIS is a forest landscape model that simulates the interaction of large landscape processes and forest successional dynamics at tree species level. We discuss how object-oriented design (OOD) approaches such as modularity, abstraction and encapsulation are integrated into the design of LANDIS. We show that using OOD approaches, model decisions (olden as model...

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.

Mistletoe-induced growth reductions at the forest stand scale.

PubMed

Kollas, Chris; Gutsch, Martin; Hommel, Robert; Lasch-Born, Petra; Suckow, Felicitas

2018-05-01

The hemiparasite European mistletoe (Viscum album L.) adversely affects growth and reproduction of the host Scots pine (Pinus sylvestris L.) and in consequence may lead to tree death. Here, we aimed to estimate mistletoe-induced losses in timber yield applying the process-based forest growth model 4C. The parasite was implemented into the eco-physiological forest growth model 4C using (literature-derived) established impacts of the parasite on the tree's water and carbon cycle. The amended model was validated simulating a sample forest stand in the Berlin area (Germany) comprising trees with and without mistletoe infection. At the same forest stand, tree core measurements were taken to evaluate simulated and observed growth. A subsample of trees were harvested to quantify biomass compartments of the tree canopy and to derive a growth function of the mistletoe population. The process-based simulations of the forest stand revealed 27% reduction in basal area increment (BAI) during the last 9 years of heavy infection, which was confirmed by the measurements (29% mean growth reduction). The long-term simulations of the forest stand before and during the parasite infection showed that the amended forest growth model 4C depicts well the BAI growth pattern during >100 years and also quantifies well the mistletoe-induced growth reductions in Scots pine stands.

The zero inflation of standing dead tree carbon stocks

Treesearch

Christopher W. Woodall; David W. MacFarlane

2012-01-01

Given the importance of standing dead trees in numerous forest ecosystem attributes/processes such as carbon (C) stocks, the USDA Forest Service’s Forest Inventory and Analysis (FIA) program began consistent nationwide sampling of standing dead trees in 1999. Modeled estimates of standing dead tree C stocks are currently used as the official C stock estimates for the...

Modeling decay rates of dead wood in a neotropical forest.

PubMed

Hérault, Bruno; Beauchêne, Jacques; Muller, Félix; Wagner, Fabien; Baraloto, Christopher; Blanc, Lilian; Martin, Jean-Michel

2010-09-01

Variation of dead wood decay rates among tropical trees remains one source of uncertainty in global models of the carbon cycle. Taking advantage of a broad forest plot network surveyed for tree mortality over a 23-year period, we measured the remaining fraction of boles from 367 dead trees from 26 neotropical species widely varying in wood density (0.23-1.24 g cm(-3)) and tree circumference at death time (31.5-272.0 cm). We modeled decay rates within a Bayesian framework assuming a first order differential equation to model the decomposition process and tested for the effects of forest management (selective logging vs. unexploited), of mode of death (standing vs. downed) and of topographical levels (bottomlands vs. hillsides vs. hilltops) on wood decay rates. The general decay model predicts the observed remaining fraction of dead wood (R2 = 60%) with only two biological predictors: tree circumference at death time and wood specific density. Neither selective logging nor local topography had a differential effect on wood decay rates. Including the mode of death into the model revealed that standing dead trees decomposed faster than downed dead trees, but the gain of model accuracy remains rather marginal. Overall, these results suggest that the release of carbon from tropical dead trees to the atmosphere can be simply estimated using tree circumference at death time and wood density.

Using Decision Trees for Estimating Mode Choice of Trips in Buca-Izmir

NASA Astrophysics Data System (ADS)

Oral, L. O.; Tecim, V.

2013-05-01

Decision makers develop transportation plans and models for providing sustainable transport systems in urban areas. Mode Choice is one of the stages in transportation modelling. Data mining techniques can discover factors affecting the mode choice. These techniques can be applied with knowledge process approach. In this study a data mining process model is applied to determine the factors affecting the mode choice with decision trees techniques by considering individual trip behaviours from household survey data collected within Izmir Transportation Master Plan. From this perspective transport mode choice problem is solved on a case in district of Buca-Izmir, Turkey with CRISP-DM knowledge process model.

Determining the Role of Sediment Deposition and Transport in the Formation and Maintenance of Tree Islands in the Florida Everglades

NASA Astrophysics Data System (ADS)

Mitchell-Bruker, S.; Childers, D.; Ross, M.; Leonard, L.; Solo-Gabriel, H.; Stothoff, S.

2002-05-01

Tree islands are a prominent feature in the Everglades ridge and slough wetlands. These tree islands are believed to be a remnant of the historical pre-drainage flow system. Within Everglades National Park, hardwood hammock and bayhead tree islands commonly form as teardrop-shaped mounds, rising above the sawgrass marsh. These tree islands are usually oriented along the direction of surface water flow, with the highest elevation and widest part of the island at the upstream head. The island narrows as it descends into the marsh at the downstream end, terminating in a tail that sometimes includes a zone of dead or dying sawgrass. The shape and orientation of the tree islands suggests that surface water flow has been instrumental in their formation, however occasional flow measurements indicate that the slow moving water of the Everglades does not provide sufficient energy to transport even moderate amounts of suspended sediment. This low flow velocity, coupled with the extremely low turbidity of the Everglades water suggests that if sediment transport and deposition processes are instrumental in forming tree islands, the process is probably occurring over short distances and long time intervals. It is also possible that concentration and transport of nutrients is an important element in tree island formation. Because the Everglades marsh is a low nutrient environment, processes that create areas of increased phosphorous concentration result in changes in the vegetation. Because many hardwood hammock and bayhead tree islands have heads that are situated on bedrock highs, the higher and drier elevation of the head allows for trees to grow. These trees could concentrate phosphorous either by acting as wildlife attractors, or by acting as \\x8Dphosphorous pumpsŒ, transporting groundwater with high concentrations of phosphorous through the roots to the tree. We are characterizing vegetation, litter fall, sediments, surface water flow, hydrologic gradients and nutrient gradients on tree islands and in the surrounding marsh. These data will be analyzed using statistical and hydrologic models to test the hypothesis that surface water flow is an essential force in forming and maintaining tree islands. A sediment and nutrient transport model is being developed to apply these data to scenarios for flow in a vegetated wetland. By constraining model parameters to the limits supported by these data, the full range of possible flow and transport scenarios can be tested in the model. These model results, along with statistical analysis will be used to support or reject the hypothesis that sediment and nutrient transport are key components in the formation of hardwood hammock and bay head tree islands.

Forest understory trees can be segmented accurately within sufficiently dense airborne laser scanning point clouds.

PubMed

Hamraz, Hamid; Contreras, Marco A; Zhang, Jun

2017-07-28

Airborne laser scanning (LiDAR) point clouds over large forested areas can be processed to segment individual trees and subsequently extract tree-level information. Existing segmentation procedures typically detect more than 90% of overstory trees, yet they barely detect 60% of understory trees because of the occlusion effect of higher canopy layers. Although understory trees provide limited financial value, they are an essential component of ecosystem functioning by offering habitat for numerous wildlife species and influencing stand development. Here we model the occlusion effect in terms of point density. We estimate the fractions of points representing different canopy layers (one overstory and multiple understory) and also pinpoint the required density for reasonable tree segmentation (where accuracy plateaus). We show that at a density of ~170 pt/m² understory trees can likely be segmented as accurately as overstory trees. Given the advancements of LiDAR sensor technology, point clouds will affordably reach this required density. Using modern computational approaches for big data, the denser point clouds can efficiently be processed to ultimately allow accurate remote quantification of forest resources. The methodology can also be adopted for other similar remote sensing or advanced imaging applications such as geological subsurface modelling or biomedical tissue analysis.

Process-based modeling of species' responses to climate change - a proof of concept using western North American trees

NASA Astrophysics Data System (ADS)

Evans, M. E.; Merow, C.; Record, S.; Menlove, J.; Gray, A.; Cundiff, J.; McMahon, S.; Enquist, B. J.

2013-12-01

Current attempts to forecast how species' distributions will change in response to climate change suffer under a fundamental trade-off: between modeling many species superficially vs. few species in detail (between correlative vs. mechanistic models). The goals of this talk are two-fold: first, we present a Bayesian multilevel modeling framework, dynamic range modeling (DRM), for building process-based forecasts of many species' distributions at a time, designed to address the trade-off between detail and number of distribution forecasts. In contrast to 'species distribution modeling' or 'niche modeling', which uses only species' occurrence data and environmental data, DRMs draw upon demographic data, abundance data, trait data, occurrence data, and GIS layers of climate in a single framework to account for two processes known to influence range dynamics - demography and dispersal. The vision is to use extensive databases on plant demography, distributions, and traits - in the Botanical Information and Ecology Network, the Forest Inventory and Analysis database (FIA), and the International Tree Ring Data Bank - to develop DRMs for North American trees. Second, we present preliminary results from building the core submodel of a DRM - an integral projection model (IPM) - for a sample of dominant tree species in western North America. IPMs are used to infer demographic niches - i.e., the set of environmental conditions under which population growth rate is positive - and project population dynamics through time. Based on >550,000 data points derived from FIA for nine tree species in western North America, we show IPM-based models of their current and future distributions, and discuss how IPMs can be used to forecast future forest productivity, mortality patterns, and inform efforts at assisted migration.

Automatic detection of key innovations, rate shifts, and diversity-dependence on phylogenetic trees.

PubMed

Rabosky, Daniel L

2014-01-01

A number of methods have been developed to infer differential rates of species diversification through time and among clades using time-calibrated phylogenetic trees. However, we lack a general framework that can delineate and quantify heterogeneous mixtures of dynamic processes within single phylogenies. I developed a method that can identify arbitrary numbers of time-varying diversification processes on phylogenies without specifying their locations in advance. The method uses reversible-jump Markov Chain Monte Carlo to move between model subspaces that vary in the number of distinct diversification regimes. The model assumes that changes in evolutionary regimes occur across the branches of phylogenetic trees under a compound Poisson process and explicitly accounts for rate variation through time and among lineages. Using simulated datasets, I demonstrate that the method can be used to quantify complex mixtures of time-dependent, diversity-dependent, and constant-rate diversification processes. I compared the performance of the method to the MEDUSA model of rate variation among lineages. As an empirical example, I analyzed the history of speciation and extinction during the radiation of modern whales. The method described here will greatly facilitate the exploration of macroevolutionary dynamics across large phylogenetic trees, which may have been shaped by heterogeneous mixtures of distinct evolutionary processes.

Automatic Detection of Key Innovations, Rate Shifts, and Diversity-Dependence on Phylogenetic Trees

PubMed Central

Rabosky, Daniel L.

2014-01-01

A number of methods have been developed to infer differential rates of species diversification through time and among clades using time-calibrated phylogenetic trees. However, we lack a general framework that can delineate and quantify heterogeneous mixtures of dynamic processes within single phylogenies. I developed a method that can identify arbitrary numbers of time-varying diversification processes on phylogenies without specifying their locations in advance. The method uses reversible-jump Markov Chain Monte Carlo to move between model subspaces that vary in the number of distinct diversification regimes. The model assumes that changes in evolutionary regimes occur across the branches of phylogenetic trees under a compound Poisson process and explicitly accounts for rate variation through time and among lineages. Using simulated datasets, I demonstrate that the method can be used to quantify complex mixtures of time-dependent, diversity-dependent, and constant-rate diversification processes. I compared the performance of the method to the MEDUSA model of rate variation among lineages. As an empirical example, I analyzed the history of speciation and extinction during the radiation of modern whales. The method described here will greatly facilitate the exploration of macroevolutionary dynamics across large phylogenetic trees, which may have been shaped by heterogeneous mixtures of distinct evolutionary processes. PMID:24586858

Adapting a scenario tree model for freedom from disease as surveillance progresses: the Canadian notifiable avian influenza model.

PubMed

Christensen, Jette; El Allaki, Farouk; Vallières, André

2014-05-01

Scenario tree models with temporal discounting have been applied in four continents to support claims of freedom from animal disease. Recently, a second (new) model was developed for the same population and disease. This is a natural development because surveillance is a dynamic process that needs to adapt to changing circumstances - the difficulty is the justification for, documentation of, presentation of and the acceptance of the changes. Our objective was to propose a systematic approach to present changes to an existing scenario tree model for freedom from disease. We used the example of how we adapted the deterministic Canadian Notifiable Avian Influenza scenario tree model published in 2011 to a stochastic scenario tree model where the definition of sub-populations and the estimation of probability of introduction of the pathogen were modified. We found that the standardized approach by Vanderstichel et al. (2013) with modifications provided a systematic approach to make and present changes to an existing scenario tree model. We believe that the new 2013 CanNAISS scenario tree model is a better model than the 2011 model because the 2013 model included more surveillance data. In particular, the new data on Notifiable Avian Influenza in Canada from the last 5 years were used to improve input parameters and model structure. Crown Copyright © 2014. Published by Elsevier B.V. All rights reserved.

Faults Discovery By Using Mined Data

NASA Technical Reports Server (NTRS)

Lee, Charles

2005-01-01

Fault discovery in the complex systems consist of model based reasoning, fault tree analysis, rule based inference methods, and other approaches. Model based reasoning builds models for the systems either by mathematic formulations or by experiment model. Fault Tree Analysis shows the possible causes of a system malfunction by enumerating the suspect components and their respective failure modes that may have induced the problem. The rule based inference build the model based on the expert knowledge. Those models and methods have one thing in common; they have presumed some prior-conditions. Complex systems often use fault trees to analyze the faults. Fault diagnosis, when error occurs, is performed by engineers and analysts performing extensive examination of all data gathered during the mission. International Space Station (ISS) control center operates on the data feedback from the system and decisions are made based on threshold values by using fault trees. Since those decision-making tasks are safety critical and must be done promptly, the engineers who manually analyze the data are facing time challenge. To automate this process, this paper present an approach that uses decision trees to discover fault from data in real-time and capture the contents of fault trees as the initial state of the trees.

Tomographic Image Reconstruction Using an Interpolation Method for Tree Decay Detection

Treesearch

Hailin Feng; Guanghui Li; Sheng Fu; Xiping Wang

2014-01-01

Stress wave velocity has been traditionally regarded as an indicator of the extent of damage inside wood. This paper aimed to detect internal decay of urban trees through reconstructing tomographic image of the cross section of a tree trunk. A grid model covering the cross section area of a tree trunk was defined with some assumptions. Stress wave data were processed...

Behavior and sensitivity of an optimal tree diameter growth model under data uncertainty

Treesearch

Don C. Bragg

2005-01-01

Using loblolly pine, shortleaf pine, white oak, and northern red oak as examples, this paper considers the behavior of potential relative increment (PRI) models of optimal tree diameter growth under data uncertainity. Recommendations on intial sample size and the PRI iteractive curve fitting process are provided. Combining different state inventories prior to PRI model...

Tree injury and mortality in fires: developing process-based models

Treesearch

Bret W. Butler; Matthew B. Dickinson

2010-01-01

Wildland fire managers are often required to predict tree injury and mortality when planning a prescribed burn or when considering wildfire management options; and, currently, statistical models based on post-fire observations are the only tools available for this purpose. Implicit in the derivation of statistical models is the assumption that they are strictly...

Prokaryotic evolution and the tree of life are two different things

PubMed Central

Bapteste, Eric; O'Malley, Maureen A; Beiko, Robert G; Ereshefsky, Marc; Gogarten, J Peter; Franklin-Hall, Laura; Lapointe, François-Joseph; Dupré, John; Dagan, Tal; Boucher, Yan; Martin, William

2009-01-01

Background The concept of a tree of life is prevalent in the evolutionary literature. It stems from attempting to obtain a grand unified natural system that reflects a recurrent process of species and lineage splittings for all forms of life. Traditionally, the discipline of systematics operates in a similar hierarchy of bifurcating (sometimes multifurcating) categories. The assumption of a universal tree of life hinges upon the process of evolution being tree-like throughout all forms of life and all of biological time. In multicellular eukaryotes, the molecular mechanisms and species-level population genetics of variation do indeed mainly cause a tree-like structure over time. In prokaryotes, they do not. Prokaryotic evolution and the tree of life are two different things, and we need to treat them as such, rather than extrapolating from macroscopic life to prokaryotes. In the following we will consider this circumstance from philosophical, scientific, and epistemological perspectives, surmising that phylogeny opted for a single model as a holdover from the Modern Synthesis of evolution. Results It was far easier to envision and defend the concept of a universal tree of life before we had data from genomes. But the belief that prokaryotes are related by such a tree has now become stronger than the data to support it. The monistic concept of a single universal tree of life appears, in the face of genome data, increasingly obsolete. This traditional model to describe evolution is no longer the most scientifically productive position to hold, because of the plurality of evolutionary patterns and mechanisms involved. Forcing a single bifurcating scheme onto prokaryotic evolution disregards the non-tree-like nature of natural variation among prokaryotes and accounts for only a minority of observations from genomes. Conclusion Prokaryotic evolution and the tree of life are two different things. Hence we will briefly set out alternative models to the tree of life to study their evolution. Ultimately, the plurality of evolutionary patterns and mechanisms involved, such as the discontinuity of the process of evolution across the prokaryote-eukaryote divide, summons forth a pluralistic approach to studying evolution. Reviewers This article was reviewed by Ford Doolittle, John Logsdon and Nicolas Galtier. PMID:19788731

Prokaryotic evolution and the tree of life are two different things.

PubMed

Bapteste, Eric; O'Malley, Maureen A; Beiko, Robert G; Ereshefsky, Marc; Gogarten, J Peter; Franklin-Hall, Laura; Lapointe, François-Joseph; Dupré, John; Dagan, Tal; Boucher, Yan; Martin, William

2009-09-29

The concept of a tree of life is prevalent in the evolutionary literature. It stems from attempting to obtain a grand unified natural system that reflects a recurrent process of species and lineage splittings for all forms of life. Traditionally, the discipline of systematics operates in a similar hierarchy of bifurcating (sometimes multifurcating) categories. The assumption of a universal tree of life hinges upon the process of evolution being tree-like throughout all forms of life and all of biological time. In multicellular eukaryotes, the molecular mechanisms and species-level population genetics of variation do indeed mainly cause a tree-like structure over time. In prokaryotes, they do not. Prokaryotic evolution and the tree of life are two different things, and we need to treat them as such, rather than extrapolating from macroscopic life to prokaryotes. In the following we will consider this circumstance from philosophical, scientific, and epistemological perspectives, surmising that phylogeny opted for a single model as a holdover from the Modern Synthesis of evolution. It was far easier to envision and defend the concept of a universal tree of life before we had data from genomes. But the belief that prokaryotes are related by such a tree has now become stronger than the data to support it. The monistic concept of a single universal tree of life appears, in the face of genome data, increasingly obsolete. This traditional model to describe evolution is no longer the most scientifically productive position to hold, because of the plurality of evolutionary patterns and mechanisms involved. Forcing a single bifurcating scheme onto prokaryotic evolution disregards the non-tree-like nature of natural variation among prokaryotes and accounts for only a minority of observations from genomes. Prokaryotic evolution and the tree of life are two different things. Hence we will briefly set out alternative models to the tree of life to study their evolution. Ultimately, the plurality of evolutionary patterns and mechanisms involved, such as the discontinuity of the process of evolution across the prokaryote-eukaryote divide, summons forth a pluralistic approach to studying evolution. This article was reviewed by Ford Doolittle, John Logsdon and Nicolas Galtier.

Modeling of Water Flow Processes in the Soil-Plant-Atmosphere System: The Soil-Tree-Atmosphere Continuum Model

NASA Astrophysics Data System (ADS)

Massoud, E. C.; Vrugt, J. A.

2015-12-01

Trees and forests play a key role in controlling the water and energy balance at the land-air surface. This study reports on the calibration of an integrated soil-tree-atmosphere continuum (STAC) model using Bayesian inference with the DREAM algorithm and temporal observations of soil moisture content, matric head, sap flux, and leaf water potential from the King's River Experimental Watershed (KREW) in the southern Sierra Nevada mountain range in California. Water flow through the coupled system is described using the Richards' equation with both the soil and tree modeled as a porous medium with nonlinear soil and tree water relationships. Most of the model parameters appear to be reasonably well defined by calibration against the observed data. The posterior mean simulation reproduces the observed soil and tree data quite accurately, but a systematic mismatch is observed between early afternoon measured and simulated sap fluxes. We will show how this points to a structural error in the STAC-model and suggest and test an alternative hypothesis for root water uptake that alleviates this problem.

Using incident response trees as a tool for risk management of online financial services.

PubMed

Gorton, Dan

2014-09-01

The article introduces the use of probabilistic risk assessment for modeling the incident response process of online financial services. The main contribution is the creation of incident response trees, using event tree analysis, which provides us with a visual tool and a systematic way to estimate the probability of a successful incident response process against the currently known risk landscape, making it possible to measure the balance between front-end and back-end security measures. The model is presented using an illustrative example, and is then applied to the incident response process of a Swedish bank. Access to relevant data is verified and the applicability and usability of the proposed model is verified using one year of historical data. Potential advantages and possible shortcomings are discussed, referring to both the design phase and the operational phase, and future work is presented. © 2014 Society for Risk Analysis.

Model-based conifer crown surface reconstruction from multi-ocular high-resolution aerial imagery

NASA Astrophysics Data System (ADS)

Sheng, Yongwei

2000-12-01

Tree crown parameters such as width, height, shape and crown closure are desirable in forestry and ecological studies, but they are time-consuming and labor intensive to measure in the field. The stereoscopic capability of high-resolution aerial imagery provides a way to crown surface reconstruction. Existing photogrammetric algorithms designed to map terrain surfaces, however, cannot adequately extract crown surfaces, especially for steep conifer crowns. Considering crown surface reconstruction in a broader context of tree characterization from aerial images, we develop a rigorous perspective tree image formation model to bridge image-based tree extraction and crown surface reconstruction, and an integrated model-based approach to conifer crown surface reconstruction. Based on the fact that most conifer crowns are in a solid geometric form, conifer crowns are modeled as a generalized hemi-ellipsoid. Both the automatic and semi-automatic approaches are investigated to optimal tree model development from multi-ocular images. The semi-automatic 3D tree interpreter developed in this thesis is able to efficiently extract reliable tree parameters and tree models in complicated tree stands. This thesis starts with a sophisticated stereo matching algorithm, and incorporates tree models to guide stereo matching. The following critical problems are addressed in the model-based surface reconstruction process: (1) the problem of surface model composition from tree models, (2) the occlusion problem in disparity prediction from tree models, (3) the problem of integrating the predicted disparities into image matching, (4) the tree model edge effect reduction on the disparity map, (5) the occlusion problem in orthophoto production, and (6) the foreshortening problem in image matching, which is very serious for conifer crown surfaces. Solutions to the above problems are necessary for successful crown surface reconstruction. The model-based approach was applied to recover the canopy surface of a dense redwood stand using tri-ocular high-resolution images scanned from 1:2,400 aerial photographs. The results demonstrate the approach's ability to reconstruct complicated stands. The model-based approach proposed in this thesis is potentially applicable to other surfaces recovering problems with a priori knowledge about objects.

Artificial Neural Networks for Processing Graphs with Application to Image Understanding: A Survey

NASA Astrophysics Data System (ADS)

Bianchini, Monica; Scarselli, Franco

In graphical pattern recognition, each data is represented as an arrangement of elements, that encodes both the properties of each element and the relations among them. Hence, patterns are modelled as labelled graphs where, in general, labels can be attached to both nodes and edges. Artificial neural networks able to process graphs are a powerful tool for addressing a great variety of real-world problems, where the information is naturally organized in entities and relationships among entities and, in fact, they have been widely used in computer vision, f.i. in logo recognition, in similarity retrieval, and for object detection. In this chapter, we propose a survey of neural network models able to process structured information, with a particular focus on those architectures tailored to address image understanding applications. Starting from the original recursive model (RNNs), we subsequently present different ways to represent images - by trees, forests of trees, multiresolution trees, directed acyclic graphs with labelled edges, general graphs - and, correspondingly, neural network architectures appropriate to process such structures.

A Lidar Point Cloud Based Procedure for Vertical Canopy Structure Analysis And 3D Single Tree Modelling in Forest

PubMed Central

Wang, Yunsheng; Weinacker, Holger; Koch, Barbara

2008-01-01

A procedure for both vertical canopy structure analysis and 3D single tree modelling based on Lidar point cloud is presented in this paper. The whole area of research is segmented into small study cells by a raster net. For each cell, a normalized point cloud whose point heights represent the absolute heights of the ground objects is generated from the original Lidar raw point cloud. The main tree canopy layers and the height ranges of the layers are detected according to a statistical analysis of the height distribution probability of the normalized raw points. For the 3D modelling of individual trees, individual trees are detected and delineated not only from the top canopy layer but also from the sub canopy layer. The normalized points are resampled into a local voxel space. A series of horizontal 2D projection images at the different height levels are then generated respect to the voxel space. Tree crown regions are detected from the projection images. Individual trees are then extracted by means of a pre-order forest traversal process through all the tree crown regions at the different height levels. Finally, 3D tree crown models of the extracted individual trees are reconstructed. With further analyses on the 3D models of individual tree crowns, important parameters such as crown height range, crown volume and crown contours at the different height levels can be derived. PMID:27879916

Using decision trees to characterize verbal communication during change and stuck episodes in the therapeutic process

PubMed Central

Masías, Víctor H.; Krause, Mariane; Valdés, Nelson; Pérez, J. C.; Laengle, Sigifredo

2015-01-01

Methods are needed for creating models to characterize verbal communication between therapists and their patients that are suitable for teaching purposes without losing analytical potential. A technique meeting these twin requirements is proposed that uses decision trees to identify both change and stuck episodes in therapist-patient communication. Three decision tree algorithms (C4.5, NBTree, and REPTree) are applied to the problem of characterizing verbal responses into change and stuck episodes in the therapeutic process. The data for the problem is derived from a corpus of 8 successful individual therapy sessions with 1760 speaking turns in a psychodynamic context. The decision tree model that performed best was generated by the C4.5 algorithm. It delivered 15 rules characterizing the verbal communication in the two types of episodes. Decision trees are a promising technique for analyzing verbal communication during significant therapy events and have much potential for use in teaching practice on changes in therapeutic communication. The development of pedagogical methods using decision trees can support the transmission of academic knowledge to therapeutic practice. PMID:25914657

Using decision trees to characterize verbal communication during change and stuck episodes in the therapeutic process.

PubMed

Masías, Víctor H; Krause, Mariane; Valdés, Nelson; Pérez, J C; Laengle, Sigifredo

2015-01-01

Methods are needed for creating models to characterize verbal communication between therapists and their patients that are suitable for teaching purposes without losing analytical potential. A technique meeting these twin requirements is proposed that uses decision trees to identify both change and stuck episodes in therapist-patient communication. Three decision tree algorithms (C4.5, NBTree, and REPTree) are applied to the problem of characterizing verbal responses into change and stuck episodes in the therapeutic process. The data for the problem is derived from a corpus of 8 successful individual therapy sessions with 1760 speaking turns in a psychodynamic context. The decision tree model that performed best was generated by the C4.5 algorithm. It delivered 15 rules characterizing the verbal communication in the two types of episodes. Decision trees are a promising technique for analyzing verbal communication during significant therapy events and have much potential for use in teaching practice on changes in therapeutic communication. The development of pedagogical methods using decision trees can support the transmission of academic knowledge to therapeutic practice.

3D Tree Dimensionality Assessment Using Photogrammetry and Small Unmanned Aerial Vehicles

PubMed Central

2015-01-01

Detailed, precise, three-dimensional (3D) representations of individual trees are a prerequisite for an accurate assessment of tree competition, growth, and morphological plasticity. Until recently, our ability to measure the dimensionality, spatial arrangement, shape of trees, and shape of tree components with precision has been constrained by technological and logistical limitations and cost. Traditional methods of forest biometrics provide only partial measurements and are labor intensive. Active remote technologies such as LiDAR operated from airborne platforms provide only partial crown reconstructions. The use of terrestrial LiDAR is laborious, has portability limitations and high cost. In this work we capitalized on recent improvements in the capabilities and availability of small unmanned aerial vehicles (UAVs), light and inexpensive cameras, and developed an affordable method for obtaining precise and comprehensive 3D models of trees and small groups of trees. The method employs slow-moving UAVs that acquire images along predefined trajectories near and around targeted trees, and computer vision-based approaches that process the images to obtain detailed tree reconstructions. After we confirmed the potential of the methodology via simulation we evaluated several UAV platforms, strategies for image acquisition, and image processing algorithms. We present an original, step-by-step workflow which utilizes open source programs and original software. We anticipate that future development and applications of our method will improve our understanding of forest self-organization emerging from the competition among trees, and will lead to a refined generation of individual-tree-based forest models. PMID:26393926

3D Tree Dimensionality Assessment Using Photogrammetry and Small Unmanned Aerial Vehicles.

PubMed

Gatziolis, Demetrios; Lienard, Jean F; Vogs, Andre; Strigul, Nikolay S

2015-01-01

Detailed, precise, three-dimensional (3D) representations of individual trees are a prerequisite for an accurate assessment of tree competition, growth, and morphological plasticity. Until recently, our ability to measure the dimensionality, spatial arrangement, shape of trees, and shape of tree components with precision has been constrained by technological and logistical limitations and cost. Traditional methods of forest biometrics provide only partial measurements and are labor intensive. Active remote technologies such as LiDAR operated from airborne platforms provide only partial crown reconstructions. The use of terrestrial LiDAR is laborious, has portability limitations and high cost. In this work we capitalized on recent improvements in the capabilities and availability of small unmanned aerial vehicles (UAVs), light and inexpensive cameras, and developed an affordable method for obtaining precise and comprehensive 3D models of trees and small groups of trees. The method employs slow-moving UAVs that acquire images along predefined trajectories near and around targeted trees, and computer vision-based approaches that process the images to obtain detailed tree reconstructions. After we confirmed the potential of the methodology via simulation we evaluated several UAV platforms, strategies for image acquisition, and image processing algorithms. We present an original, step-by-step workflow which utilizes open source programs and original software. We anticipate that future development and applications of our method will improve our understanding of forest self-organization emerging from the competition among trees, and will lead to a refined generation of individual-tree-based forest models.

Simulation-Based Model Checking for Nondeterministic Systems and Rare Events

DTIC Science & Technology

2016-03-24

year, we have investigated AO* search and Monte Carlo Tree Search algorithms to complement and enhance CMU’s SMCMDP. 1 Final Report, March 14... tree , so we can use it to find the probability of reachability for a property in PRISM’s Probabilistic LTL. By finding the maximum probability of...savings, particularly when handling very large models. 2.3 Monte Carlo Tree Search The Monte Carlo sampling process in SMCMDP can take a long time to

Proposed Hydrodynamic Model Increases the Ability of Land-Surface Models to Capture Intra-Daily Dynamics of Transpiration and Canopy Structure Effects

NASA Astrophysics Data System (ADS)

Matheny, A. M.; Bohrer, G.; Mirfenderesgi, G.; Schafer, K. V.; Ivanov, V. Y.

2014-12-01

Hydraulic limitations are known to control transpiration in forest ecosystems when the soil is drying or when the vapor pressure deficit between the air and stomata is very large, but they can also impact stomatal apertures under conditions of adequate soil moisture and lower evaporative demand. We use the NACP dataset of latent heat flux measurements and model observations for multiple sites and models to demonstrate models' difficulties in capturing intra-daily hysteresis. We hypothesize that this is a result of un-resolved afternoon stomata closure due to hydrodynamic stresses. The current formulations for stomatal conductance and the empirical coupling between stomatal conductance and soil moisture used by these models does not resolve the hydrodynamic process of water movement from the soil to the leaves. This approach does not take advantage of advances in our understanding of water flow and storage in the trees, or of tree and canopy structure. A more thorough representation of the tree-hydrodynamic processes could potentially remedy this significant source of model error. In a forest plot at the University of Michigan Biological Station, we use measurements of sap flux and leaf water potential to demonstrate that trees of similar type - late successional deciduous trees - have very different hydrodynamic strategies that lead to differences in their temporal patterns of stomatal conductance and thus hysteretic cycles of transpiration. These differences will lead to large differences in conductance and water use based on the species composition of the forest. We also demonstrate that the size and shape of the tree branching system leads to differences in extent of hydrodynamic stress, which may change the forest respiration patterns as the forest grows and ages. We propose a framework to resolve tree hydrodynamics in global and regional models based on the Finite-Elements Tree-Crown Hydrodynamics model (FETCH) -a hydrodynamic model that can resolve the fast dynamics of stomatal conductance. FETCH simulates water flow through a tree as a system of porous media conduits and calculates the amount of hydraulic limitation to stomatal conductance, given the atmospheric and biological variables from the global model, and could replace the current empirical formulation for stomatal adjustment based on soil moisture.

A Decision Tree for Nonmetric Sex Assessment from the Skull.

PubMed

Langley, Natalie R; Dudzik, Beatrix; Cloutier, Alesia

2018-01-01

This study uses five well-documented cranial nonmetric traits (glabella, mastoid process, mental eminence, supraorbital margin, and nuchal crest) and one additional trait (zygomatic extension) to develop a validated decision tree for sex assessment. The decision tree was built and cross-validated on a sample of 293 U.S. White individuals from the William M. Bass Donated Skeletal Collection. Ordinal scores from the six traits were analyzed using the partition modeling option in JMP Pro 12. A holdout sample of 50 skulls was used to test the model. The most accurate decision tree includes three variables: glabella, zygomatic extension, and mastoid process. This decision tree yielded 93.5% accuracy on the training sample, 94% on the cross-validated sample, and 96% on a holdout validation sample. Linear weighted kappa statistics indicate acceptable agreement among observers for these variables. Mental eminence should be avoided, and definitions and figures should be referenced carefully to score nonmetric traits. © 2017 American Academy of Forensic Sciences.

Research on the discharge characteristics for water tree in crosslinked polyethylene cable based on plasma-chemical model

NASA Astrophysics Data System (ADS)

Fan, Yang; Qi, Yang; Bing, Gao; Rong, Xia; Yanjie, Le; Iroegbu, Paul Ikechukwu

2018-03-01

Water tree is the predominant defect in high-voltage crosslinked polyethylene cables. The microscopic mechanism in the discharge process is not fully understood; hence, a drawback is created towards an effective method to evaluate the insulation status. In order to investigate the growth of water tree, a plasma-chemical model is developed. The dynamic characteristics of the discharge process including voltage waveform, current waveform, electron density, electric potential, and electric field intensity are analyzed. Our results show that the distorted electric field is the predominant contributing factor of electron avalanche formation, which inevitably leads to the formation of pulse current. In addition, it is found that characteristic parameters such as the pulse width and pulse number have a great relevance to the length of water tree. Accordingly, the growth of water tree can be divided into the initial stage, development stage, and pre-breakdown stage, which provides a reference for evaluating the deteriorated stages of crosslinked polyethylene cables.

Variation across mitochondrial gene trees provides evidence for systematic error: How much gene tree variation is biological?

PubMed

Richards, Emilie J; Brown, Jeremy M; Barley, Anthony J; Chong, Rebecca A; Thomson, Robert C

2018-02-19

The use of large genomic datasets in phylogenetics has highlighted extensive topological variation across genes. Much of this discordance is assumed to result from biological processes. However, variation among gene trees can also be a consequence of systematic error driven by poor model fit, and the relative importance of biological versus methodological factors in explaining gene tree variation is a major unresolved question. Using mitochondrial genomes to control for biological causes of gene tree variation, we estimate the extent of gene tree discordance driven by systematic error and employ posterior prediction to highlight the role of model fit in producing this discordance. We find that the amount of discordance among mitochondrial gene trees is similar to the amount of discordance found in other studies that assume only biological causes of variation. This similarity suggests that the role of systematic error in generating gene tree variation is underappreciated and critical evaluation of fit between assumed models and the data used for inference is important for the resolution of unresolved phylogenetic questions.

Forest fire effects on transpiration: process modeling of sapwood area reduction

NASA Astrophysics Data System (ADS)

Michaletz, Sean; Johnson, Edward

2010-05-01

Transpiration is a hydrological process that is strongly affected by forest fires. In crown fires, canopy fine fuels (foliage, buds, and small branches) combust, which kills individual trees and stops transpiration of the entire stand. In surface fires (intensities ≤ 2500 kW m-1), however, effects on transpiration are less predictable becuase heat transfer from the passing fireline can injure or kill fine roots, leaves, and sapwood; post-fire transpiration of forest stands is thus governed by fire effects on individual tree water budgets. Here, we consider fire effects on cross-sectional sapwood area. A two-dimensional model of transient bole heating is used to estimate radial isotherms for a range of fireline intensities typical of surface fires. Isotherms are then used to drive three processes by which heat may reduce sapwood area: 1) necrosis of living cells in contact with xylem conduits, which prevents repair of natural embolism; 2) relaxation of viscoelastic conduit wall polymers (cellulose, hemicelloluse, and lignin), which reduces cross-sectional conduit area; and 3) boiling of metastable water under tension, which causes conduit embolism. Results show that these processes operate on different time scales, suggesting that fire effects on transpiration vary with time since fire. The model can be linked with a three-dimensional physical fire spread model to predict size-dependent effects on individual trees, which can be used to estimate scaling of individual tree and stand-level transpiration.

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

PubMed Central

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

2014-01-01

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

Applying and Individual-Based Model to Simultaneously Evaluate Net Ecosystem Production and Tree Diameter Increment

NASA Astrophysics Data System (ADS)

Fang, F. J.

2017-12-01

Reconciling observations at fundamentally different scales is central in understanding the global carbon cycle. This study investigates a model-based melding of forest inventory data, remote-sensing data and micrometeorological-station data ("flux towers" estimating forest heat, CO2 and H2O fluxes). The individual tree-based model FORCCHN was used to evaluate the tree DBH increment and forest carbon fluxes. These are the first simultaneous simulations of the forest carbon budgets from flux towers and individual-tree growth estimates of forest carbon budgets using the continuous forest inventory data — under circumstances in which both predictions can be tested. Along with the global implications of such findings, this also improves the capacity for forest sustainable management and the comprehensive understanding of forest ecosystems. In forest ecology, diameter at breast height (DBH) of a tree significantly determines an individual tree's cross-sectional sapwood area, its biomass and carbon storage. Evaluation the annual DBH increment (ΔDBH) of an individual tree is central to understanding tree growth and forest ecology. Ecosystem Carbon flux is a consequence of key ecosystem processes in the forest-ecosystem carbon cycle, Gross and Net Primary Production (GPP and NPP, respectively) and Net Ecosystem Respiration (NEP). All of these closely relate with tree DBH changes and tree death. Despite advances in evaluating forest carbon fluxes with flux towers and forest inventories for individual tree ΔDBH, few current ecological models can simultaneously quantify and predict the tree ΔDBH and forest carbon flux.

A Novel Modelling Approach for Predicting Forest Growth and Yield under Climate Change.

PubMed

Ashraf, M Irfan; Meng, Fan-Rui; Bourque, Charles P-A; MacLean, David A

2015-01-01

Global climate is changing due to increasing anthropogenic emissions of greenhouse gases. Forest managers need growth and yield models that can be used to predict future forest dynamics during the transition period of present-day forests under a changing climatic regime. In this study, we developed a forest growth and yield model that can be used to predict individual-tree growth under current and projected future climatic conditions. The model was constructed by integrating historical tree growth records with predictions from an ecological process-based model using neural networks. The new model predicts basal area (BA) and volume growth for individual trees in pure or mixed species forests. For model development, tree-growth data under current climatic conditions were obtained using over 3000 permanent sample plots from the Province of Nova Scotia, Canada. Data to reflect tree growth under a changing climatic regime were projected with JABOWA-3 (an ecological process-based model). Model validation with designated data produced model efficiencies of 0.82 and 0.89 in predicting individual-tree BA and volume growth. Model efficiency is a relative index of model performance, where 1 indicates an ideal fit, while values lower than zero means the predictions are no better than the average of the observations. Overall mean prediction error (BIAS) of basal area and volume growth predictions was nominal (i.e., for BA: -0.0177 cm(2) 5-year(-1) and volume: 0.0008 m(3) 5-year(-1)). Model variability described by root mean squared error (RMSE) in basal area prediction was 40.53 cm(2) 5-year(-1) and 0.0393 m(3) 5-year(-1) in volume prediction. The new modelling approach has potential to reduce uncertainties in growth and yield predictions under different climate change scenarios. This novel approach provides an avenue for forest managers to generate required information for the management of forests in transitional periods of climate change. Artificial intelligence technology has substantial potential in forest modelling.

A Novel Modelling Approach for Predicting Forest Growth and Yield under Climate Change

PubMed Central

Ashraf, M. Irfan; Meng, Fan-Rui; Bourque, Charles P.-A.; MacLean, David A.

2015-01-01

Global climate is changing due to increasing anthropogenic emissions of greenhouse gases. Forest managers need growth and yield models that can be used to predict future forest dynamics during the transition period of present-day forests under a changing climatic regime. In this study, we developed a forest growth and yield model that can be used to predict individual-tree growth under current and projected future climatic conditions. The model was constructed by integrating historical tree growth records with predictions from an ecological process-based model using neural networks. The new model predicts basal area (BA) and volume growth for individual trees in pure or mixed species forests. For model development, tree-growth data under current climatic conditions were obtained using over 3000 permanent sample plots from the Province of Nova Scotia, Canada. Data to reflect tree growth under a changing climatic regime were projected with JABOWA-3 (an ecological process-based model). Model validation with designated data produced model efficiencies of 0.82 and 0.89 in predicting individual-tree BA and volume growth. Model efficiency is a relative index of model performance, where 1 indicates an ideal fit, while values lower than zero means the predictions are no better than the average of the observations. Overall mean prediction error (BIAS) of basal area and volume growth predictions was nominal (i.e., for BA: -0.0177 cm2 5-year-1 and volume: 0.0008 m3 5-year-1). Model variability described by root mean squared error (RMSE) in basal area prediction was 40.53 cm2 5-year-1 and 0.0393 m3 5-year-1 in volume prediction. The new modelling approach has potential to reduce uncertainties in growth and yield predictions under different climate change scenarios. This novel approach provides an avenue for forest managers to generate required information for the management of forests in transitional periods of climate change. Artificial intelligence technology has substantial potential in forest modelling. PMID:26173081

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.

Climatic correlates of tree mortality in water- and energy-limited forests

USGS Publications Warehouse

Das, Adrian J.; Stephenson, Nathan L.; Flint, Alan; Das, Tapash; van Mantgem, Phillip J.

2013-01-01

Recent increases in tree mortality rates across the western USA are correlated with increasing temperatures, but mechanisms remain unresolved. Specifically, increasing mortality could predominantly be a consequence of temperature-induced increases in either (1) drought stress, or (2) the effectiveness of tree-killing insects and pathogens. Using long-term data from California’s Sierra Nevada mountain range, we found that in water-limited (low-elevation) forests mortality was unambiguously best modeled by climatic water deficit, consistent with the first mechanism. In energy-limited (high-elevation) forests deficit models were only equivocally better than temperature models, suggesting that the second mechanism is increasingly important in these forests. We could not distinguish between models predicting mortality using absolute versus relative changes in water deficit, and these two model types led to different forecasts of mortality vulnerability under future climate scenarios. Our results provide evidence for differing climatic controls of tree mortality in water- and energy-limited forests, while highlighting the need for an improved understanding of tree mortality processes.

Climatic correlates of tree mortality in water- and energy-limited forests.

PubMed

Das, Adrian J; Stephenson, Nathan L; Flint, Alan; Das, Tapash; van Mantgem, Phillip J

2013-01-01

Recent increases in tree mortality rates across the western USA are correlated with increasing temperatures, but mechanisms remain unresolved. Specifically, increasing mortality could predominantly be a consequence of temperature-induced increases in either (1) drought stress, or (2) the effectiveness of tree-killing insects and pathogens. Using long-term data from California's Sierra Nevada mountain range, we found that in water-limited (low-elevation) forests mortality was unambiguously best modeled by climatic water deficit, consistent with the first mechanism. In energy-limited (high-elevation) forests deficit models were only equivocally better than temperature models, suggesting that the second mechanism is increasingly important in these forests. We could not distinguish between models predicting mortality using absolute versus relative changes in water deficit, and these two model types led to different forecasts of mortality vulnerability under future climate scenarios. Our results provide evidence for differing climatic controls of tree mortality in water- and energy-limited forests, while highlighting the need for an improved understanding of tree mortality processes.

Climatic Correlates of Tree Mortality in Water- and Energy-Limited Forests

PubMed Central

Das, Adrian J.; Stephenson, Nathan L.; Flint, Alan; Das, Tapash; van Mantgem, Phillip J.

2013-01-01

Recent increases in tree mortality rates across the western USA are correlated with increasing temperatures, but mechanisms remain unresolved. Specifically, increasing mortality could predominantly be a consequence of temperature-induced increases in either (1) drought stress, or (2) the effectiveness of tree-killing insects and pathogens. Using long-term data from California’s Sierra Nevada mountain range, we found that in water-limited (low-elevation) forests mortality was unambiguously best modeled by climatic water deficit, consistent with the first mechanism. In energy-limited (high-elevation) forests deficit models were only equivocally better than temperature models, suggesting that the second mechanism is increasingly important in these forests. We could not distinguish between models predicting mortality using absolute versus relative changes in water deficit, and these two model types led to different forecasts of mortality vulnerability under future climate scenarios. Our results provide evidence for differing climatic controls of tree mortality in water- and energy-limited forests, while highlighting the need for an improved understanding of tree mortality processes. PMID:23936118

Evaluation of four methods for estimating leaf area of isolated trees

Treesearch

P.J. Peper; E.G. McPherson

2003-01-01

The accurate modeling of the physiological and functional processes of urban forests requires information on the leaf area of urban tree species. Several non-destructive, indirect leaf area sampling methods have shown good performance for homogenous canopies. These methods have not been evaluated for use in urban settings where trees are typically isolated and...

Tree mortality from drought, insects, and their interactions in a changing climate

Treesearch

William R. L. Anderegg; Jeffrey A. Hicke; Rosie A. Fisher; Craig D. Allen; Juliann Aukema; Barbara Bentz; Sharon Hood; Jeremy W. Lichstein; Alison K. Macalady; Nate McDowell; Yude Pan; Kenneth Raffa; Anna Sala; John D. Shaw; Nathan L. Stephenson; Christina Tague; Melanie Zeppel

2015-01-01

Climate change is expected to drive increased tree mortality through drought, heat stress, and insect attacks, with manifold impacts on forest ecosystems. Yet, climate-induced tree mortality and biotic disturbance agents are largely absent from process-based ecosystem models. Using data sets from the western USA and associated studies, we present a framework for...

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

A Test of Carbon and Oxygen Stable Isotope Ratio Process Models in Tree Rings.

NASA Astrophysics Data System (ADS)

Roden, J. S.; Farquhar, G. D.

2008-12-01

Stable isotopes ratios of carbon and oxygen in tree ring cellulose have been used to infer environmental change. Process-based models have been developed to clarify the potential of historic tree ring records for meaningful paleoclimatic reconstructions. However, isotopic variation can be influenced by multiple environmental factors making simplistic interpretations problematic. Recently, the dual isotope approach, where the variation in one stable isotope ratio (e.g. oxygen) is used to constrain the interpretation of variation in another (e.g. carbon), has been shown to have the potential to de-convolute isotopic analysis. However, this approach requires further testing to determine its applicability for paleo-reconstructions using tree-ring time series. We present a study where the information needed to parameterize mechanistic models for both carbon and oxygen stable isotope ratios were collected in controlled environment chambers for two species (Pinus radiata and Eucalyptus globulus). The seedlings were exposed to treatments designed to modify leaf temperature, transpiration rates, stomatal conductance and photosynthetic capacity. Both species were grown for over 100 days under two humidity regimes that differed by 20%. Stomatal conductance was significantly different between species and for seedlings under drought conditions but not between other treatments or humidity regimes. The treatments produced large differences in transpiration rate and photosynthesis. Treatments that effected photosynthetic rates but not stomatal conductance influenced carbon isotope discrimination more than those that influenced primarily conductance. The various treatments produced a range in oxygen isotope ratios of 7 ‰. Process models predicted greater oxygen isotope enrichment in tree ring cellulose than observed. The oxygen isotope ratios of bulk leaf water were reasonably well predicted by current steady-state models. However, the fractional difference between models that predict bulk leaf water versus the site of evaporation did not increase with transpiration rates. In conclusion, although the dual isotope approach may better constrain interpretation of isotopic variation, more work is required before its predictive power can be applied to tree-ring archives.

Modeling the relationships among internal defect features and external Appalachian hardwood log defect indicators

Treesearch

R. Edward Thomas

2009-01-01

As a hardwood tree grows and develops, surface defects such as branch stubs and wounds are overgrown. Evidence of these defects remain on the log surface for decades and in many instances for the life of the tree. As the tree grows the defect is encapsulated or grown over by new wood. During this process the appearance of the defect in the tree's bark changes. The...

Using Fault Trees to Advance Understanding of Diagnostic Errors.

PubMed

Rogith, Deevakar; Iyengar, M Sriram; Singh, Hardeep

2017-11-01

Diagnostic errors annually affect at least 5% of adults in the outpatient setting in the United States. Formal analytic techniques are only infrequently used to understand them, in part because of the complexity of diagnostic processes and clinical work flows involved. In this article, diagnostic errors were modeled using fault tree analysis (FTA), a form of root cause analysis that has been successfully used in other high-complexity, high-risk contexts. How factors contributing to diagnostic errors can be systematically modeled by FTA to inform error understanding and error prevention is demonstrated. A team of three experts reviewed 10 published cases of diagnostic error and constructed fault trees. The fault trees were modeled according to currently available conceptual frameworks characterizing diagnostic error. The 10 trees were then synthesized into a single fault tree to identify common contributing factors and pathways leading to diagnostic error. FTA is a visual, structured, deductive approach that depicts the temporal sequence of events and their interactions in a formal logical hierarchy. The visual FTA enables easier understanding of causative processes and cognitive and system factors, as well as rapid identification of common pathways and interactions in a unified fashion. In addition, it enables calculation of empirical estimates for causative pathways. Thus, fault trees might provide a useful framework for both quantitative and qualitative analysis of diagnostic errors. Future directions include establishing validity and reliability by modeling a wider range of error cases, conducting quantitative evaluations, and undertaking deeper exploration of other FTA capabilities. Copyright © 2017 The Joint Commission. Published by Elsevier Inc. All rights reserved.

The user's guide to STEMS (Stand and Tree Evaluation and Modeling System).

Treesearch

David M. Belcher

1981-01-01

Presents the structure of STEMS, a computer program for projecting growth of individual trees within the Lake States Region, and discusses its input, processing, major subsystems, and output. Includes an example projection.

Empirical Succession Mapping and Data Assimilation to Constrain Demographic Processes in an Ecosystem Model

NASA Astrophysics Data System (ADS)

Kelly, R.; Andrews, T.; Dietze, M.

2015-12-01

Shifts in ecological communities in response to environmental change have implications for biodiversity, ecosystem function, and feedbacks to global climate change. Community composition is fundamentally the product of demography, but demographic processes are simplified or missing altogether in many ecosystem, Earth system, and species distribution models. This limitation arises in part because demographic data are noisy and difficult to synthesize. As a consequence, demographic processes are challenging to formulate in models in the first place, and to verify and constrain with data thereafter. Here, we used a novel analysis of the USFS Forest Inventory Analysis to improve the representation of demography in an ecosystem model. First, we created an Empirical Succession Mapping (ESM) based on ~1 million individual tree observations from the eastern U.S. to identify broad demographic patterns related to forest succession and disturbance. We used results from this analysis to guide reformulation of the Ecosystem Demography model (ED), an existing forest simulator with explicit tree demography. Results from the ESM reveal a coherent, cyclic pattern of change in temperate forest tree size and density over the eastern U.S. The ESM captures key ecological processes including succession, self-thinning, and gap-filling, and quantifies the typical trajectory of these processes as a function of tree size and stand density. Recruitment is most rapid in early-successional stands with low density and mean diameter, but slows as stand density increases; mean diameter increases until thinning promotes recruitment of small-diameter trees. Strikingly, the upper bound of size-density space that emerges in the ESM conforms closely to the self-thinning power law often observed in ecology. The ED model obeys this same overall size-density boundary, but overestimates plot-level growth, mortality, and fecundity rates, leading to unrealistic emergent demographic patterns. In particular, the current ED formulation cannot capture steady state dynamics evident in the ESM. Ongoing efforts are aimed at reformulating ED to more closely approach overall forest dynamics evident in the ESM, and then assimilating inventory data to constrain model parameters and initial conditions.

Efficient Exploration of the Space of Reconciled Gene Trees

PubMed Central

Szöllősi, Gergely J.; Rosikiewicz, Wojciech; Boussau, Bastien; Tannier, Eric; Daubin, Vincent

2013-01-01

Gene trees record the combination of gene-level events, such as duplication, transfer and loss (DTL), and species-level events, such as speciation and extinction. Gene tree–species tree reconciliation methods model these processes by drawing gene trees into the species tree using a series of gene and species-level events. The reconstruction of gene trees based on sequence alone almost always involves choosing between statistically equivalent or weakly distinguishable relationships that could be much better resolved based on a putative species tree. To exploit this potential for accurate reconstruction of gene trees, the space of reconciled gene trees must be explored according to a joint model of sequence evolution and gene tree–species tree reconciliation. Here we present amalgamated likelihood estimation (ALE), a probabilistic approach to exhaustively explore all reconciled gene trees that can be amalgamated as a combination of clades observed in a sample of gene trees. We implement the ALE approach in the context of a reconciliation model (Szöllősi et al. 2013), which allows for the DTL of genes. We use ALE to efficiently approximate the sum of the joint likelihood over amalgamations and to find the reconciled gene tree that maximizes the joint likelihood among all such trees. We demonstrate using simulations that gene trees reconstructed using the joint likelihood are substantially more accurate than those reconstructed using sequence alone. Using realistic gene tree topologies, branch lengths, and alignment sizes, we demonstrate that ALE produces more accurate gene trees even if the model of sequence evolution is greatly simplified. Finally, examining 1099 gene families from 36 cyanobacterial genomes we find that joint likelihood-based inference results in a striking reduction in apparent phylogenetic discord, with respectively. 24%, 59%, and 46% reductions in the mean numbers of duplications, transfers, and losses per gene family. The open source implementation of ALE is available from https://github.com/ssolo/ALE.git. [amalgamation; gene tree reconciliation; gene tree reconstruction; lateral gene transfer; phylogeny.] PMID:23925510

Integrating LIDAR and forest inventories to fill the trees outside forests data gap

Treesearch

Kristofer D. Johnson; Richard Birdsey; Jason Cole; Anu Swatantran; Jarlath O' Neil-Dunne; Ralph Dubayah; Andrew Lister

2015-01-01

Forest inventories are commonly used to estimate total tree biomass of forest land even though they are not traditionally designed to measure biomass of trees outside forests (TOF). The consequence may be an inaccurate representation of all of the aboveground biomass, which propagates error to the outputs of spatial and process models that rely on the inventory data....

Age-Dependent and Lineage-Dependent Speciation and Extinction in the Imbalance of Phylogenetic Trees.

PubMed

Holman, Eric W

2017-11-01

It is known that phylogenetic trees are more imbalanced than expected from a birth-death model with constant rates of speciation and extinction, and also that imbalance can be better fit by allowing the rate of speciation to decrease as the age of the parent species increases. If imbalance is measured in more detail, at nodes within trees as a function of the number of species descended from the nodes, age-dependent models predict levels of imbalance comparable to real trees for small numbers of descendent species, but predicted imbalance approaches an asymptote not found in real trees as the number of descendent species becomes large. Age-dependence must therefore be complemented by another process such as inheritance of different rates along different lineages, which is known to predict insufficient imbalance at nodes with few descendent species, but can predict increasing imbalance with increasing numbers of descendent species. [Crump-Mode-Jagers process; diversification; macroevolution; taxon sampling; tree of life.]. © The Author(s) 2017. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Estimating drought induced tree mortality in the Amazon rainforest: A simulation study with a focus on plant hydraulic processes

NASA Astrophysics Data System (ADS)

Papastefanou, P.; Fleischer, K.; Hickler, T.; Grams, T.; Lapola, D.; Quesada, C. A.; Zang, C.; Rammig, A.

2017-12-01

The Amazon basin was recently hit by severe drought events that were unprecedented in their severity and spatial extent, e.g. during 2005, 2010 and 2015/2016. Significant amounts of biomass were lost, turning large parts of the rainforest from a carbon sink into a carbon source. It is assumed that drought-induced tree mortality from hydraulic failure played an important role during these events and may become more frequent in the Amazon region in the future. Many state-of-the-art dynamic vegetation models do not include plant hydraulic processes and fail to reproduce observed rainforest responses to drought events, such as e.g. increased tree mortality. We address this research gap by developing a simple plant-hydraulic module for the dynamic vegetation model LPJ-GUESS. This plant-hydraulic module uses leaf water potential and cavitation as baseline processes to simulate tree mortality under drought stress. Furthermore, we introduce different plant strategies in the model, which describe e.g. differences in the stomatal regulation under drought stress. To parameterize and evaluate our hydraulic module, we use a set of available observational data from the Amazon region. We apply our model to the Amazon Basin and highlight similarities and differences across other measured and predicted drought responses, e.g. extrapolated observations and data derived from satellite measurements. Our results highlight the importance of including plant hydraulic processes in dynamic vegetation models to correctly predict vegetation dynamics under drought stress and show major differences on the vegetation dynamics depending on the selected plant strategies. We also identify gaps in process understanding of the triggering factors, the extent and the consequences of drought responses that hampers our ability to predict potential impact of future drought events on the Amazon rainforest.

Quantifying Standing Dead Tree Volume and Structural Loss with Voxelized Terrestrial Lidar Data

NASA Astrophysics Data System (ADS)

Popescu, S. C.; Putman, E.

2017-12-01

Standing dead trees (SDTs) are an important forest component and impact a variety of ecosystem processes, yet the carbon pool dynamics of SDTs are poorly constrained in terrestrial carbon cycling models. The ability to model wood decay and carbon cycling in relation to detectable changes in tree structure and volume over time would greatly improve such models. The overall objective of this study was to provide automated aboveground volume estimates of SDTs and automated procedures to detect, quantify, and characterize structural losses over time with terrestrial lidar data. The specific objectives of this study were: 1) develop an automated SDT volume estimation algorithm providing accurate volume estimates for trees scanned in dense forests; 2) develop an automated change detection methodology to accurately detect and quantify SDT structural loss between subsequent terrestrial lidar observations; and 3) characterize the structural loss rates of pine and oak SDTs in southeastern Texas. A voxel-based volume estimation algorithm, "TreeVolX", was developed and incorporates several methods designed to robustly process point clouds of varying quality levels. The algorithm operates on horizontal voxel slices by segmenting the slice into distinct branch or stem sections then applying an adaptive contour interpolation and interior filling process to create solid reconstructed tree models (RTMs). TreeVolX estimated large and small branch volume with an RMSE of 7.3% and 13.8%, respectively. A voxel-based change detection methodology was developed to accurately detect and quantify structural losses and incorporated several methods to mitigate the challenges presented by shifting tree and branch positions as SDT decay progresses. The volume and structural loss of 29 SDTs, composed of Pinus taeda and Quercus stellata, were successfully estimated using multitemporal terrestrial lidar observations over elapsed times ranging from 71 - 753 days. Pine and oak structural loss rates were characterized by estimating the amount of volumetric loss occurring in 20 equal-interval height bins of each SDT. Results showed that large pine snags exhibited more rapid structural loss in comparison to medium-sized oak snags in this study.

A Bayesian Supertree Model for Genome-Wide Species Tree Reconstruction

PubMed Central

De Oliveira Martins, Leonardo; Mallo, Diego; Posada, David

2016-01-01

Current phylogenomic data sets highlight the need for species tree methods able to deal with several sources of gene tree/species tree incongruence. At the same time, we need to make most use of all available data. Most species tree methods deal with single processes of phylogenetic discordance, namely, gene duplication and loss, incomplete lineage sorting (ILS) or horizontal gene transfer. In this manuscript, we address the problem of species tree inference from multilocus, genome-wide data sets regardless of the presence of gene duplication and loss and ILS therefore without the need to identify orthologs or to use a single individual per species. We do this by extending the idea of Maximum Likelihood (ML) supertrees to a hierarchical Bayesian model where several sources of gene tree/species tree disagreement can be accounted for in a modular manner. We implemented this model in a computer program called guenomu whose inputs are posterior distributions of unrooted gene tree topologies for multiple gene families, and whose output is the posterior distribution of rooted species tree topologies. We conducted extensive simulations to evaluate the performance of our approach in comparison with other species tree approaches able to deal with more than one leaf from the same species. Our method ranked best under simulated data sets, in spite of ignoring branch lengths, and performed well on empirical data, as well as being fast enough to analyze relatively large data sets. Our Bayesian supertree method was also very successful in obtaining better estimates of gene trees, by reducing the uncertainty in their distributions. In addition, our results show that under complex simulation scenarios, gene tree parsimony is also a competitive approach once we consider its speed, in contrast to more sophisticated models. PMID:25281847

Weighted Statistical Binning: Enabling Statistically Consistent Genome-Scale Phylogenetic Analyses

PubMed Central

Bayzid, Md Shamsuzzoha; Mirarab, Siavash; Boussau, Bastien; Warnow, Tandy

2015-01-01

Because biological processes can result in different loci having different evolutionary histories, species tree estimation requires multiple loci from across multiple genomes. While many processes can result in discord between gene trees and species trees, incomplete lineage sorting (ILS), modeled by the multi-species coalescent, is considered to be a dominant cause for gene tree heterogeneity. Coalescent-based methods have been developed to estimate species trees, many of which operate by combining estimated gene trees, and so are called "summary methods". Because summary methods are generally fast (and much faster than more complicated coalescent-based methods that co-estimate gene trees and species trees), they have become very popular techniques for estimating species trees from multiple loci. However, recent studies have established that summary methods can have reduced accuracy in the presence of gene tree estimation error, and also that many biological datasets have substantial gene tree estimation error, so that summary methods may not be highly accurate in biologically realistic conditions. Mirarab et al. (Science 2014) presented the "statistical binning" technique to improve gene tree estimation in multi-locus analyses, and showed that it improved the accuracy of MP-EST, one of the most popular coalescent-based summary methods. Statistical binning, which uses a simple heuristic to evaluate "combinability" and then uses the larger sets of genes to re-calculate gene trees, has good empirical performance, but using statistical binning within a phylogenomic pipeline does not have the desirable property of being statistically consistent. We show that weighting the re-calculated gene trees by the bin sizes makes statistical binning statistically consistent under the multispecies coalescent, and maintains the good empirical performance. Thus, "weighted statistical binning" enables highly accurate genome-scale species tree estimation, and is also statistically consistent under the multi-species coalescent model. New data used in this study are available at DOI: http://dx.doi.org/10.6084/m9.figshare.1411146, and the software is available at https://github.com/smirarab/binning. PMID:26086579

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

Sarrack, A.G.

The purpose of this report is to document fault tree analyses which have been completed for the Defense Waste Processing Facility (DWPF) safety analysis. Logic models for equipment failures and human error combinations that could lead to flammable gas explosions in various process tanks, or failure of critical support systems were developed for internal initiating events and for earthquakes. These fault trees provide frequency estimates for support systems failures and accidents that could lead to radioactive and hazardous chemical releases both on-site and off-site. Top event frequency results from these fault trees will be used in further APET analyses tomore » calculate accident risk associated with DWPF facility operations. This report lists and explains important underlying assumptions, provides references for failure data sources, and briefly describes the fault tree method used. Specific commitments from DWPF to provide new procedural/administrative controls or system design changes are listed in the ''Facility Commitments'' section. The purpose of the ''Assumptions'' section is to clarify the basis for fault tree modeling, and is not necessarily a list of items required to be protected by Technical Safety Requirements (TSRs).« less

Binary partition tree analysis based on region evolution and its application to tree simplification.

PubMed

Lu, Huihai; Woods, John C; Ghanbari, Mohammed

2007-04-01

Pyramid image representations via tree structures are recognized methods for region-based image analysis. Binary partition trees can be applied which document the merging process with small details found at the bottom levels and larger ones close to the root. Hindsight of the merging process is stored within the tree structure and provides the change histories of an image property from the leaf to the root node. In this work, the change histories are modelled by evolvement functions and their second order statistics are analyzed by using a knee function. Knee values show the reluctancy of each merge. We have systematically formulated these findings to provide a novel framework for binary partition tree analysis, where tree simplification is demonstrated. Based on an evolvement function, for each upward path in a tree, the tree node associated with the first reluctant merge is considered as a pruning candidate. The result is a simplified version providing a reduced solution space and still complying with the definition of a binary tree. The experiments show that image details are preserved whilst the number of nodes is dramatically reduced. An image filtering tool also results which preserves object boundaries and has applications for segmentation.

An improved classification tree analysis of high cost modules based upon an axiomatic definition of complexity

NASA Technical Reports Server (NTRS)

Tian, Jianhui; Porter, Adam; Zelkowitz, Marvin V.

1992-01-01

Identification of high cost modules has been viewed as one mechanism to improve overall system reliability, since such modules tend to produce more than their share of problems. A decision tree model was used to identify such modules. In this current paper, a previously developed axiomatic model of program complexity is merged with the previously developed decision tree process for an improvement in the ability to identify such modules. This improvement was tested using data from the NASA Software Engineering Laboratory.

Modeling tree growth and stable isotope ratios of white spruce in western Alaska.

NASA Astrophysics Data System (ADS)

Boucher, Etienne; Andreu-Hayles, Laia; Field, Robert; Oelkers, Rose; D'Arrigo, Rosanne

2017-04-01

Summer temperatures are assumed to exert a dominant control on physiological processes driving forest productivity in interior Alaska. However, despite the recent warming of the last few decades, numerous lines of evidence indicate that the enhancing effect of summer temperatures on high latitude forest populations has been weakening. First, satellite-derived indices of photosynthetic activity, such as the Normalized-Difference Vegetation Index (NDVI, 1982-2005), show overall declines in productivity in the interior boreal forests. Second, some white spruce tree ring series strongly diverge from summer temperatures during the second half of the 20th century, indicating a persistent loss of temperature sensitivity of tree ring proxies. Thus, the physiological response of treeline forests to ongoing climate change cannot be accurately predicted, especially from correlation analysis. Here, we make use of a process-based dendroecological model (MAIDENiso) to elucidate the complex linkages between global warming and increases in atmospheric CO2 concentration [CO2] with the response of treeline white spruce stands in interior Alaska (Seward). In order to fully capture the array of processes controlling tree growth in the area, multiple physiological indicators of white spruce productivity are used as target variables: NDVI images, ring widths (RW), maximum density (MXD) and newly measured carbon and oxygen stable isotope ratios from ring cellulose. Based on these data, we highlight the processes and mechanisms responsible for the apparent loss of sensitivity of white spruce trees to recent climate warming and [CO2] increase in order to elucidate the sensitivity and vulnerability of these trees to climate change.

Modeling transcriptional networks regulating secondary growth and wood formation in forest trees

Treesearch

Lijun Liu; Vladimir Filkov; Andrew Groover

2013-01-01

The complex interactions among the genes that underlie a biological process can be modeled and presented as a transcriptional network, in which genes (nodes) and their interactions (edges) are shown in a graphical form similar to a wiring diagram. A large number of genes have been identified that are expressed during the radial woody growth of tree stems (secondary...

Comparative study of biodegradability prediction of chemicals using decision trees, functional trees, and logistic regression.

PubMed

Chen, Guangchao; Li, Xuehua; Chen, Jingwen; Zhang, Ya-Nan; Peijnenburg, Willie J G M

2014-12-01

Biodegradation is the principal environmental dissipation process of chemicals. As such, it is a dominant factor determining the persistence and fate of organic chemicals in the environment, and is therefore of critical importance to chemical management and regulation. In the present study, the authors developed in silico methods assessing biodegradability based on a large heterogeneous set of 825 organic compounds, using the techniques of the C4.5 decision tree, the functional inner regression tree, and logistic regression. External validation was subsequently carried out by 2 independent test sets of 777 and 27 chemicals. As a result, the functional inner regression tree exhibited the best predictability with predictive accuracies of 81.5% and 81.0%, respectively, on the training set (825 chemicals) and test set I (777 chemicals). Performance of the developed models on the 2 test sets was subsequently compared with that of the Estimation Program Interface (EPI) Suite Biowin 5 and Biowin 6 models, which also showed a better predictability of the functional inner regression tree model. The model built in the present study exhibits a reasonable predictability compared with existing models while possessing a transparent algorithm. Interpretation of the mechanisms of biodegradation was also carried out based on the models developed. © 2014 SETAC.

Recruiting Conventional Tree Architecture Models into State-of-the-Art LiDAR Mapping for Investigating Tree Growth Habits in Structure.

PubMed

Lin, Yi; Jiang, Miao; Pellikka, Petri; Heiskanen, Janne

2018-01-01

Mensuration of tree growth habits is of considerable importance for understanding forest ecosystem processes and forest biophysical responses to climate changes. However, the complexity of tree crown morphology that is typically formed after many years of growth tends to render it a non-trivial task, even for the state-of-the-art 3D forest mapping technology-light detection and ranging (LiDAR). Fortunately, botanists have deduced the large structural diversity of tree forms into only a limited number of tree architecture models, which can present a-priori knowledge about tree structure, growth, and other attributes for different species. This study attempted to recruit Hallé architecture models (HAMs) into LiDAR mapping to investigate tree growth habits in structure. First, following the HAM-characterized tree structure organization rules, we run the kernel procedure of tree species classification based on the LiDAR-collected point clouds using a support vector machine classifier in the leave-one-out-for-cross-validation mode. Then, the HAM corresponding to each of the classified tree species was identified based on expert knowledge, assisted by the comparison of the LiDAR-derived feature parameters. Next, the tree growth habits in structure for each of the tree species were derived from the determined HAM. In the case of four tree species growing in the boreal environment, the tests indicated that the classification accuracy reached 85.0%, and their growth habits could be derived by qualitative and quantitative means. Overall, the strategy of recruiting conventional HAMs into LiDAR mapping for investigating tree growth habits in structure was validated, thereby paving a new way for efficiently reflecting tree growth habits and projecting forest structure dynamics.

Recruiting Conventional Tree Architecture Models into State-of-the-Art LiDAR Mapping for Investigating Tree Growth Habits in Structure

PubMed Central

Lin, Yi; Jiang, Miao; Pellikka, Petri; Heiskanen, Janne

2018-01-01

Mensuration of tree growth habits is of considerable importance for understanding forest ecosystem processes and forest biophysical responses to climate changes. However, the complexity of tree crown morphology that is typically formed after many years of growth tends to render it a non-trivial task, even for the state-of-the-art 3D forest mapping technology—light detection and ranging (LiDAR). Fortunately, botanists have deduced the large structural diversity of tree forms into only a limited number of tree architecture models, which can present a-priori knowledge about tree structure, growth, and other attributes for different species. This study attempted to recruit Hallé architecture models (HAMs) into LiDAR mapping to investigate tree growth habits in structure. First, following the HAM-characterized tree structure organization rules, we run the kernel procedure of tree species classification based on the LiDAR-collected point clouds using a support vector machine classifier in the leave-one-out-for-cross-validation mode. Then, the HAM corresponding to each of the classified tree species was identified based on expert knowledge, assisted by the comparison of the LiDAR-derived feature parameters. Next, the tree growth habits in structure for each of the tree species were derived from the determined HAM. In the case of four tree species growing in the boreal environment, the tests indicated that the classification accuracy reached 85.0%, and their growth habits could be derived by qualitative and quantitative means. Overall, the strategy of recruiting conventional HAMs into LiDAR mapping for investigating tree growth habits in structure was validated, thereby paving a new way for efficiently reflecting tree growth habits and projecting forest structure dynamics. PMID:29515616

Evolutionary inference via the Poisson Indel Process.

PubMed

Bouchard-Côté, Alexandre; Jordan, Michael I

2013-01-22

We address the problem of the joint statistical inference of phylogenetic trees and multiple sequence alignments from unaligned molecular sequences. This problem is generally formulated in terms of string-valued evolutionary processes along the branches of a phylogenetic tree. The classic evolutionary process, the TKF91 model [Thorne JL, Kishino H, Felsenstein J (1991) J Mol Evol 33(2):114-124] is a continuous-time Markov chain model composed of insertion, deletion, and substitution events. Unfortunately, this model gives rise to an intractable computational problem: The computation of the marginal likelihood under the TKF91 model is exponential in the number of taxa. In this work, we present a stochastic process, the Poisson Indel Process (PIP), in which the complexity of this computation is reduced to linear. The Poisson Indel Process is closely related to the TKF91 model, differing only in its treatment of insertions, but it has a global characterization as a Poisson process on the phylogeny. Standard results for Poisson processes allow key computations to be decoupled, which yields the favorable computational profile of inference under the PIP model. We present illustrative experiments in which Bayesian inference under the PIP model is compared with separate inference of phylogenies and alignments.

Evolutionary inference via the Poisson Indel Process

PubMed Central

Bouchard-Côté, Alexandre; Jordan, Michael I.

2013-01-01

We address the problem of the joint statistical inference of phylogenetic trees and multiple sequence alignments from unaligned molecular sequences. This problem is generally formulated in terms of string-valued evolutionary processes along the branches of a phylogenetic tree. The classic evolutionary process, the TKF91 model [Thorne JL, Kishino H, Felsenstein J (1991) J Mol Evol 33(2):114–124] is a continuous-time Markov chain model composed of insertion, deletion, and substitution events. Unfortunately, this model gives rise to an intractable computational problem: The computation of the marginal likelihood under the TKF91 model is exponential in the number of taxa. In this work, we present a stochastic process, the Poisson Indel Process (PIP), in which the complexity of this computation is reduced to linear. The Poisson Indel Process is closely related to the TKF91 model, differing only in its treatment of insertions, but it has a global characterization as a Poisson process on the phylogeny. Standard results for Poisson processes allow key computations to be decoupled, which yields the favorable computational profile of inference under the PIP model. We present illustrative experiments in which Bayesian inference under the PIP model is compared with separate inference of phylogenies and alignments. PMID:23275296

Modeling whole-tree carbon assimilation rate using observed transpiration rates and needle sugar carbon isotope ratios.

PubMed

Hu, Jia; Moore, David J P; Riveros-Iregui, Diego A; Burns, Sean P; Monson, Russell K

2010-03-01

*Understanding controls over plant-atmosphere CO(2) exchange is important for quantifying carbon budgets across a range of spatial and temporal scales. In this study, we used a simple approach to estimate whole-tree CO(2) assimilation rate (A(Tree)) in a subalpine forest ecosystem. *We analysed the carbon isotope ratio (delta(13)C) of extracted needle sugars and combined it with the daytime leaf-to-air vapor pressure deficit to estimate tree water-use efficiency (WUE). The estimated WUE was then combined with observations of tree transpiration rate (E) using sap flow techniques to estimate A(Tree). Estimates of A(Tree) for the three dominant tree species in the forest were combined with species distribution and tree size to estimate and gross primary productivity (GPP) using an ecosystem process model. *A sensitivity analysis showed that estimates of A(Tree) were more sensitive to dynamics in E than delta(13)C. At the ecosystem scale, the abundance of lodgepole pine trees influenced seasonal dynamics in GPP considerably more than Engelmann spruce and subalpine fir because of its greater sensitivity of E to seasonal climate variation. *The results provide the framework for a nondestructive method for estimating whole-tree carbon assimilation rate and ecosystem GPP over daily-to weekly time scales.

Simulated Tree Growth across the Northern Hemisphere and the Seasonality of Climate Signals Encoded within Tree-ring Widths

NASA Astrophysics Data System (ADS)

Li, X.; St George, S.

2013-12-01

Both dendrochronological theory and regional and global networks of tree-ring width measurements indicate that trees can respond to climate variations quite differently from one location to another. To explain these geographical differences at hemispheric scale, we used a process-based model of tree-ring formation (the Vaganov-Shashkin model) to simulate tree growth at over 6000 locations across the Northern Hemisphere. We compared the seasonality and strength of climate signals in the simulated tree-ring records against parallel analysis conducted on a hemispheric network of real tree-ring observations, tested the ability of the model to reproduce behaviors that emerge from large networks of tree-ring widths and used the model outputs to explain why the network exhibits these behaviors. The simulated tree-ring records are consistent with observations with respect to the seasonality and relative strength of the encoded climate signals, and time-related changes in these climate signals can be predicted using the modeled relative growth rate due to temperature or soil moisture. The positive imprint of winter (DJF) precipitation is strongest in simulations from the American Southwest and northern Mexico as well as selected locations in the Mediterranean and central Asia. Summer (JJA) precipitation has higher positive correlations with simulations in the mid-latitudes, but some high-latitude coastal sites exhibit a negative association. The influence of summer temperature is mainly positive at high-latitude or high-altitude sites and negative in the mid-latitudes. The absolute magnitude of climate correlations are generally higher in simulations than in observations, but the pattern and geographical differences remain the same, demonstrating that the model has skill in reproducing tree-ring growth response to climate variability in the Northern Hemisphere. Because the model uses only temperature, precipitation and latitude as input and is not adjusted for species or other biological factors, the fact that the climate response of the simulations largely agrees with the observations may imply that climate, rather than biology, is the main factor that influences large-scale patterns of the climate information recorded by tree rings. Our results also suggest that the Vaganov-Shashkin model could be used to estimate the likely climate response of trees in ';frontier' areas that have not been sampled extensively. Seasonal Climate Correlations of Simulated Tree-ring Records

Tree-Structured Digital Organisms Model

NASA Astrophysics Data System (ADS)

Suzuki, Teruhiko; Nobesawa, Shiho; Tahara, Ikuo

Tierra and Avida are well-known models of digital organisms. They describe a life process as a sequence of computation codes. A linear sequence model may not be the only way to describe a digital organism, though it is very simple for a computer-based model. Thus we propose a new digital organism model based on a tree structure, which is rather similar to the generic programming. With our model, a life process is a combination of various functions, as if life in the real world is. This implies that our model can easily describe the hierarchical structure of life, and it can simulate evolutionary computation through mutual interaction of functions. We verified our model by simulations that our model can be regarded as a digital organism model according to its definitions. Our model even succeeded in creating species such as viruses and parasites.

MODELING TREE LEVEL PROCESSES

EPA Science Inventory

An overview of three main types of simulation approach (explanatory, abstraction, and estimation) is presented, along with a discussion of their capabilities limitations, and the steps required for their validation. A process model being developed through the Forest Response Prog...

Majority rule has transition ratio 4 on Yule trees under a 2-state symmetric model.

PubMed

Mossel, Elchanan; Steel, Mike

2014-11-07

Inferring the ancestral state at the root of a phylogenetic tree from states observed at the leaves is a problem arising in evolutionary biology. The simplest technique - majority rule - estimates the root state by the most frequently occurring state at the leaves. Alternative methods - such as maximum parsimony - explicitly take the tree structure into account. Since either method can outperform the other on particular trees, it is useful to consider the accuracy of the methods on trees generated under some evolutionary null model, such as a Yule pure-birth model. In this short note, we answer a recently posed question concerning the performance of majority rule on Yule trees under a symmetric 2-state Markovian substitution model of character state change. We show that majority rule is accurate precisely when the ratio of the birth (speciation) rate of the Yule process to the substitution rate exceeds the value 4. By contrast, maximum parsimony has been shown to be accurate only when this ratio is at least 6. Our proof relies on a second moment calculation, coupling, and a novel application of a reflection principle. Copyright © 2014 Elsevier Ltd. All rights reserved.

Simultaneous inference of phylogenetic and transmission trees in infectious disease outbreaks

PubMed Central

2017-01-01

Whole-genome sequencing of pathogens from host samples becomes more and more routine during infectious disease outbreaks. These data provide information on possible transmission events which can be used for further epidemiologic analyses, such as identification of risk factors for infectivity and transmission. However, the relationship between transmission events and sequence data is obscured by uncertainty arising from four largely unobserved processes: transmission, case observation, within-host pathogen dynamics and mutation. To properly resolve transmission events, these processes need to be taken into account. Recent years have seen much progress in theory and method development, but existing applications make simplifying assumptions that often break up the dependency between the four processes, or are tailored to specific datasets with matching model assumptions and code. To obtain a method with wider applicability, we have developed a novel approach to reconstruct transmission trees with sequence data. Our approach combines elementary models for transmission, case observation, within-host pathogen dynamics, and mutation, under the assumption that the outbreak is over and all cases have been observed. We use Bayesian inference with MCMC for which we have designed novel proposal steps to efficiently traverse the posterior distribution, taking account of all unobserved processes at once. This allows for efficient sampling of transmission trees from the posterior distribution, and robust estimation of consensus transmission trees. We implemented the proposed method in a new R package phybreak. The method performs well in tests of both new and published simulated data. We apply the model to five datasets on densely sampled infectious disease outbreaks, covering a wide range of epidemiological settings. Using only sampling times and sequences as data, our analyses confirmed the original results or improved on them: the more realistic infection times place more confidence in the inferred transmission trees. PMID:28545083

Simultaneous inference of phylogenetic and transmission trees in infectious disease outbreaks.

PubMed

Klinkenberg, Don; Backer, Jantien A; Didelot, Xavier; Colijn, Caroline; Wallinga, Jacco

2017-05-01

Whole-genome sequencing of pathogens from host samples becomes more and more routine during infectious disease outbreaks. These data provide information on possible transmission events which can be used for further epidemiologic analyses, such as identification of risk factors for infectivity and transmission. However, the relationship between transmission events and sequence data is obscured by uncertainty arising from four largely unobserved processes: transmission, case observation, within-host pathogen dynamics and mutation. To properly resolve transmission events, these processes need to be taken into account. Recent years have seen much progress in theory and method development, but existing applications make simplifying assumptions that often break up the dependency between the four processes, or are tailored to specific datasets with matching model assumptions and code. To obtain a method with wider applicability, we have developed a novel approach to reconstruct transmission trees with sequence data. Our approach combines elementary models for transmission, case observation, within-host pathogen dynamics, and mutation, under the assumption that the outbreak is over and all cases have been observed. We use Bayesian inference with MCMC for which we have designed novel proposal steps to efficiently traverse the posterior distribution, taking account of all unobserved processes at once. This allows for efficient sampling of transmission trees from the posterior distribution, and robust estimation of consensus transmission trees. We implemented the proposed method in a new R package phybreak. The method performs well in tests of both new and published simulated data. We apply the model to five datasets on densely sampled infectious disease outbreaks, covering a wide range of epidemiological settings. Using only sampling times and sequences as data, our analyses confirmed the original results or improved on them: the more realistic infection times place more confidence in the inferred transmission trees.

Combining a generic process-based productivity model classification method to predict the presence and absence species in the Pacific Northwest, U.S.A

Treesearch

Nicholas C. Coops; Richard H. Waring; Todd A. Schroeder

2009-01-01

Although long-lived tree species experience considerable environmental variation over their life spans, their geographical distributions reflect sensitivity mainly to mean monthly climatic conditions.We introduce an approach that incorporates a physiologically based growth model to illustrate how a half-dozen tree species differ in their responses to monthly variation...

Sampling intensity and normalizations: Exploring cost-driving factors in nationwide mapping of tree canopy cover

Treesearch

John Tipton; Gretchen Moisen; Paul Patterson; Thomas A. Jackson; John Coulston

2012-01-01

There are many factors that will determine the final cost of modeling and mapping tree canopy cover nationwide. For example, applying a normalization process to Landsat data used in the models is important in standardizing reflectance values among scenes and eliminating visual seams in the final map product. However, normalization at the national scale is expensive and...

[Effects of sampling plot number on tree species distribution prediction under climate change].

PubMed

Liang, Yu; He, Hong-Shi; Wu, Zhi-Wei; Li, Xiao-Na; Luo, Xu

2013-05-01

Based on the neutral landscapes under different degrees of landscape fragmentation, this paper studied the effects of sampling plot number on the prediction of tree species distribution at landscape scale under climate change. The tree species distribution was predicted by the coupled modeling approach which linked an ecosystem process model with a forest landscape model, and three contingent scenarios and one reference scenario of sampling plot numbers were assumed. The differences between the three scenarios and the reference scenario under different degrees of landscape fragmentation were tested. The results indicated that the effects of sampling plot number on the prediction of tree species distribution depended on the tree species life history attributes. For the generalist species, the prediction of their distribution at landscape scale needed more plots. Except for the extreme specialist, landscape fragmentation degree also affected the effects of sampling plot number on the prediction. With the increase of simulation period, the effects of sampling plot number on the prediction of tree species distribution at landscape scale could be changed. For generalist species, more plots are needed for the long-term simulation.

Determinants of farmers' tree planting investment decision as a degraded landscape management strategy in the central highlands of Ethiopia

NASA Astrophysics Data System (ADS)

Gessesse, B.; Bewket, W.; Bräuning, A.

2015-11-01

Land degradation due to lack of sustainable land management practices are one of the critical challenges in many developing countries including Ethiopia. This study explores the major determinants of farm level tree planting decision as a land management strategy in a typical framing and degraded landscape of the Modjo watershed, Ethiopia. The main data were generated from household surveys and analysed using descriptive statistics and binary logistic regression model. The model significantly predicted farmers' tree planting decision (Chi-square = 37.29, df = 15, P<0.001). Besides, the computed significant value of the model suggests that all the considered predictor variables jointly influenced the farmers' decision to plant trees as a land management strategy. In this regard, the finding of the study show that local land-users' willingness to adopt tree growing decision is a function of a wide range of biophysical, institutional, socioeconomic and household level factors, however, the likelihood of household size, productive labour force availability, the disparity of schooling age, level of perception of the process of deforestation and the current land tenure system have positively and significantly influence on tree growing investment decisions in the study watershed. Eventually, the processes of land use conversion and land degradation are serious which in turn have had adverse effects on agricultural productivity, local food security and poverty trap nexus. Hence, devising sustainable and integrated land management policy options and implementing them would enhance ecological restoration and livelihood sustainability in the study watershed.

Determinants of farmers' tree-planting investment decisions as a degraded landscape management strategy in the central highlands of Ethiopia

NASA Astrophysics Data System (ADS)

Gessesse, Berhan; Bewket, Woldeamlak; Bräuning, Achim

2016-04-01

Land degradation due to lack of sustainable land management practices is one of the critical challenges in many developing countries including Ethiopia. This study explored the major determinants of farm-level tree-planting decisions as a land management strategy in a typical farming and degraded landscape of the Modjo watershed, Ethiopia. The main data were generated from household surveys and analysed using descriptive statistics and a binary logistic regression model. The model significantly predicted farmers' tree-planting decisions (χ2 = 37.29, df = 15, P < 0.001). Besides, the computed significant value of the model revealed that all the considered predictor variables jointly influenced the farmers' decisions to plant trees as a land management strategy. The findings of the study demonstrated that the adoption of tree-growing decisions by local land users was a function of a wide range of biophysical, institutional, socioeconomic and household-level factors. In this regard, the likelihood of household size, productive labour force availability, the disparity of schooling age, level of perception of the process of deforestation and the current land tenure system had a critical influence on tree-growing investment decisions in the study watershed. Eventually, the processes of land-use conversion and land degradation were serious, which in turn have had adverse effects on agricultural productivity, local food security and poverty trap nexus. Hence, the study recommended that devising and implementing sustainable land management policy options would enhance ecological restoration and livelihood sustainability in the study watershed.

Tree growth and competition in an old-growth Picea abies forest of boreal Sweden: influence of tree spatial patterning

USGS Publications Warehouse

Fraver, Shawn; D'Amato, Anthony W.; Bradford, John B.; Jonsson, Bengt Gunnar; Jönsson, Mari; Esseen, Per-Anders

2013-01-01

Question: What factors best characterize tree competitive environments in this structurally diverse old-growth forest, and do these factors vary spatially within and among stands? Location: Old-growth Picea abies forest of boreal Sweden. Methods: Using long-term, mapped permanent plot data augmented with dendrochronological analyses, we evaluated the effect of neighbourhood competition on focal tree growth by means of standard competition indices, each modified to include various metrics of trees size, neighbour mortality weighting (for neighbours that died during the inventory period), and within-neighbourhood tree clustering. Candidate models were evaluated using mixed-model linear regression analyses, with mean basal area increment as the response variable. We then analysed stand-level spatial patterns of competition indices and growth rates (via kriging) to determine if the relationship between these patterns could further elucidate factors influencing tree growth. Results: Inter-tree competition clearly affected growth rates, with crown volume being the size metric most strongly influencing the neighbourhood competitive environment. Including neighbour tree mortality weightings in models only slightly improved descriptions of competitive interactions. Although the within-neighbourhood clustering index did not improve model predictions, competition intensity was influenced by the underlying stand-level tree spatial arrangement: stand-level clustering locally intensified competition and reduced tree growth, whereas in the absence of such clustering, inter-tree competition played a lesser role in constraining tree growth. Conclusions: Our findings demonstrate that competition continues to influence forest processes and structures in an old-growth system that has not experienced major disturbances for at least two centuries. The finding that the underlying tree spatial pattern influenced the competitive environment suggests caution in interpreting traditional tree competition studies, in which tree spatial patterning is typically not taken into account. Our findings highlight the importance of forest structure – particularly the spatial arrangement of trees – in regulating inter-tree competition and growth in structurally diverse forests, and they provide insight into the causes and consequences of heterogeneity in this old-growth system.

MPTinR: analysis of multinomial processing tree models in R.

PubMed

Singmann, Henrik; Kellen, David

2013-06-01

We introduce MPTinR, a software package developed for the analysis of multinomial processing tree (MPT) models. MPT models represent a prominent class of cognitive measurement models for categorical data with applications in a wide variety of fields. MPTinR is the first software for the analysis of MPT models in the statistical programming language R, providing a modeling framework that is more flexible than standalone software packages. MPTinR also introduces important features such as (1) the ability to calculate the Fisher information approximation measure of model complexity for MPT models, (2) the ability to fit models for categorical data outside the MPT model class, such as signal detection models, (3) a function for model selection across a set of nested and nonnested candidate models (using several model selection indices), and (4) multicore fitting. MPTinR is available from the Comprehensive R Archive Network at http://cran.r-project.org/web/packages/MPTinR/ .

Section-Based Tree Species Identification Using Airborne LIDAR Point Cloud

NASA Astrophysics Data System (ADS)

Yao, C.; Zhang, X.; Liu, H.

2017-09-01

The application of LiDAR data in forestry initially focused on mapping forest community, particularly and primarily intended for largescale forest management and planning. Then with the smaller footprint and higher sampling density LiDAR data available, detecting individual tree overstory, estimating crowns parameters and identifying tree species are demonstrated practicable. This paper proposes a section-based protocol of tree species identification taking palm tree as an example. Section-based method is to detect objects through certain profile among different direction, basically along X-axis or Y-axis. And this method improve the utilization of spatial information to generate accurate results. Firstly, separate the tree points from manmade-object points by decision-tree-based rules, and create Crown Height Mode (CHM) by subtracting the Digital Terrain Model (DTM) from the digital surface model (DSM). Then calculate and extract key points to locate individual trees, thus estimate specific tree parameters related to species information, such as crown height, crown radius, and cross point etc. Finally, with parameters we are able to identify certain tree species. Comparing to species information measured on ground, the portion correctly identified trees on all plots could reach up to 90.65 %. The identification result in this research demonstrate the ability to distinguish palm tree using LiDAR point cloud. Furthermore, with more prior knowledge, section-based method enable the process to classify trees into different classes.

The fundamental theorem of asset pricing under default and collateral in finite discrete time

NASA Astrophysics Data System (ADS)

Alvarez-Samaniego, Borys; Orrillo, Jaime

2006-08-01

We consider a financial market where time and uncertainty are modeled by a finite event-tree. The event-tree has a length of N, a unique initial node at the initial date, and a continuum of branches at each node of the tree. Prices and returns of J assets are modeled, respectively, by a R2JxR2J-valued stochastic process . In this framework we prove a version of the Fundamental Theorem of Asset Pricing which applies to defaultable securities backed by exogenous collateral suffering a contingent linear depreciation.

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

PubMed

Liang, Ying; Liao, Bo; Zhu, Wen

2017-01-01

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

Constructing event trees for volcanic crises

USGS Publications Warehouse

Newhall, C.; Hoblitt, R.

2002-01-01

Event trees are useful frameworks for discussing probabilities of possible outcomes of volcanic unrest. Each branch of the tree leads from a necessary prior event to a more specific outcome, e.g., from an eruption to a pyroclastic flow. Where volcanic processes are poorly understood, probability estimates might be purely empirical - utilizing observations of past and current activity and an assumption that the future will mimic the past or follow a present trend. If processes are better understood, probabilities might be estimated from a theoritical model, either subjectively or by numerical simulations. Use of Bayes' theorem aids in the estimation of how fresh unrest raises (or lowers) the probabilities of eruptions. Use of event trees during volcanic crises can help volcanologists to critically review their analysis of hazard, and help officials and individuals to compare volcanic risks with more familiar risks. Trees also emphasize the inherently probabilistic nature of volcano forecasts, with multiple possible outcomes.

Integrated pipeline for inferring the evolutionary history of a gene family embedded in the species tree: a case study on the STIMATE gene family.

PubMed

Song, Jia; Zheng, Sisi; Nguyen, Nhung; Wang, Youjun; Zhou, Yubin; Lin, Kui

2017-10-03

Because phylogenetic inference is an important basis for answering many evolutionary problems, a large number of algorithms have been developed. Some of these algorithms have been improved by integrating gene evolution models with the expectation of accommodating the hierarchy of evolutionary processes. To the best of our knowledge, however, there still is no single unifying model or algorithm that can take all evolutionary processes into account through a stepwise or simultaneous method. On the basis of three existing phylogenetic inference algorithms, we built an integrated pipeline for inferring the evolutionary history of a given gene family; this pipeline can model gene sequence evolution, gene duplication-loss, gene transfer and multispecies coalescent processes. As a case study, we applied this pipeline to the STIMATE (TMEM110) gene family, which has recently been reported to play an important role in store-operated Ca 2+ entry (SOCE) mediated by ORAI and STIM proteins. We inferred their phylogenetic trees in 69 sequenced chordate genomes. By integrating three tree reconstruction algorithms with diverse evolutionary models, a pipeline for inferring the evolutionary history of a gene family was developed, and its application was demonstrated.

treeman: an R package for efficient and intuitive manipulation of phylogenetic trees.

PubMed

Bennett, Dominic J; Sutton, Mark D; Turvey, Samuel T

2017-01-07

Phylogenetic trees are hierarchical structures used for representing the inter-relationships between biological entities. They are the most common tool for representing evolution and are essential to a range of fields across the life sciences. The manipulation of phylogenetic trees-in terms of adding or removing tips-is often performed by researchers not just for reasons of management but also for performing simulations in order to understand the processes of evolution. Despite this, the most common programming language among biologists, R, has few class structures well suited to these tasks. We present an R package that contains a new class, called TreeMan, for representing the phylogenetic tree. This class has a list structure allowing phylogenetic trees to be manipulated more efficiently. Computational running times are reduced because of the ready ability to vectorise and parallelise methods. Development is also improved due to fewer lines of code being required for performing manipulation processes. We present three use cases-pinning missing taxa to a supertree, simulating evolution with a tree-growth model and detecting significant phylogenetic turnover-that demonstrate the new package's speed and simplicity.

Phylogenetic Invariants for Metazoan Mitochondrial Genome Evolution.

PubMed

Sankoff; Blanchette

1998-01-01

The method of phylogenetic invariants was developed to apply to aligned sequence data generated, according to a stochastic substitution model, for N species related through an unknown phylogenetic tree. The invariants are functions of the probabilities of the observable N-tuples, which are identically zero, over all choices of branch length, for some trees. Evaluating the invariants associated with all possible trees, using observed N-tuple frequencies over all sequence positions, enables us to rapidly infer the generating tree. An aspect of evolution at the genomic level much studied recently is the rearrangements of gene order along the chromosome from one species to another. Instead of the substitutions responsible for sequence evolution, we examine the non-local processes responsible for genome rearrangements such as inversion of arbitrarily long segments of chromosomes. By treating the potential adjacency of each possible pair of genes as a position", an appropriate substitution" model can be recognized as governing the rearrangement process, and a probabilistically principled phylogenetic inference can be set up. We calculate the invariants for this process for N=5, and apply them to mitochondrial genome data from coelomate metazoans, showing how they resolve key aspects of branching order.

A Nonstationary Markov Model Detects Directional Evolution in Hymenopteran Morphology.

PubMed

Klopfstein, Seraina; Vilhelmsen, Lars; Ronquist, Fredrik

2015-11-01

Directional evolution has played an important role in shaping the morphological, ecological, and molecular diversity of life. However, standard substitution models assume stationarity of the evolutionary process over the time scale examined, thus impeding the study of directionality. Here we explore a simple, nonstationary model of evolution for discrete data, which assumes that the state frequencies at the root differ from the equilibrium frequencies of the homogeneous evolutionary process along the rest of the tree (i.e., the process is nonstationary, nonreversible, but homogeneous). Within this framework, we develop a Bayesian approach for testing directional versus stationary evolution using a reversible-jump algorithm. Simulations show that when only data from extant taxa are available, the success in inferring directionality is strongly dependent on the evolutionary rate, the shape of the tree, the relative branch lengths, and the number of taxa. Given suitable evolutionary rates (0.1-0.5 expected substitutions between root and tips), accounting for directionality improves tree inference and often allows correct rooting of the tree without the use of an outgroup. As an empirical test, we apply our method to study directional evolution in hymenopteran morphology. We focus on three character systems: wing veins, muscles, and sclerites. We find strong support for a trend toward loss of wing veins and muscles, while stationarity cannot be ruled out for sclerites. Adding fossil and time information in a total-evidence dating approach, we show that accounting for directionality results in more precise estimates not only of the ancestral state at the root of the tree, but also of the divergence times. Our model relaxes the assumption of stationarity and reversibility by adding a minimum of additional parameters, and is thus well suited to studying the nature of the evolutionary process in data sets of limited size, such as morphology and ecology. © The Author(s) 2015. Published by Oxford University Press, on behalf of the Society of Systematic Biologists.

Performance Analysis of a Pole and Tree Trunk Detection Method for Mobile Laser Scanning Data

NASA Astrophysics Data System (ADS)

Lehtomäki, M.; Jaakkola, A.; Hyyppä, J.; Kukko, A.; Kaartinen, H.

2011-09-01

Dense point clouds can be collected efficiently from large areas using mobile laser scanning (MLS) technology. Accurate MLS data can be used for detailed 3D modelling of the road surface and objects around it. The 3D models can be utilised, for example, in street planning and maintenance and noise modelling. Utility poles, traffic signs, and lamp posts can be considered an important part of road infrastructure. Poles and trees stand out from the environment and should be included in realistic 3D models. Detection of narrow vertical objects, such as poles and tree trunks, from MLS data was studied. MLS produces huge amounts of data and, therefore, processing methods should be as automatic as possible and for the methods to be practical, the algorithms should run in an acceptable time. The automatic pole detection method tested in this study is based on first finding point clusters that are good candidates for poles and then separating poles and tree trunks from other clusters using features calculated from the clusters and by applying a mask that acts as a model of a pole. The method achieved detection rates of 77.7% and 69.7% in the field tests while 81.0% and 86.5% of the detected targets were correct. Pole-like targets that were surrounded by other objects, such as tree trunks that were inside branches, were the most difficult to detect. Most of the false detections came from wall structures, which could be corrected in further processing.

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.

Size-Class Effect Contributes to Tree Species Assembly through Influencing Dispersal in Tropical Forests

PubMed Central

Hu, Yue-Hua; Kitching, Roger L.; Lan, Guo-Yu; Zhang, Jiao-Lin; Sha, Li-Qing; Cao, Min

2014-01-01

We have investigated the processes of community assembly using size classes of trees. Specifically our work examined (1) whether point process models incorporating an effect of size-class produce more realistic summary outcomes than do models without this effect; (2) which of three selected models incorporating, respectively environmental effects, dispersal and the joint-effect of both of these, is most useful in explaining species-area relationships (SARs) and point dispersion patterns. For this evaluation we used tree species data from the 50-ha forest dynamics plot in Barro Colorado Island, Panama and the comparable 20 ha plot at Bubeng, Southwest China. Our results demonstrated that incorporating an size-class effect dramatically improved the SAR estimation at both the plots when the dispersal only model was used. The joint effect model produced similar improvement but only for the 50-ha plot in Panama. The point patterns results were not improved by incorporation of size-class effects using any of the three models. Our results indicate that dispersal is likely to be a key process determining both SARs and point patterns. The environment-only model and joint-effects model were effective at the species level and the community level, respectively. We conclude that it is critical to use multiple summary characteristics when modelling spatial patterns at the species and community levels if a comprehensive understanding of the ecological processes that shape species’ distributions is sought; without this results may have inherent biases. By influencing dispersal, the effect of size-class contributes to species assembly and enhances our understanding of species coexistence. PMID:25251538

Heat Transfer Processes Linking Fire Behavior and Tree Mortality

NASA Astrophysics Data System (ADS)

Michaletz, S. T.; Johnson, E. A.

2004-12-01

Traditional methods for predicting post-fire tree mortality employ statistical models which neglect the processes linking fire behavior to physiological mortality mechanisms. Here we present a physical process approach which predicts tree mortality by linking fireline intensity with lateral (vascular cambium) and apical (vegetative bud) meristem necrosis. We use a linefire plume model with independently validated conduction and lumped capacitance heat transfer analyses to predict lethal meristem temperatures in tree stems, branches, and buds. These models show that meristem necrosis in large diameter (Bi ≥ 0.3) stems/branches is governed by meristem height, bark thickness, and bark water content, while meristem necrosis in small diameter (Bi < 0.3) branches/buds is governed by meristem height, branch/bud size, branch/bud water content, and foliage architecture. To investigate effects of interspecfic variation in these properties, we compare model results for Picea glauca (Moench) Voss and Pinus contorta Loudon var. latifolia Engelm. at fireline intensities from 50 to 3000 kWm-1. Parameters are obtained from allometric models which relate stem/branch diameter to bark thickness and height, as well as bark and bud water content data collected in the southern Canadian Rocky Mountains. Variation in foliage architecture is quantified using forced convection heat transfer coefficients measured in a laminar flow wind tunnel at Re from 100 to 2000, typical for branches/buds in a linefire plume. Results indicate that in unfoliated stems/branches, P. glauca meristems are more protected due to thicker bark, whereas in foliated branches/buds, P. contorta meristems are more protected due to larger bud size and foliage architecture.

Tree mortality from drought, insects, and their interactions in a changing climate

USGS Publications Warehouse

Anderegg, William R.L.; Hicke, Jeffrey A.; Fisher, Rosie A.; Allen, Craig D.; Aukema, Juliann E.; Bentz, Barbara; Hood, Sharon; Lichstein, Jeremy W.; Macalady, Alison K.; McDowell, Nate G.; Pan, Yude; Raffa, Kenneth; Sala, Anna; Shaw, John D.; Stephenson, Nathan L.; Tague, Christina L.; Zeppel, Melanie

2015-01-01

Climate change is expected to drive increased tree mortality through drought, heat stress, and insect attacks, with manifold impacts on forest ecosystems. Yet, climate-induced tree mortality and biotic disturbance agents are largely absent from process-based ecosystem models. Using data sets from the western USA and associated studies, we present a framework for determining the relative contribution of drought stress, insect attack, and their interactions, which is critical for modeling mortality in future climates. We outline a simple approach that identifies the mechanisms associated with two guilds of insects – bark beetles and defoliators – which are responsible for substantial tree mortality. We then discuss cross-biome patterns of insect-driven tree mortality and draw upon available evidence contrasting the prevalence of insect outbreaks in temperate and tropical regions. We conclude with an overview of tools and promising avenues to address major challenges. Ultimately, a multitrophic approach that captures tree physiology, insect populations, and tree–insect interactions will better inform projections of forest ecosystem responses to climate change.

Taking the pulse of mountains: Ecosystem responses to climatic variability

USGS Publications Warehouse

Fagre, Daniel B.; Peterson, David L.; Hessl, Amy E.

2003-01-01

An integrated program of ecosystem modeling and field studies in the mountains of the Pacific Northwest (U.S.A.) has quantified many of the ecological processes affected by climatic variability. Paleoecological and contemporary ecological data in forest ecosystems provided model parameterization and validation at broad spatial and temporal scales for tree growth, tree regeneration and treeline movement. For subalpine tree species, winter precipitation has a strong negative correlation with growth; this relationship is stronger at higher elevations and west-side sites (which have more precipitation). Temperature affects tree growth at some locations with respect to length of growing season (spring) and severity of drought at drier sites (summer). Furthermore, variable but predictable climate-growth relationships across elevation gradients suggest that tree species respond differently to climate at different locations, making a uniform response of these species to future climatic change unlikely. Multi-decadal variability in climate also affects ecosystem processes. Mountain hemlock growth at high-elevation sites is negatively correlated with winter snow depth and positively correlated with the winter Pacific Decadal Oscillation (PDO) index. At low elevations, the reverse is true. Glacier mass balance and fire severity are also linked to PDO. Rapid establishment of trees in subalpine ecosystems during this century is increasing forest cover and reducing meadow cover at many subalpine locations in the western U.S.A. and precipitation (snow depth) is a critical variable regulating conifer expansion. Lastly, modeling potential future ecosystem conditions suggests that increased climatic variability will result in increasing forest fire size and frequency, and reduced net primary productivity in drier, east-side forest ecosystems. As additional empirical data and modeling output become available, we will improve our ability to predict the effects of climatic change across a broad range of climates and mountain ecosystems in the northwestern U.S.A.

Climate variability drives recent tree mortality in Europe.

PubMed

Neumann, Mathias; Mues, Volker; Moreno, Adam; Hasenauer, Hubert; Seidl, Rupert

2017-11-01

Tree mortality is an important process in forest ecosystems, frequently hypothesized to be highly climate sensitive. Yet, tree death remains one of the least understood processes of forest dynamics. Recently, changes in tree mortality have been observed in forests around the globe, which could profoundly affect ecosystem functioning and services provisioning to society. We describe continental-scale patterns of recent tree mortality from the only consistent pan-European forest monitoring network, identifying recent mortality hotspots in southern and northern Europe. Analyzing 925,462 annual observations of 235,895 trees between 2000 and 2012, we determine the influence of climate variability and tree age on interannual variation in tree mortality using Cox proportional hazard models. Warm summers as well as high seasonal variability in precipitation increased the likelihood of tree death. However, our data also suggest that reduced cold-induced mortality could compensate increased mortality related to peak temperatures in a warming climate. Besides climate variability, age was an important driver of tree mortality, with individual mortality probability decreasing with age over the first century of a trees life. A considerable portion of the observed variation in tree mortality could be explained by satellite-derived net primary productivity, suggesting that widely available remote sensing products can be used as an early warning indicator of widespread tree mortality. Our findings advance the understanding of patterns of large-scale tree mortality by demonstrating the influence of seasonal and diurnal climate variation, and highlight the potential of state-of-the-art remote sensing to anticipate an increased likelihood of tree mortality in space and time. © 2017 John Wiley & Sons Ltd.

Simulation of dendritic growth reveals necessary and sufficient parameters to describe the shapes of dendritic trees

NASA Astrophysics Data System (ADS)

Trottier, Olivier; Ganguly, Sujoy; Bowne-Anderson, Hugo; Liang, Xin; Howard, Jonathon

For the last 120 years, the development of neuronal shapes has been of great interest to the scientific community. Over the last 30 years, significant work has been done on the molecular processes responsible for dendritic development. In our ongoing research, we use the class IV sensory neurons of the Drosophila melanogaster larva as a model system to understand the growth of dendritic arbors. Our main goal is to elucidate the mechanisms that the neuron uses to determine the shape of its dendritic tree. We have observed the development of the class IV neuron's dendritic tree in the larval stage and have concluded that morphogenesis is defined by 3 distinct processes: 1) branch growth, 2) branching and 3) branch retraction. As the first step towards understanding dendritic growth, we have implemented these three processes in a computational model. Our simulations are able to reproduce the branch length distribution, number of branches and fractal dimension of the class IV neurons for a small range of parameters.

20th century changes in carbon isotopes and water-use efficiency: tree-ring-based evaluation of the CLM4.5 and LPX-Bern models

DOE PAGES

Keller, Kathrin M.; Lienert, Sebastian; Bozbiyik, Anil; ...

2017-05-24

Measurements of the stable carbon isotope ratio ( δ 13C) on annual tree rings offer new opportunities to evaluate mechanisms of variations in photosynthesis and stomatal conductance under changing CO 2 and climate conditions, especially in conjunction with process-based biogeochemical model simulations. The isotopic discrimination is indicative of the ratio between the CO 2 partial pressure in the intercellular cavities and the atmosphere ( c i/ c a) and of the ratio of assimilation to stomatal conductance, termed intrinsic water-use efficiency (iWUE). We performed isotope-enabled simulations over the industrial period with the land biosphere module (CLM4.5) of the Community Earthmore » System Model and the Land Surface Processes and Exchanges (LPX-Bern) dynamic global vegetation model. Results for C3 tree species show good agreement with a global compilation of δ 13C measurements on leaves, though modeled 13C discrimination by C3 trees is smaller in arid regions than measured. A compilation of 76 tree-ring records, mainly from Europe, boreal Asia, and western North America, suggests on average small 20th century changes in isotopic discrimination and in c i/ c a and an increase in iWUE of about 27% since 1900. LPX-Bern results match these century-scale reconstructions, supporting the idea that the physiology of stomata has evolved to optimize trade-offs between carbon gain by assimilation and water loss by transpiration. In contrast, CLM4.5 simulates an increase in discrimination and in turn a change in iWUE that is almost twice as large as that revealed by the tree-ring data. Factorial simulations show that these changes are mainly in response to rising atmospheric CO 2. The results suggest that the downregulation of c i/ c a and of photosynthesis by nitrogen limitation is possibly too strong in the standard setup of CLM4.5 or that there may be problems associated with the implementation of conductance, assimilation, and related adjustment processes on long-term environmental changes.« less

20th century changes in carbon isotopes and water-use efficiency: tree-ring-based evaluation of the CLM4.5 and LPX-Bern models

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

Keller, Kathrin M.; Lienert, Sebastian; Bozbiyik, Anil

Measurements of the stable carbon isotope ratio ( δ 13C) on annual tree rings offer new opportunities to evaluate mechanisms of variations in photosynthesis and stomatal conductance under changing CO 2 and climate conditions, especially in conjunction with process-based biogeochemical model simulations. The isotopic discrimination is indicative of the ratio between the CO 2 partial pressure in the intercellular cavities and the atmosphere ( c i/ c a) and of the ratio of assimilation to stomatal conductance, termed intrinsic water-use efficiency (iWUE). We performed isotope-enabled simulations over the industrial period with the land biosphere module (CLM4.5) of the Community Earthmore » System Model and the Land Surface Processes and Exchanges (LPX-Bern) dynamic global vegetation model. Results for C3 tree species show good agreement with a global compilation of δ 13C measurements on leaves, though modeled 13C discrimination by C3 trees is smaller in arid regions than measured. A compilation of 76 tree-ring records, mainly from Europe, boreal Asia, and western North America, suggests on average small 20th century changes in isotopic discrimination and in c i/ c a and an increase in iWUE of about 27% since 1900. LPX-Bern results match these century-scale reconstructions, supporting the idea that the physiology of stomata has evolved to optimize trade-offs between carbon gain by assimilation and water loss by transpiration. In contrast, CLM4.5 simulates an increase in discrimination and in turn a change in iWUE that is almost twice as large as that revealed by the tree-ring data. Factorial simulations show that these changes are mainly in response to rising atmospheric CO 2. The results suggest that the downregulation of c i/ c a and of photosynthesis by nitrogen limitation is possibly too strong in the standard setup of CLM4.5 or that there may be problems associated with the implementation of conductance, assimilation, and related adjustment processes on long-term environmental changes.« less

20th century changes in carbon isotopes and water-use efficiency: tree-ring-based evaluation of the CLM4.5 and LPX-Bern models

NASA Astrophysics Data System (ADS)

Keller, Kathrin M.; Lienert, Sebastian; Bozbiyik, Anil; Stocker, Thomas F.; Churakova (Sidorova), Olga V.; Frank, David C.; Klesse, Stefan; Koven, Charles D.; Leuenberger, Markus; Riley, William J.; Saurer, Matthias; Siegwolf, Rolf; Weigt, Rosemarie B.; Joos, Fortunat

2017-05-01

Measurements of the stable carbon isotope ratio (δ13C) on annual tree rings offer new opportunities to evaluate mechanisms of variations in photosynthesis and stomatal conductance under changing CO2 and climate conditions, especially in conjunction with process-based biogeochemical model simulations. The isotopic discrimination is indicative of the ratio between the CO2 partial pressure in the intercellular cavities and the atmosphere (ci/ca) and of the ratio of assimilation to stomatal conductance, termed intrinsic water-use efficiency (iWUE). We performed isotope-enabled simulations over the industrial period with the land biosphere module (CLM4.5) of the Community Earth System Model and the Land Surface Processes and Exchanges (LPX-Bern) dynamic global vegetation model. Results for C3 tree species show good agreement with a global compilation of δ13C measurements on leaves, though modeled 13C discrimination by C3 trees is smaller in arid regions than measured. A compilation of 76 tree-ring records, mainly from Europe, boreal Asia, and western North America, suggests on average small 20th century changes in isotopic discrimination and in ci/ca and an increase in iWUE of about 27 % since 1900. LPX-Bern results match these century-scale reconstructions, supporting the idea that the physiology of stomata has evolved to optimize trade-offs between carbon gain by assimilation and water loss by transpiration. In contrast, CLM4.5 simulates an increase in discrimination and in turn a change in iWUE that is almost twice as large as that revealed by the tree-ring data. Factorial simulations show that these changes are mainly in response to rising atmospheric CO2. The results suggest that the downregulation of ci/ca and of photosynthesis by nitrogen limitation is possibly too strong in the standard setup of CLM4.5 or that there may be problems associated with the implementation of conductance, assimilation, and related adjustment processes on long-term environmental changes.

Implementation of a Goal-Based Systems Engineering Process Using the Systems Modeling Language (SysML)

NASA Technical Reports Server (NTRS)

Breckenridge, Jonathan T.; Johnson, Stephen B.

2013-01-01

This paper describes the core framework used to implement a Goal-Function Tree (GFT) based systems engineering process using the Systems Modeling Language. It defines a set of principles built upon by the theoretical approach described in the InfoTech 2013 ISHM paper titled "Goal-Function Tree Modeling for Systems Engineering and Fault Management" presented by Dr. Stephen B. Johnson. Using the SysML language, the principles in this paper describe the expansion of the SysML language as a baseline in order to: hierarchically describe a system, describe that system functionally within success space, and allocate detection mechanisms to success functions for system protection.

Adaptive segmentation of cerebrovascular tree in time-of-flight magnetic resonance angiography.

PubMed

Hao, J T; Li, M L; Tang, F L

2008-01-01

Accurate segmentation of the human vasculature is an important prerequisite for a number of clinical procedures, such as diagnosis, image-guided neurosurgery and pre-surgical planning. In this paper, an improved statistical approach to extracting whole cerebrovascular tree in time-of-flight magnetic resonance angiography is proposed. Firstly, in order to get a more accurate segmentation result, a localized observation model is proposed instead of defining the observation model over the entire dataset. Secondly, for the binary segmentation, an improved Iterative Conditional Model (ICM) algorithm is presented to accelerate the segmentation process. The experimental results showed that the proposed algorithm can obtain more satisfactory segmentation results and save more processing time than conventional approaches, simultaneously.

Wood phenology: from organ-scale processes to terrestrial ecosystem models

NASA Astrophysics Data System (ADS)

Delpierre, Nicolas; Guillemot, Joannès

2016-04-01

In temperate and boreal trees, a dormancy period prevents organ development during adverse climatic conditions. Whereas the phenology of leaves and flowers has received considerable attention, to date, little is known regarding the phenology of other tree organs such as wood, fine roots, fruits and reserve compounds. In this presentation, we review both the role of environmental drivers in determining the phenology of wood and the models used to predict its phenology in temperate and boreal forest trees. Temperature is a key driver of the resumption of wood activity in spring. There is no such clear dominant environmental cue involved in the cessation of wood formation in autumn, but temperature and water stress appear as prominent factors. We show that wood phenology is a key driver of the interannual variability of wood growth in temperate tree species. Incorporating representations of wood phenology in a terrestrial ecosystem model substantially improved the simulation of wood growth under current climate.

Simulating Urban Tree Effects on Air, Water, and Heat Pollution Mitigation: iTree-Hydro Model

NASA Astrophysics Data System (ADS)

Yang, Y.; Endreny, T. A.; Nowak, D.

2011-12-01

Urban and suburban development changes land surface thermal, radiative, porous, and roughness properties and pollutant loading rates, with the combined effect leading to increased air, water, and heat pollution (e.g., urban heat islands). In this research we present the USDA Forest Service urban forest ecosystem and hydrology model, iTree Eco and Hydro, used to analyze how tree cover can deliver valuable ecosystem services to mitigate air, water, and heat pollution. Air pollution mitigation is simulated by dry deposition processes based on detected pollutant levels for CO, NO2, SO2, O3 and atmospheric stability and leaf area indices. Water quality mitigation is simulated with event mean concentration loading algorithms for N, P, metals, and TSS, and by green infrastructure pollutant filtering algorithms that consider flow path dispersal areas. Urban cooling considers direct shading and indirect evapotranspiration. Spatially distributed estimates of hourly tree evapotranspiration during the growing season are used to estimate human thermal comfort. Two main factors regulating evapotranspiration are soil moisture and canopy radiation. Spatial variation of soil moisture is represented by a modified urban topographic index and radiation for each tree is modified by considering aspect, slope and shade from surrounding buildings or hills. We compare the urban cooling algorithms used in iTree-Hydro with the urban canopy and land surface physics schemes used in the Weather Research and Forecasting model. We conclude by identifying biophysical feedbacks between tree-modulated air and water quality environmental services and how these may respond to urban heating and cooling. Improvements to this iTree model are intended to assist managers identify valuable tree services for urban living.

Tree mortality from drought, insects, and their interactions in a changing climate.

PubMed

Anderegg, William R L; Hicke, Jeffrey A; Fisher, Rosie A; Allen, Craig D; Aukema, Juliann; Bentz, Barbara; Hood, Sharon; Lichstein, Jeremy W; Macalady, Alison K; McDowell, Nate; Pan, Yude; Raffa, Kenneth; Sala, Anna; Shaw, John D; Stephenson, Nathan L; Tague, Christina; Zeppel, Melanie

2015-11-01

Climate change is expected to drive increased tree mortality through drought, heat stress, and insect attacks, with manifold impacts on forest ecosystems. Yet, climate-induced tree mortality and biotic disturbance agents are largely absent from process-based ecosystem models. Using data sets from the western USA and associated studies, we present a framework for determining the relative contribution of drought stress, insect attack, and their interactions, which is critical for modeling mortality in future climates. We outline a simple approach that identifies the mechanisms associated with two guilds of insects - bark beetles and defoliators - which are responsible for substantial tree mortality. We then discuss cross-biome patterns of insect-driven tree mortality and draw upon available evidence contrasting the prevalence of insect outbreaks in temperate and tropical regions. We conclude with an overview of tools and promising avenues to address major challenges. Ultimately, a multitrophic approach that captures tree physiology, insect populations, and tree-insect interactions will better inform projections of forest ecosystem responses to climate change. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

On joint subtree distributions under two evolutionary models.

PubMed

Wu, Taoyang; Choi, Kwok Pui

2016-04-01

In population and evolutionary biology, hypotheses about micro-evolutionary and macro-evolutionary processes are commonly tested by comparing the shape indices of empirical evolutionary trees with those predicted by neutral models. A key ingredient in this approach is the ability to compute and quantify distributions of various tree shape indices under random models of interest. As a step to meet this challenge, in this paper we investigate the joint distribution of cherries and pitchforks (that is, subtrees with two and three leaves) under two widely used null models: the Yule-Harding-Kingman (YHK) model and the proportional to distinguishable arrangements (PDA) model. Based on two novel recursive formulae, we propose a dynamic approach to numerically compute the exact joint distribution (and hence the marginal distributions) for trees of any size. We also obtained insights into the statistical properties of trees generated under these two models, including a constant correlation between the cherry and the pitchfork distributions under the YHK model, and the log-concavity and unimodality of the cherry distributions under both models. In addition, we show that there exists a unique change point for the cherry distributions between these two models. Copyright © 2015 Elsevier Inc. All rights reserved.

Wave processes in the human cardiovascular system: The measuring complex, computing models, and diagnostic analysis

NASA Astrophysics Data System (ADS)

Ganiev, R. F.; Reviznikov, D. L.; Rogoza, A. N.; Slastushenskiy, Yu. V.; Ukrainskiy, L. E.

2017-03-01

A description of a complex approach to investigation of nonlinear wave processes in the human cardiovascular system based on a combination of high-precision methods of measuring a pulse wave, mathematical methods of processing the empirical data, and methods of direct numerical modeling of hemodynamic processes in an arterial tree is given.

EDNA: Expert fault digraph analysis using CLIPS

NASA Technical Reports Server (NTRS)

Dixit, Vishweshwar V.

1990-01-01

Traditionally fault models are represented by trees. Recently, digraph models have been proposed (Sack). Digraph models closely imitate the real system dependencies and hence are easy to develop, validate and maintain. However, they can also contain directed cycles and analysis algorithms are hard to find. Available algorithms tend to be complicated and slow. On the other hand, the tree analysis (VGRH, Tayl) is well understood and rooted in vast research effort and analytical techniques. The tree analysis algorithms are sophisticated and orders of magnitude faster. Transformation of a digraph (cyclic) into trees (CLP, LP) is a viable approach to blend the advantages of the representations. Neither the digraphs nor the trees provide the ability to handle heuristic knowledge. An expert system, to capture the engineering knowledge, is essential. We propose an approach here, namely, expert network analysis. We combine the digraph representation and tree algorithms. The models are augmented by probabilistic and heuristic knowledge. CLIPS, an expert system shell from NASA-JSC will be used to develop a tool. The technique provides the ability to handle probabilities and heuristic knowledge. Mixed analysis, some nodes with probabilities, is possible. The tool provides graphics interface for input, query, and update. With the combined approach it is expected to be a valuable tool in the design process as well in the capture of final design knowledge.

Individual Tree Crown Delineation Using Multi-Wavelength Titan LIDAR Data

NASA Astrophysics Data System (ADS)

Naveed, F.; Hu, B.

2017-10-01

The inability to detect the Emerald Ash Borer (EAB) at an early stage has led to the enumerable loss of different species of ash trees. Due to the increasing risk being posed by the EAB, a robust and accurate method is needed for identifying Individual Tree Crowns (ITCs) that are at a risk of being infected or are already diseased. This paper attempts to outline an ITC delineation method that employs airborne multi-spectral Light Detection and Ranging (LiDAR) to accurately delineate tree crowns. The raw LiDAR data were initially pre-processed to generate the Digital Surface Models (DSM) and Digital Elevation Models (DEM) using an iterative progressive TIN (Triangulated Irregular Network) densification method. The DSM and DEM were consequently used for Canopy Height Model (CHM) generation, from which the structural information pertaining to the size and shape of the tree crowns was obtained. The structural information along with the spectral information was used to segment ITCs using a region growing algorithm. The availability of the multi-spectral LiDAR data allows for delineation of crowns that have otherwise homogenous structural characteristics and hence cannot be isolated from the CHM alone. This study exploits the spectral data to derive initial approximations of individual tree tops and consequently grow those regions based on the spectral constraints of the individual trees.

[Introduction and advantage analysis of the stepwise method for the construction of vascular trees].

PubMed

Zhang, Yan; Xie, Haiwei; Zhu, Kai

2010-08-01

A new method for constructing the model of vascular trees was proposed in this paper. By use of this method, the arterial trees in good agreement with the actual structure could be grown. In this process, all vessels in the vascular tree were divided into two groups: the conveying vessels, and the delivering branches. And different branches could be built by different ways. Firstly, the distributing rules of conveying vessels were ascertained by use of measurement data, and then the conveying vessels were constructed in accordance to the statistical rule and optimization criterion. Lastly, delivering branches were modeled by constrained constructive optimization (CCO) on the conveying vessel-trees which had already been generated. In order to compare the CCO method and stepwise method proposed here, two 3D arterial trees of human tongue were grown with their vascular tree having a special structure. Based on the corrosion casts of real arterial tree of human tongue, the data about the two trees constructed by different methods were compared and analyzed, including the averaged segment diameters at respective levels, the distribution and the diameters of the branches of first level at respective directions. The results show that the vascular tree built by stepwise method is more similar to the true arterial of human tongue when compared against the tree built by CCO method.

Measurement of tree canopy architecture

NASA Technical Reports Server (NTRS)

Martens, S. N.; Ustin, S. L.; Norman, J. M.

1991-01-01

The lack of accurate extensive geometric data on tree canopies has retarded development and validation of radiative transfer models. A stratified sampling method was devised to measure the three-dimensional geometry of 16 walnut trees which had received irrigation treatments of either 100 or 33 per cent of evapotranspirational (ET) demand for the previous two years. Graphic reconstructions of the three-dimensional geometry were verified by 58 independent measurements. The distributions of stem- and leaf-size classes, lengths, and angle classes were determined and used to calculate leaf area index (LAI), stem area, and biomass. Reduced irrigation trees have lower biomass of stems, leaves and fruit, lower LAI, steeper leaf angles and altered biomass allocation to large stems. These data can be used in ecological models that link canopy processes with remotely sensed measurements.

Modeling of larch forest dynamics under a changing climate in eastern Siberia

NASA Astrophysics Data System (ADS)

Nakai, T.; Kumagai, T.; Iijima, Y.; Ohta, T.; Kotani, A.; Maximov, T. C.; Hiyama, T.

2017-12-01

According to the projection by an earth system model under RCP8.5 scenario, boreal forest in eastern Siberia (near Yakutsk) is predicted to experience significant changes in climate, in which the mean annual air temperature is projected to be positive and the annual precipitation will be doubled by the end of 21st century. Since the forest in this region is underlain by continuous permafrost, both increasing temperature and precipitation can affect the dynamics of forest through the soil water processes. To investigate such effects, we adopted a newly developed terrestrial ecosystem dynamics model named S-TEDy (SEIB-DGVM-originated Terrestrial Ecosystem Dynamics model), which mechanistically simulates "the way of life" of each individual tree and resulting tree mortality under the future climate conditions. This model was first developed for the simulation of the dynamics of a tropical rainforest in the Borneo Island, and successfully reproduced higher mortality of large trees due to a prolonged drought induced by ENSO event of 1997-1998. To apply this model to a larch forest in eastern Siberia, we are developing a soil submodel to consider the effect of thawing-freezing processes. We will present a simulation results using the future climate projection.

Bayesian inference on multiscale models for poisson intensity estimation: applications to photon-limited image denoising.

PubMed

Lefkimmiatis, Stamatios; Maragos, Petros; Papandreou, George

2009-08-01

We present an improved statistical model for analyzing Poisson processes, with applications to photon-limited imaging. We build on previous work, adopting a multiscale representation of the Poisson process in which the ratios of the underlying Poisson intensities (rates) in adjacent scales are modeled as mixtures of conjugate parametric distributions. Our main contributions include: 1) a rigorous and robust regularized expectation-maximization (EM) algorithm for maximum-likelihood estimation of the rate-ratio density parameters directly from the noisy observed Poisson data (counts); 2) extension of the method to work under a multiscale hidden Markov tree model (HMT) which couples the mixture label assignments in consecutive scales, thus modeling interscale coefficient dependencies in the vicinity of image edges; 3) exploration of a 2-D recursive quad-tree image representation, involving Dirichlet-mixture rate-ratio densities, instead of the conventional separable binary-tree image representation involving beta-mixture rate-ratio densities; and 4) a novel multiscale image representation, which we term Poisson-Haar decomposition, that better models the image edge structure, thus yielding improved performance. Experimental results on standard images with artificially simulated Poisson noise and on real photon-limited images demonstrate the effectiveness of the proposed techniques.

Tree-, stand- and site-specific controls on landscape-scale patterns of transpiration

NASA Astrophysics Data System (ADS)

Hassler, Sibylle; Markus, Weiler; Theresa, Blume

2017-04-01

Transpiration is a key process in the hydrological cycle and a sound understanding and quantification of transpiration and its spatial variability is essential for management decisions as well as for improving the parameterisation of hydrological and soil-vegetation-atmosphere transfer models. For individual trees, transpiration is commonly estimated by measuring sap flow. Besides evaporative demand and water availability, tree-specific characteristics such as species, size or social status control sap flow amounts of individual trees. Within forest stands, properties such as species composition, basal area or stand density additionally affect sap flow, for example via competition mechanisms. Finally, sap flow patterns might also be influenced by landscape-scale characteristics such as geology, slope position or aspect because they affect water and energy availability; however, little is known about the dynamic interplay of these controls. We studied the relative importance of various tree-, stand- and site-specific characteristics with multiple linear regression models to explain the variability of sap velocity measurements in 61 beech and oak trees, located at 24 sites spread over a 290 km2-catchment in Luxembourg. For each of 132 consecutive days of the growing season of 2014 we modelled the daily sap velocities of these 61 trees and determined the importance of the different predictors. Results indicate that a combination of tree-, stand- and site-specific factors controls sap velocity patterns in the landscape, namely tree species, tree diameter, the stand density, geology and aspect. Compared to these predictors, spatial variability of atmospheric demand and soil moisture explains only a small fraction of the variability in the daily datasets. However, the temporal dynamics of the explanatory power of the tree-specific characteristics, especially species, are correlated to the temporal dynamics of potential evaporation. Thus, transpiration estimates at the landscape scale would benefit from not only considering hydro-meteorological drivers, but also including tree, stand and site characteristics in order to improve the spatial representation of transpiration for hydrological and soil-vegetation-atmosphere transfer models.

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

Beyond ROC Curvature: Strength Effects and Response Time Data Support Continuous-Evidence Models of Recognition Memory

ERIC Educational Resources Information Center

Dube, Chad; Starns, Jeffrey J.; Rotello, Caren M.; Ratcliff, Roger

2012-01-01

A classic question in the recognition memory literature is whether retrieval is best described as a continuous-evidence process consistent with signal detection theory (SDT), or a threshold process consistent with many multinomial processing tree (MPT) models. Because receiver operating characteristics (ROCs) based on confidence ratings are…

Merging tree ring chronologies and climate system model simulated temperature by optimal interpolation algorithm in North America

NASA Astrophysics Data System (ADS)

Chen, Xin; Xing, Pei; Luo, Yong; Zhao, Zongci; Nie, Suping; Huang, Jianbin; Wang, Shaowu; Tian, Qinhua

2015-04-01

A new dataset of annual mean surface temperature has been constructed over North America in recent 500 years by performing optimal interpolation (OI) algorithm. Totally, 149 series totally were screened out including 69 tree ring width (MXD) and 80 tree ring width (TRW) chronologies are screened from International Tree Ring Data Bank (ITRDB). The simulated annual mean surface temperature derives from the past1000 experiment results of Community Climate System Model version 4 (CCSM4). Different from existing research that applying data assimilation approach to (General Circulation Models) GCMs simulation, the errors of both the climate model simulation and tree ring reconstruction were considered, with a view to combining the two parts in an optimal way. Variance matching (VM) was employed to calibrate tree ring chronologies on CRUTEM4v, and corresponding errors were estimated through leave-one-out process. Background error covariance matrix was estimated from samples of simulation results in a running 30-year window in a statistical way. Actually, the background error covariance matrix was calculated locally within the scanning range (2000km in this research). Thus, the merging process continued with a time-varying local gain matrix. The merging method (MM) was tested by two kinds of experiments, and the results indicated standard deviation of errors can be reduced by about 0.3 degree centigrade lower than tree ring reconstructions and 0.5 degree centigrade lower than model simulation. During the recent Obvious decadal variability can be identified in MM results including the evident cooling (0.10 degree per decade) in 1940-60s, wherein the model simulation exhibit a weak increasing trend (0.05 degree per decade) instead. MM results revealed a compromised spatial pattern of the linear trend of surface temperature during a typical period (1601-1800 AD) in Little Ice Age, which basically accorded with the phase transitions of the Pacific decadal oscillation (PDO) and Atlantic multi-decadal oscillation (AMO). Through the empirical orthogonal functions and power spectrum analysis, it was demonstrated that, compared with the pure simulations of CCSM4, MM made significant improvement of decadal variability for the gridded temperature in North America by merging the temperature-sensitive tree ring records.

Bayesian Total-Evidence Dating Reveals the Recent Crown Radiation of Penguins

PubMed Central

Heath, Tracy A.; Ksepka, Daniel T.; Stadler, Tanja; Welch, David; Drummond, Alexei J.

2017-01-01

The total-evidence approach to divergence time dating uses molecular and morphological data from extant and fossil species to infer phylogenetic relationships, species divergence times, and macroevolutionary parameters in a single coherent framework. Current model-based implementations of this approach lack an appropriate model for the tree describing the diversification and fossilization process and can produce estimates that lead to erroneous conclusions. We address this shortcoming by providing a total-evidence method implemented in a Bayesian framework. This approach uses a mechanistic tree prior to describe the underlying diversification process that generated the tree of extant and fossil taxa. Previous attempts to apply the total-evidence approach have used tree priors that do not account for the possibility that fossil samples may be direct ancestors of other samples, that is, ancestors of fossil or extant species or of clades. The fossilized birth–death (FBD) process explicitly models the diversification, fossilization, and sampling processes and naturally allows for sampled ancestors. This model was recently applied to estimate divergence times based on molecular data and fossil occurrence dates. We incorporate the FBD model and a model of morphological trait evolution into a Bayesian total-evidence approach to dating species phylogenies. We apply this method to extant and fossil penguins and show that the modern penguins radiated much more recently than has been previously estimated, with the basal divergence in the crown clade occurring at \\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{upgreek} \\usepackage{mathrsfs} \\setlength{\\oddsidemargin}{-69pt} \\begin{document} }{}${\\sim}12.7$\\end{document} Ma and most splits leading to extant species occurring in the last 2 myr. Our results demonstrate that including stem-fossil diversity can greatly improve the estimates of the divergence times of crown taxa. The method is available in BEAST2 (version 2.4) software www.beast2.org with packages SA (version at least 1.1.4) and morph-models (version at least 1.0.4) installed. [Birth–death process; calibration; divergence times; MCMC; phylogenetics.] PMID:28173531

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.

Oak decline around the world

Treesearch

Kurt W. Gottschalk; Philip M. Wargo

1997-01-01

Oak (Quercus spp.) decline is a malady related to the consequences of stress and successful attack of stressed trees by opportunistic (secondary) organisms (Wargo et al. 1983). It is a progressive process where trees decline in health for several years before they die. Houston (1981) developed a model of declines that is presented in Figure 1. So...

Equipment and Supplies For Collecting, Processing, Storing, and Testing Forest Tree Seed

Treesearch

F.T. Bonner

1977-01-01

This publication is a directory of information on equipment and supplies used in handling and treating tree seed. The use of each device is briefly described. Specifications such as size, capacity, or model number are given. Manufacturers' or suppliers' names are listed, and users of the equipment are identified.

Prediction of strontium bromide laser efficiency using cluster and decision tree analysis

NASA Astrophysics Data System (ADS)

Iliev, Iliycho; Gocheva-Ilieva, Snezhana; Kulin, Chavdar

2018-01-01

Subject of investigation is a new high-powered strontium bromide (SrBr2) vapor laser emitting in multiline region of wavelengths. The laser is an alternative to the atom strontium lasers and electron free lasers, especially at the line 6.45 μm which line is used in surgery for medical processing of biological tissues and bones with minimal damage. In this paper the experimental data from measurements of operational and output characteristics of the laser are statistically processed by means of cluster analysis and tree-based regression techniques. The aim is to extract the more important relationships and dependences from the available data which influence the increase of the overall laser efficiency. There are constructed and analyzed a set of cluster models. It is shown by using different cluster methods that the seven investigated operational characteristics (laser tube diameter, length, supplied electrical power, and others) and laser efficiency are combined in 2 clusters. By the built regression tree models using Classification and Regression Trees (CART) technique there are obtained dependences to predict the values of efficiency, and especially the maximum efficiency with over 95% accuracy.

Investigation on electrical tree propagation in polyethylene based on etching method

NASA Astrophysics Data System (ADS)

Shi, Zexiang; Zhang, Xiaohong; Wang, Kun; Gao, Junguo; Guo, Ning

2017-11-01

To investigate the characteristic of electrical tree propagation in semi-crystalline polymers, the low-density polyethylene (LDPE) samples containing electrical trees are cut into slices by using ultramicrotome. Then the slice samples are etched by potassium permanganate etchant. Finally, the crystalline structure and the electrical tree propagation path in samples are observed by polarized light microscopy (PLM). According to the observation, the LDPE spherocrystal structure model is established on the basis of crystallization kinetics and morphology of polymers. And the electrical tree growth process in LDPE is discussed based on the free volume breakdown theory, the molecular chain relaxation theory, the electromechanical force theory, the thermal expansion effect and the space charge shielding effect.

A New Model for Acquiescence at the Interface of Psychometrics and Cognitive Psychology.

PubMed

Plieninger, Hansjörg; Heck, Daniel W

2018-05-29

When measuring psychological traits, one has to consider that respondents often show content-unrelated response behavior in answering questionnaires. To disentangle the target trait and two such response styles, extreme responding and midpoint responding, Böckenholt ( 2012a ) developed an item response model based on a latent processing tree structure. We propose a theoretically motivated extension of this model to also measure acquiescence, the tendency to agree with both regular and reversed items. Substantively, our approach builds on multinomial processing tree (MPT) models that are used in cognitive psychology to disentangle qualitatively distinct processes. Accordingly, the new model for response styles assumes a mixture distribution of affirmative responses, which are either determined by the underlying target trait or by acquiescence. In order to estimate the model parameters, we rely on Bayesian hierarchical estimation of MPT models. In simulations, we show that the model provides unbiased estimates of response styles and the target trait, and we compare the new model and Böckenholt's model in a recovery study. An empirical example from personality psychology is used for illustrative purposes.

Universal scaling in the branching of the tree of life.

PubMed

Herrada, E Alejandro; Tessone, Claudio J; Klemm, Konstantin; Eguíluz, Víctor M; Hernández-García, Emilio; Duarte, Carlos M

2008-07-23

Understanding the patterns and processes of diversification of life in the planet is a key challenge of science. The Tree of Life represents such diversification processes through the evolutionary relationships among the different taxa, and can be extended down to intra-specific relationships. Here we examine the topological properties of a large set of interspecific and intraspecific phylogenies and show that the branching patterns follow allometric rules conserved across the different levels in the Tree of Life, all significantly departing from those expected from the standard null models. The finding of non-random universal patterns of phylogenetic differentiation suggests that similar evolutionary forces drive diversification across the broad range of scales, from macro-evolutionary to micro-evolutionary processes, shaping the diversity of life on the planet.

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

Measuring and modelling interception loss by an isolated olive tree in a traditional olive grove - pasture system

NASA Astrophysics Data System (ADS)

Nóbrega, Cristina; Pereira, Fernando L.; Valente, Fernanda

2015-04-01

Water losses associated to the rainfall interception process by trees can be an important component of the local hydrologic balance and must be accounted for when implementing any sustainable water management programme. In many dry areas of the Mediterranean region where agro-forestry systems are common, those programmes are crucial to foster adequate water conservation measures. Recent studies have shown that the evaluation of interception loss in sparse forests or tree plantations should be made for individual trees, being the total value determined as the sum of the individual contributions. Following this approach, rainfall interception was measured and modelled over two years, in an isolated Olea europeaea L. tree, in a traditional low-density olive grove in Castelo Branco, central Portugal. Total interception loss over the experimental period was 243.5 mm, on a tree crown projected area basis, corresponding to 18.0% of gross rainfall (Pg). Modelling made for each rainfall event using the sparse version of the Gash model, slightly underestimated interception loss with a value of 240.5 mm, i.e., 17.8 % ofPg. Modelling quality, evaluated according to a number of criteria, was good, allowing the conclusion that the methodology used was adequate. Modelling was also made on a daily basis, i.e., assuming a single storm per rainday. In this case, interception loss was overestimated by 12%, mostly because 72% of all rainfall events lasted for more than a day.

Learning a constrained conditional random field for enhanced segmentation of fallen trees in ALS point clouds

NASA Astrophysics Data System (ADS)

Polewski, Przemyslaw; Yao, Wei; Heurich, Marco; Krzystek, Peter; Stilla, Uwe

2018-06-01

In this study, we present a method for improving the quality of automatic single fallen tree stem segmentation in ALS data by applying a specialized constrained conditional random field (CRF). The entire processing pipeline is composed of two steps. First, short stem segments of equal length are detected and a subset of them is selected for further processing, while in the second step the chosen segments are merged to form entire trees. The first step is accomplished using the specialized CRF defined on the space of segment labelings, capable of finding segment candidates which are easier to merge subsequently. To achieve this, the CRF considers not only the features of every candidate individually, but incorporates pairwise spatial interactions between adjacent segments into the model. In particular, pairwise interactions include a collinearity/angular deviation probability which is learned from training data as well as the ratio of spatial overlap, whereas unary potentials encode a learned probabilistic model of the laser point distribution around each segment. Each of these components enters the CRF energy with its own balance factor. To process previously unseen data, we first calculate the subset of segments for merging on a grid of balance factors by minimizing the CRF energy. Then, we perform the merging and rank the balance configurations according to the quality of their resulting merged trees, obtained from a learned tree appearance model. The final result is derived from the top-ranked configuration. We tested our approach on 5 plots from the Bavarian Forest National Park using reference data acquired in a field inventory. Compared to our previous segment selection method without pairwise interactions, an increase in detection correctness and completeness of up to 7 and 9 percentage points, respectively, was observed.

Identification and Characterization of Liver MicroRNAs of the Chinese Tree Shrew via Deep Sequencing.

PubMed

Feng, Yue; Feng, Yue-Mei; Feng, Yang; Lu, Caixia; Liu, Li; Sun, Xiaomei; Dai, Jiejie; Xia, Xueshan

2015-10-01

Chinese tree shrew (Tupaia belangeri chinensis) is a small animal that possess many features, which are valuable in biomedical research, as experimental models. Currently, there are numerous attempts to utilize tree shrews as models for hepatitis C virus (HCV) infection. This study aimed to construct a liver microRNA (miRNA) data of the tree shrew. Three second filial generation tree shrews were used in this study. Total RNA was extracted from each liver of the tree shrew and equal quality mixed, then reverse-transcribed to complementary DNA (cDNA). The cDNAs were amplified by polymerase chain reaction and subjected to high-throughput sequencing. A total of 2060 conserved miRNAs were identified through alignment with the mature miRNAs in miRBase 20.0 database. The gene ontology and Kyoto encyclopedia of genes and genomes analyses of the target genes of the miRNAs revealed several candidate miRNAs, genes and pathways that may involve in the process of HCV infection. The abundance of miR-122 and Let-7 families and their other characteristics provided us more evidences for the utilization of this animal, as a potential model for HCV infection and other related biomedical research. Moreover, 80 novel microRNAs were predicted using the software Mireap. The top 3 abundant miRNAs were validated in other tree samples, based on stem-loop quantitative reverse transcription-polymerase chain reaction. According to the liver microRNA data of Chinese tree shrew, characteristics of the miR-122 and Let-7 families further highlight the suitability of tree shrew as the animal model in HCV research.

Very High Resolution Tree Cover Mapping for Continental United States using Deep Convolutional Neural Networks

NASA Technical Reports Server (NTRS)

Ganguly, Sangram; Kalia, Subodh; Li, Shuang; Michaelis, Andrew; Nemani, Ramakrishna R.; Saatchi, Sassan A

2017-01-01

Uncertainties in input land cover estimates contribute to a significant bias in modeled above ground biomass (AGB) and carbon estimates from satellite-derived data. The resolution of most currently used passive remote sensing products is not sufficient to capture tree canopy cover of less than ca. 10-20 percent, limiting their utility to estimate canopy cover and AGB for trees outside of forest land. In our study, we created a first of its kind Continental United States (CONUS) tree cover map at a spatial resolution of 1-m for the 2010-2012 epoch using the USDA NAIP imagery to address the present uncertainties in AGB estimates. The process involves different tasks including data acquisition ingestion to pre-processing and running a state-of-art encoder-decoder based deep convolutional neural network (CNN) algorithm for automatically generating a tree non-tree map for almost a quarter million scenes. The entire processing chain including generation of the largest open source existing aerial satellite image training database was performed at the NEX supercomputing and storage facility. We believe the resulting forest cover product will substantially contribute to filling the gaps in ongoing carbon and ecological monitoring research and help quantifying the errors and uncertainties in derived products.

PCA based feature reduction to improve the accuracy of decision tree c4.5 classification

NASA Astrophysics Data System (ADS)

Nasution, M. Z. F.; Sitompul, O. S.; Ramli, M.

2018-03-01

Splitting attribute is a major process in Decision Tree C4.5 classification. However, this process does not give a significant impact on the establishment of the decision tree in terms of removing irrelevant features. It is a major problem in decision tree classification process called over-fitting resulting from noisy data and irrelevant features. In turns, over-fitting creates misclassification and data imbalance. Many algorithms have been proposed to overcome misclassification and overfitting on classifications Decision Tree C4.5. Feature reduction is one of important issues in classification model which is intended to remove irrelevant data in order to improve accuracy. The feature reduction framework is used to simplify high dimensional data to low dimensional data with non-correlated attributes. In this research, we proposed a framework for selecting relevant and non-correlated feature subsets. We consider principal component analysis (PCA) for feature reduction to perform non-correlated feature selection and Decision Tree C4.5 algorithm for the classification. From the experiments conducted using available data sets from UCI Cervical cancer data set repository with 858 instances and 36 attributes, we evaluated the performance of our framework based on accuracy, specificity and precision. Experimental results show that our proposed framework is robust to enhance classification accuracy with 90.70% accuracy rates.

Very High Resolution Tree Cover Mapping for Continental United States using Deep Convolutional Neural Networks

NASA Astrophysics Data System (ADS)

Ganguly, S.; Kalia, S.; Li, S.; Michaelis, A.; Nemani, R. R.; Saatchi, S.

2017-12-01

Uncertainties in input land cover estimates contribute to a significant bias in modeled above gound biomass (AGB) and carbon estimates from satellite-derived data. The resolution of most currently used passive remote sensing products is not sufficient to capture tree canopy cover of less than ca. 10-20 percent, limiting their utility to estimate canopy cover and AGB for trees outside of forest land. In our study, we created a first of its kind Continental United States (CONUS) tree cover map at a spatial resolution of 1-m for the 2010-2012 epoch using the USDA NAIP imagery to address the present uncertainties in AGB estimates. The process involves different tasks including data acquisition/ingestion to pre-processing and running a state-of-art encoder-decoder based deep convolutional neural network (CNN) algorithm for automatically generating a tree/non-tree map for almost a quarter million scenes. The entire processing chain including generation of the largest open source existing aerial/satellite image training database was performed at the NEX supercomputing and storage facility. We believe the resulting forest cover product will substantially contribute to filling the gaps in ongoing carbon and ecological monitoring research and help quantifying the errors and uncertainties in derived products.

New analytic results for speciation times in neutral models.

PubMed

Gernhard, Tanja

2008-05-01

In this paper, we investigate the standard Yule model, and a recently studied model of speciation and extinction, the "critical branching process." We develop an analytic way-as opposed to the common simulation approach-for calculating the speciation times in a reconstructed phylogenetic tree. Simple expressions for the density and the moments of the speciation times are obtained. Methods for dating a speciation event become valuable, if for the reconstructed phylogenetic trees, no time scale is available. A missing time scale could be due to supertree methods, morphological data, or molecular data which violates the molecular clock. Our analytic approach is, in particular, useful for the model with extinction, since simulations of birth-death processes which are conditioned on obtaining n extant species today are quite delicate. Further, simulations are very time consuming for big n under both models.

Rate of tree carbon accumulation increases continuously with tree size.

PubMed

Stephenson, N L; Das, A J; Condit, R; Russo, S E; Baker, P J; Beckman, N G; Coomes, D A; Lines, E R; Morris, W K; Rüger, N; Alvarez, E; Blundo, C; Bunyavejchewin, S; Chuyong, G; Davies, S J; Duque, A; Ewango, C N; Flores, O; Franklin, J F; Grau, H R; Hao, Z; Harmon, M E; Hubbell, S P; Kenfack, D; Lin, Y; Makana, J-R; Malizia, A; Malizia, L R; Pabst, R J; Pongpattananurak, N; Su, S-H; Sun, I-F; Tan, S; Thomas, D; van Mantgem, P J; Wang, X; Wiser, S K; Zavala, M A

2014-03-06

Forests are major components of the global carbon cycle, providing substantial feedback to atmospheric greenhouse gas concentrations. Our ability to understand and predict changes in the forest carbon cycle--particularly net primary productivity and carbon storage--increasingly relies on models that represent biological processes across several scales of biological organization, from tree leaves to forest stands. Yet, despite advances in our understanding of productivity at the scales of leaves and stands, no consensus exists about the nature of productivity at the scale of the individual tree, in part because we lack a broad empirical assessment of whether rates of absolute tree mass growth (and thus carbon accumulation) decrease, remain constant, or increase as trees increase in size and age. Here we present a global analysis of 403 tropical and temperate tree species, showing that for most species mass growth rate increases continuously with tree size. Thus, large, old trees do not act simply as senescent carbon reservoirs but actively fix large amounts of carbon compared to smaller trees; at the extreme, a single big tree can add the same amount of carbon to the forest within a year as is contained in an entire mid-sized tree. The apparent paradoxes of individual tree growth increasing with tree size despite declining leaf-level and stand-level productivity can be explained, respectively, by increases in a tree's total leaf area that outpace declines in productivity per unit of leaf area and, among other factors, age-related reductions in population density. Our results resolve conflicting assumptions about the nature of tree growth, inform efforts to undertand and model forest carbon dynamics, and have additional implications for theories of resource allocation and plant senescence.

If BZ medium did spanning trees these would be the same trees as Physarum built

NASA Astrophysics Data System (ADS)

Adamatzky, Andrew

2009-03-01

A sub-excitable Belousov-Zhabotinsky (BZ) medium exhibits self-localized wave-fragments which may travel for relatively long time preserving their shape. Using Oregonator model of the BZ medium we imitate foraging behavior of a true slime mold, Physarum polycephalum, on a nutrient-poor substrate. We show that given erosion post-processing operations the BZ medium can approximate a spanning tree of a planar set and thus is computationally equivalent to Physarum in the domain of proximity graph construction.

Assimilation of pseudo-tree-ring-width observations into an atmospheric general circulation model

NASA Astrophysics Data System (ADS)

Acevedo, Walter; Fallah, Bijan; Reich, Sebastian; Cubasch, Ulrich

2017-05-01

Paleoclimate data assimilation (DA) is a promising technique to systematically combine the information from climate model simulations and proxy records. Here, we investigate the assimilation of tree-ring-width (TRW) chronologies into an atmospheric global climate model using ensemble Kalman filter (EnKF) techniques and a process-based tree-growth forward model as an observation operator. Our results, within a perfect-model experiment setting, indicate that the "online DA" approach did not outperform the "off-line" one, despite its considerable additional implementation complexity. On the other hand, it was observed that the nonlinear response of tree growth to surface temperature and soil moisture does deteriorate the operation of the time-averaged EnKF methodology. Moreover, for the first time we show that this skill loss appears significantly sensitive to the structure of the growth rate function, used to represent the principle of limiting factors (PLF) within the forward model. In general, our experiments showed that the error reduction achieved by assimilating pseudo-TRW chronologies is modulated by the magnitude of the yearly internal variability in the model. This result might help the dendrochronology community to optimize their sampling efforts.

Multiscale model of a freeze–thaw process for tree sap exudation

PubMed Central

Graf, Isabell; Ceseri, Maurizio; Stockie, John M.

2015-01-01

Sap transport in trees has long fascinated scientists, and a vast literature exists on experimental and modelling studies of trees during the growing season when large negative stem pressures are generated by transpiration from leaves. Much less attention has been paid to winter months when trees are largely dormant but nonetheless continue to exhibit interesting flow behaviour. A prime example is sap exudation, which refers to the peculiar ability of sugar maple (Acer saccharum) and related species to generate positive stem pressure while in a leafless state. Experiments demonstrate that ambient temperatures must oscillate about the freezing point before significantly heightened stem pressures are observed, but the precise causes of exudation remain unresolved. The prevailing hypothesis attributes exudation to a physical process combining freeze–thaw and osmosis, which has some support from experimental studies but remains a subject of active debate. We address this knowledge gap by developing the first mathematical model for exudation, while also introducing several essential modifications to this hypothesis. We derive a multiscale model consisting of a nonlinear system of differential equations governing phase change and transport within wood cells, coupled to a suitably homogenized equation for temperature on the macroscale. Numerical simulations yield stem pressures that are consistent with experiments and provide convincing evidence that a purely physical mechanism is capable of capturing exudation. PMID:26400199

Multiscale model of a freeze-thaw process for tree sap exudation.

PubMed

Graf, Isabell; Ceseri, Maurizio; Stockie, John M

2015-10-06

Sap transport in trees has long fascinated scientists, and a vast literature exists on experimental and modelling studies of trees during the growing season when large negative stem pressures are generated by transpiration from leaves. Much less attention has been paid to winter months when trees are largely dormant but nonetheless continue to exhibit interesting flow behaviour. A prime example is sap exudation, which refers to the peculiar ability of sugar maple (Acer saccharum) and related species to generate positive stem pressure while in a leafless state. Experiments demonstrate that ambient temperatures must oscillate about the freezing point before significantly heightened stem pressures are observed, but the precise causes of exudation remain unresolved. The prevailing hypothesis attributes exudation to a physical process combining freeze-thaw and osmosis, which has some support from experimental studies but remains a subject of active debate. We address this knowledge gap by developing the first mathematical model for exudation, while also introducing several essential modifications to this hypothesis. We derive a multiscale model consisting of a nonlinear system of differential equations governing phase change and transport within wood cells, coupled to a suitably homogenized equation for temperature on the macroscale. Numerical simulations yield stem pressures that are consistent with experiments and provide convincing evidence that a purely physical mechanism is capable of capturing exudation. © 2015 The Author(s).

A Multiscale Simulation Framework to Investigate Hydrobiogeochemical Processes in the Groundwater-Surface Water Interaction Zone

NASA Astrophysics Data System (ADS)

Scheibe, T. D.; Yang, X.; Song, X.; Chen, X.; Hammond, G. E.; Song, H. S.; Hou, Z.; Murray, C. J.; Tartakovsky, A. M.; Tartakovsky, G.; Yang, X.; Zachara, J. M.

2016-12-01

Drought-related tree mortality at a regional scale causes drastic shifts in carbon and water cycling in Southeast Asian tropical rainforests, where severe droughts are projected to occur more frequently, especially under El Niño conditions. To provide a useful tool for projecting the tropical rainforest dynamics under climate change conditions, we developed the Spatially Explicit Individual-Based (SEIB) Dynamic Global Vegetation Model (DGVM) applicable to simulating mechanistic tree mortality induced by the climatic impacts via individual-tree-scale ecophysiology such as hydraulic failure and carbon starvation. In this study, we present the new model, SEIB-originated Terrestrial Ecosystem Dynamics (S-TEDy) model, and the computation results were compared with observations collected at a field site in a Bornean tropical rainforest. Furthermore, after validating the model's performance, numerical experiments addressing a future of the tropical rainforest were conducted using some global climate model (GCM) simulation outputs.

Implementation of a Goal-Based Systems Engineering Process Using the Systems Modeling Language (SysML)

NASA Technical Reports Server (NTRS)

Patterson, Jonathan D.; Breckenridge, Jonathan T.; Johnson, Stephen B.

2013-01-01

Building upon the purpose, theoretical approach, and use of a Goal-Function Tree (GFT) being presented by Dr. Stephen B. Johnson, described in a related Infotech 2013 ISHM abstract titled "Goal-Function Tree Modeling for Systems Engineering and Fault Management", this paper will describe the core framework used to implement the GFTbased systems engineering process using the Systems Modeling Language (SysML). These two papers are ideally accepted and presented together in the same Infotech session. Statement of problem: SysML, as a tool, is currently not capable of implementing the theoretical approach described within the "Goal-Function Tree Modeling for Systems Engineering and Fault Management" paper cited above. More generally, SysML's current capabilities to model functional decompositions in the rigorous manner required in the GFT approach are limited. The GFT is a new Model-Based Systems Engineering (MBSE) approach to the development of goals and requirements, functions, and its linkage to design. As a growing standard for systems engineering, it is important to develop methods to implement GFT in SysML. Proposed Method of Solution: Many of the central concepts of the SysML language are needed to implement a GFT for large complex systems. In the implementation of those central concepts, the following will be described in detail: changes to the nominal SysML process, model view definitions and examples, diagram definitions and examples, and detailed SysML construct and stereotype definitions.

Ecohydrologic Changes due to Tree Expansion into Tundra in the Polar Urals, Russia

NASA Astrophysics Data System (ADS)

Ivanov, V. Y.; Wang, J.; El Sharif, H. A.; Liu, D.; Sheshukov, A. Y.; Mazepa, V.; Shiyatov, S.; Sokolov, A.

2017-12-01

The Arctic has been warming at an accelerating rate over the last several decades and the changing climate has caused the invasion of trees and shrubs into tundra across the polar regions of Alaska, Canada, and Russia. These vegetation changes may have the potential to impact regional hydrology and climate. This study aims to develop mechanistic and quantitative understanding of implications of forest encroachment into tundra. Specifically, for several areas with well-documented larch and spruce expansion in the Polar Urals and southern Yamal Peninsula of Russia over 1960-2010s, we hypothesize that the encroachment process alters the seasonality of energy budget characterized by enhanced total evapotranspiration and concomitant subsurface warming. We are collecting a comprehensive set of field observational data on micrometeorology, snow conditions, radiative fluxes, tree sap flows, soil temperature, moisture, and heat fluxes, and active layer thickness. A novel model of maximum entropy production (MEP) is used to derive the surface energy budgets as the partition of radiative fluxes into turbulent and conductive heat fluxes across the ecotone interface. We are presenting preliminary findings that illustrate the identified differences of seasonal snow and heat budget regimes for two contrasting sites: one of which has experienced a recent tree encroachment, while for the other this process has not yet occurred. Observed and modeled heat fluxes are used to inform a comprehensive physical model to study the impact of vegetation encroachment process on the permafrost dynamics.

Anapole dark matter annihilation into photons

NASA Astrophysics Data System (ADS)

Latimer, David C.

2017-05-01

In models of anapole dark matter (DM), the DM candidate is a Majorana fermion whose primary interaction with standard model (SM) particles is through an anapole coupling to off-shell photons. As such, at tree-level, anapole DM undergoes p-wave annihilation into SM charged fermions via a virtual photon. But, generally, Majorana fermions are polarizable, coupling to two real photons. This fact admits the possibility that anapole DM can annihilate into two photons in an s-wave process. Using an explicit model, we compute both the tree-level and diphoton contributions to the anapole DM annihilation cross section. Depending on model parameters, the s-wave process can either rival or be dwarfed by the p-wave contribution to the total annihilation cross section. Subjecting the model to astrophysical upper bounds on the s-wave annihilation mode, we rule out the model with large s-wave annihilation.

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

Modeling the Spatial Distribution and Fruiting Pattern of a Key Tree Species in a Neotropical Forest: Methodology and Potential Applications

PubMed Central

Scarpino, Samuel V.; Jansen, Patrick A.; Garzon-Lopez, Carol X.; Winkelhagen, Annemarie J. S.; Bohlman, Stephanie A.; Walsh, Peter D.

2010-01-01

Background The movement patterns of wild animals depend crucially on the spatial and temporal availability of resources in their habitat. To date, most attempts to model this relationship were forced to rely on simplified assumptions about the spatiotemporal distribution of food resources. Here we demonstrate how advances in statistics permit the combination of sparse ground sampling with remote sensing imagery to generate biological relevant, spatially and temporally explicit distributions of food resources. We illustrate our procedure by creating a detailed simulation model of fruit production patterns for Dipteryx oleifera, a keystone tree species, on Barro Colorado Island (BCI), Panama. Methodology and Principal Findings Aerial photographs providing GPS positions for large, canopy trees, the complete census of a 50-ha and 25-ha area, diameter at breast height data from haphazardly sampled trees and long-term phenology data from six trees were used to fit 1) a point process model of tree spatial distribution and 2) a generalized linear mixed-effect model of temporal variation of fruit production. The fitted parameters from these models are then used to create a stochastic simulation model which incorporates spatio-temporal variations of D. oleifera fruit availability on BCI. Conclusions and Significance We present a framework that can provide a statistical characterization of the habitat that can be included in agent-based models of animal movements. When environmental heterogeneity cannot be exhaustively mapped, this approach can be a powerful alternative. The results of our model on the spatio-temporal variation in D. oleifera fruit availability will be used to understand behavioral and movement patterns of several species on BCI. PMID:21124927

Rate of tree carbon accumulation increases continuously with tree size

USGS Publications Warehouse

Stephenson, N.L.; Das, A.J.; Condit, R.; Russo, S.E.; Baker, P.J.; Beckman, N.G.; Coomes, D.A.; Lines, E.R.; Morris, W.K.; Rüger, N.; Álvarez, E.; Blundo, C.; Bunyavejchewin, S.; Chuyong, G.; Davies, S.J.; Duque, Á.; Ewango, C.N.; Flores, O.; Franklin, J.F.; Grau, H.R.; Hao, Z.; Harmon, M.E.; Hubbell, S.P.; Kenfack, D.; Lin, Y.; Makana, J.-R.; Malizia, A.; Malizia, L.R.; Pabst, R.J.; Pongpattananurak, N.; Su, S.-H.; Sun, I-F.; Tan, S.; Thomas, D.; van Mantgem, P.J.; Wang, X.; Wiser, S.K.; Zavala, M.A.

2014-01-01

Forests are major components of the global carbon cycle, providing substantial feedback to atmospheric greenhouse gas concentrations. Our ability to understand and predict changes in the forest carbon cycle—particularly net primary productivity and carbon storage - increasingly relies on models that represent biological processes across several scales of biological organization, from tree leaves to forest stands. Yet, despite advances in our understanding of productivity at the scales of leaves and stands, no consensus exists about the nature of productivity at the scale of the individual tree, in part because we lack a broad empirical assessment of whether rates of absolute tree mass growth (and thus carbon accumulation) decrease, remain constant, or increase as trees increase in size and age. Here we present a global analysis of 403 tropical and temperate tree species, showing that for most species mass growth rate increases continuously with tree size. Thus, large, old trees do not act simply as senescent carbon reservoirs but actively fix large amounts of carbon compared to smaller trees; at the extreme, a single big tree can add the same amount of carbon to the forest within a year as is contained in an entire mid-sized tree. The apparent paradoxes of individual tree growth increasing with tree size despite declining leaf-level and stand-level productivity can be explained, respectively, by increases in a tree’s total leaf area that outpace declines in productivity per unit of leaf area and, among other factors, age-related reductions in population density. Our results resolve conflicting assumptions about the nature of tree growth, inform efforts to understand and model forest carbon dynamics, and have additional implications for theories of resource allocation and plant senescence.

Detection and Counting of Orchard Trees from Vhr Images Using a Geometrical-Optical Model and Marked Template Matching

NASA Astrophysics Data System (ADS)

Maillard, Philippe; Gomes, Marília F.

2016-06-01

This article presents an original algorithm created to detect and count trees in orchards using very high resolution images. The algorithm is based on an adaptation of the "template matching" image processing approach, in which the template is based on a "geometricaloptical" model created from a series of parameters, such as illumination angles, maximum and ambient radiance, and tree size specifications. The algorithm is tested on four images from different regions of the world and different crop types. These images all have < 1 meter spatial resolution and were downloaded from the GoogleEarth application. Results show that the algorithm is very efficient at detecting and counting trees as long as their spectral and spatial characteristics are relatively constant. For walnut, mango and orange trees, the overall accuracy was clearly above 90%. However, the overall success rate for apple trees fell under 75%. It appears that the openness of the apple tree crown is most probably responsible for this poorer result. The algorithm is fully explained with a step-by-step description. At this stage, the algorithm still requires quite a bit of user interaction. The automatic determination of most of the required parameters is under development.

Regulatory and information support for evaluation of biological productivity of Ukrainian forests and climate change

NASA Astrophysics Data System (ADS)

Lakyda, Petro; Vasylyshyn, Roman; Lakyda, Ivan

2013-04-01

Stabilization and preservation of the planet's climate system today is regarded as one of the most important global political-economic, environmental and social problems of mankind. Rising concentration of carbon dioxide in the planet's atmosphere due to anthropogenic impact is the main reason leading to global climate change. Due to the above mentioned, social demands on forests are changing their biosphere role and function of natural sink of greenhouse gases becomes top priority. It is known that one of the most essential components of biological productivity of forests is their live biomass. Absorption, long-term sequestration of carbon and generation of oxygen are secured by its components. System research of its parametric structure and development of regulatory and reference information for assessment of aboveground live biomass components of trees and stands of the main forest-forming tree species in Ukraine began over twenty-five years ago at the department of forest mensuration and forest inventory of National University of Life and Environmental Sciences of Ukraine, involving staff from other research institutions. Today, regulatory and reference materials for evaluation of parametric structure of live biomass are developed for trees of the following major forest-forming tree species of Ukraine: Scots pine of natural and artificial origin, Crimean pine, Norway spruce, silver fir, pedunculate oak, European beech, hornbeam, ash, common birch, aspen and black alder (P.I. Lakyda et al., 2011). An ongoing process on development of similar regulatory and reference materials for forest stands of the abovementioned forest-forming tree species of Ukraine is secured by scientists of departments of forest management, and forest mensuration and forest inventory. The total experimental research base is 609 temporary sample plots, where 4880 model trees were processed, including 3195 model trees with estimates of live biomass components. Laboratory studies conducted on 1743 research sections of tree stems, 809 samples of crown branches, 2560 model tree greenery branches, 346 batches of needles and 534 batches of leaves. These materials have high scientific and practical value, forming a basis for quantitative evaluation of biological productivity of forests in Ukraine, which are of great importance for mitigation of climate change. They also can be used as a data source for development of systems of models of various purposes, which find their application in Ukrainian and world forest science and practice.

Multi-test decision tree and its application to microarray data classification.

PubMed

Czajkowski, Marcin; Grześ, Marek; Kretowski, Marek

2014-05-01

The desirable property of tools used to investigate biological data is easy to understand models and predictive decisions. Decision trees are particularly promising in this regard due to their comprehensible nature that resembles the hierarchical process of human decision making. However, existing algorithms for learning decision trees have tendency to underfit gene expression data. The main aim of this work is to improve the performance and stability of decision trees with only a small increase in their complexity. We propose a multi-test decision tree (MTDT); our main contribution is the application of several univariate tests in each non-terminal node of the decision tree. We also search for alternative, lower-ranked features in order to obtain more stable and reliable predictions. Experimental validation was performed on several real-life gene expression datasets. Comparison results with eight classifiers show that MTDT has a statistically significantly higher accuracy than popular decision tree classifiers, and it was highly competitive with ensemble learning algorithms. The proposed solution managed to outperform its baseline algorithm on 14 datasets by an average 6%. A study performed on one of the datasets showed that the discovered genes used in the MTDT classification model are supported by biological evidence in the literature. This paper introduces a new type of decision tree which is more suitable for solving biological problems. MTDTs are relatively easy to analyze and much more powerful in modeling high dimensional microarray data than their popular counterparts. Copyright © 2014 Elsevier B.V. All rights reserved.

Accuracy Assessment of Crown Delineation Methods for the Individual Trees Using LIDAR Data

NASA Astrophysics Data System (ADS)

Chang, K. T.; Lin, C.; Lin, Y. C.; Liu, J. K.

2016-06-01

Forest canopy density and height are used as variables in a number of environmental applications, including the estimation of biomass, forest extent and condition, and biodiversity. The airborne Light Detection and Ranging (LiDAR) is very useful to estimate forest canopy parameters according to the generated canopy height models (CHMs). The purpose of this work is to introduce an algorithm to delineate crown parameters, e.g. tree height and crown radii based on the generated rasterized CHMs. And accuracy assessment for the extraction of volumetric parameters of a single tree is also performed via manual measurement using corresponding aerial photo pairs. A LiDAR dataset of a golf course acquired by Leica ALS70-HP is used in this study. Two algorithms, i.e. a traditional one with the subtraction of a digital elevation model (DEM) from a digital surface model (DSM), and a pit-free approach are conducted to generate the CHMs firstly. Then two algorithms, a multilevel morphological active-contour (MMAC) and a variable window filter (VWF), are implemented and used in this study for individual tree delineation. Finally, experimental results of two automatic estimation methods for individual trees can be evaluated with manually measured stand-level parameters, i.e. tree height and crown diameter. The resulting CHM generated by a simple subtraction is full of empty pixels (called "pits") that will give vital impact on subsequent analysis for individual tree delineation. The experimental results indicated that if more individual trees can be extracted, tree crown shape will became more completely in the CHM data after the pit-free process.

Patterns of thinking about phylogenetic trees: A study of student learning and the potential of tree thinking to improve comprehension of biological concepts

NASA Astrophysics Data System (ADS)

Naegle, Erin

Evolution education is a critical yet challenging component of teaching and learning biology. There is frequently an emphasis on natural selection when teaching about evolution and conducting educational research. A full understanding of evolution, however, integrates evolutionary processes, such as natural selection, with the resulting evolutionary patterns, such as species divergence. Phylogenetic trees are models of evolutionary patterns. The perspective gained from understanding biology through phylogenetic analyses is referred to as tree thinking. Due to the increasing prevalence of tree thinking in biology, understanding how to read phylogenetic trees is an important skill for students to learn. Interpreting graphics is not an intuitive process, as graphical representations are semiotic objects. This is certainly true concerning phylogenetic tree interpretation. Previous research and anecdotal evidence report that students struggle to correctly interpret trees. The objective of this research was to describe and investigate the rationale underpinning the prior knowledge of introductory biology students' tree thinking Understanding prior knowledge is valuable as prior knowledge influences future learning. In Chapter 1, qualitative methods such as semi-structured interviews were used to explore patterns of student rationale in regard to tree thinking. Seven common tree thinking misconceptions are described: (1) Equating the degree of trait similarity with the extent of relatedness, (2) Environmental change is a necessary prerequisite to evolution, (3) Essentialism of species, (4) Evolution is inherently progressive, (5) Evolution is a linear process, (6) Not all species are related, and (7) Trees portray evolution through the hybridization of species. These misconceptions are based in students' incomplete or incorrect understanding of evolution. These misconceptions are often reinforced by the misapplication of cultural conventions to make sense of trees. Chapter 2 explores the construction, validity, and reliability of a tree thinking concept inventory. Concept inventories are research based instruments that diagnose faulty reasoning among students. Such inventories are tools for improving teaching and learning of concepts. Test scores indicate that tree thinking misconceptions are held by novice and intermediate biology students. Finally, Chapter 3 presents a tree thinking rubric. The rubric aids teachers in selecting and improving introductory tree thinking learning exercises that address students' tree thinking misconceptions.

The shape and temporal dynamics of phylogenetic trees arising from geographic speciation.

PubMed

Pigot, Alex L; Phillimore, Albert B; Owens, Ian P F; Orme, C David L

2010-12-01

Phylogenetic trees often depart from the expectations of stochastic models, exhibiting imbalance in diversification among lineages and slowdowns in the rate of lineage accumulation through time. Such departures have led to a widespread perception that ecological differences among species or adaptation and subsequent niche filling are required to explain patterns of diversification. However, a key element missing from models of diversification is the geographical context of speciation and extinction. In this study, we develop a spatially explicit model of geographic range evolution and cladogenesis, where speciation arises via vicariance or peripatry, and explore the effects of these processes on patterns of diversification. We compare the results with those observed in 41 reconstructed avian trees. Our model shows that nonconstant rates of speciation and extinction are emergent properties of the apportioning of geographic ranges that accompanies speciation. The dynamics of diversification exhibit wide variation, depending on the mode of speciation, tendency for range expansion, and rate of range evolution. By varying these parameters, the model is able to capture many, but not all, of the features exhibited by birth-death trees and extant bird clades. Under scenarios with relatively stable geographic ranges, strong slowdowns in diversification rates are produced, with faster rates of range dynamics leading to constant or accelerating rates of apparent diversification. A peripatric model of speciation with stable ranges also generates highly unbalanced trees typical of bird phylogenies but fails to produce realistic range size distributions among the extant species. Results most similar to those of a birth-death process are reached under a peripatric speciation scenario with highly volatile range dynamics. Taken together, our results demonstrate that considering the geographical context of speciation and extinction provides a more conservative null model of diversification and offers a very different perspective on the phylogenetic patterns expected in the absence of ecology.

Japanese flowering cherry tree as a woody plant candidate grown in space

NASA Astrophysics Data System (ADS)

Tomita-Yokotani, K.; Yoshida, S.; Hashimoto, H.; Nyunoya, H.; Funada, R.; Katayama, T.; Suzuki, T.; Honma, T.; Nagatomo, M.; Nakamura, T.

We are proposing to raise woody plant in space for several applications Japanese flowering cherry tree is a candidate to do wood science in space Mechanism of sensing gravity and controlling shape of tree has been studied quite extensively Cherry mutants associated with gravity are telling responsible plant hormones and molecular machinery for plant adaptation against action of gravity Space experiment using our wood model contribute to understand molecular and cellular process of gravitropism in plant Tree is considered to be an important member in space agriculture to produce excess oxygen wooden materials for constructing living environment and provide biomass for cultivating mushrooms and insects Furthermore trees and their flowers improve quality of life under stressful environment in outer space

Hybrid-Lambda: simulation of multiple merger and Kingman gene genealogies in species networks and species trees.

PubMed

Zhu, Sha; Degnan, James H; Goldstien, Sharyn J; Eldon, Bjarki

2015-09-15

There has been increasing interest in coalescent models which admit multiple mergers of ancestral lineages; and to model hybridization and coalescence simultaneously. Hybrid-Lambda is a software package that simulates gene genealogies under multiple merger and Kingman's coalescent processes within species networks or species trees. Hybrid-Lambda allows different coalescent processes to be specified for different populations, and allows for time to be converted between generations and coalescent units, by specifying a population size for each population. In addition, Hybrid-Lambda can generate simulated datasets, assuming the infinitely many sites mutation model, and compute the F ST statistic. As an illustration, we apply Hybrid-Lambda to infer the time of subdivision of certain marine invertebrates under different coalescent processes. Hybrid-Lambda makes it possible to investigate biogeographic concordance among high fecundity species exhibiting skewed offspring distribution.

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".

A new conceptual framework for unifying the heterogeneity of plant-microbe interactions in forests by linking belowground measurements with large-scale modeling and remote sensing

NASA Astrophysics Data System (ADS)

Brzostek, E. R.; Phillips, R.; Fisher, J. B.

2015-12-01

Recognition of the importance of rhizosphere interactions to ecosystem processes has led to efforts to integrate these dynamics into a conceptual framework that can be tested, refined and applied across spatial scales. A new view suggests that a plant's mycorrhizal association represents a "trait integrator" for a suite of aboveground and belowground functional traits involved in coupling C-nutrient cycles, since nearly all plants associate with a single type of mycorrhizal fungi. The MANE framework predicts that tree species that associate with arbuscular mycorrhizal (AM) fungi differ from trees that associate with ectomycorrhizal (ECM) fungi in a suite of functional traits, and that such differences contribute to unique "biogeochemical syndromes" in forests with varying abundances of AM- and ECM-associated trees. To date, we have found that relative to AM trees, the leaf litter of ECM trees decomposes nearly 50% more slowly; as such, the nutrient economy of ECM-dominated stands is driven by organic forms of N and P whereas the nutrient economy of AM-dominated stands in driven by inorganic forms of N and P. Moreover, differences in the nutrient economies between AM- and ECM-dominated stands can affect the carbon (C) cost of nutrient acquisition. For example, while ECM trees allocate 2-3-fold more C to fine roots and mycorrhizal fungi, this greater investment results in the enhanced activity of enzymes that mobilize nitrogen (N) and phosphorus (P) from soil organic matter, and ultimately the greater uptake of nutrients by plants. However, this enhanced uptake by ECM trees comes at a cost to soil organic C, which declines as a function of root-accelerated N mineralization. By incorporating these dynamics into a coupled nutrient acquisition-microbial decomposition model, and scaling these processes following development of a map of mycorrhizal associations, we are now quantifying how belowground processes shape ecosystem sensitivity to global changes (e.g., rising CO2, warming) at regional- and continental-scales.

Phylogenetic analysis accounting for age-dependent death and sampling with applications to epidemics.

PubMed

Lambert, Amaury; Alexander, Helen K; Stadler, Tanja

2014-07-07

The reconstruction of phylogenetic trees based on viral genetic sequence data sequentially sampled from an epidemic provides estimates of the past transmission dynamics, by fitting epidemiological models to these trees. To our knowledge, none of the epidemiological models currently used in phylogenetics can account for recovery rates and sampling rates dependent on the time elapsed since transmission, i.e. age of infection. Here we introduce an epidemiological model where infectives leave the epidemic, by either recovery or sampling, after some random time which may follow an arbitrary distribution. We derive an expression for the likelihood of the phylogenetic tree of sampled infectives under our general epidemiological model. The analytic concept developed in this paper will facilitate inference of past epidemiological dynamics and provide an analytical framework for performing very efficient simulations of phylogenetic trees under our model. The main idea of our analytic study is that the non-Markovian epidemiological model giving rise to phylogenetic trees growing vertically as time goes by can be represented by a Markovian "coalescent point process" growing horizontally by the sequential addition of pairs of coalescence and sampling times. As examples, we discuss two special cases of our general model, described in terms of influenza and HIV epidemics. Though phrased in epidemiological terms, our framework can also be used for instance to fit macroevolutionary models to phylogenies of extant and extinct species, accounting for general species lifetime distributions. Copyright © 2014 Elsevier Ltd. All rights reserved.

Growth response of conifers in Adirondack plantations to changing environment: Model approaches based on stem-analysis

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

Pan, Y.

1993-01-01

Based on model approaches, three conifer species, red pine, Norway spruce and Scots pine grown in plantations at Pack Demonstration Forest, in the southeastern Adirondack mountains of New York, were chosen to study growth response to different environmental changes, including silvicultural treatments and changes in climate and chemical environment. Detailed stem analysis data provided a basis for constructing tree growth models. These models were organized into three groups: morphological, dynamic and predictive. The morphological model was designed to evaluate relationship between tree attributes and interactive influences of intrinsic and extrinsic factors on the annual increments. Three types of morphological patternsmore » have been characterized: space-time patterns of whole-stem rings, intrinsic wood deposition pattern along the tree-stem, and bolewood allocation ratio patterns along the tree-stem. The dynamic model reflects the growth process as a system which responds to extrinsic signal inputs, including fertilization pulses, spacing effects and climatic disturbance, as well as intrinsic feedback. Growth signals indicative of climatic effects were used to construct growth-climate models using both multivariate analysis and Kalman filter methods. The predictive model utilized GCMs and growth-climate relationships to forecast tree growth responses in relation to future scenarios of CO[sub 2]-induced climate change. Prediction results indicate that different conifer species have individualistic growth response to future climatic change and suggest possible changes in future growth and distribution of naturally occurring conifers in this region.« less

Twisted trees and inconsistency of tree estimation when gaps are treated as missing data - The impact of model mis-specification in distance corrections.

PubMed

McTavish, Emily Jane; Steel, Mike; Holder, Mark T

2015-12-01

Statistically consistent estimation of phylogenetic trees or gene trees is possible if pairwise sequence dissimilarities can be converted to a set of distances that are proportional to the true evolutionary distances. Susko et al. (2004) reported some strikingly broad results about the forms of inconsistency in tree estimation that can arise if corrected distances are not proportional to the true distances. They showed that if the corrected distance is a concave function of the true distance, then inconsistency due to long branch attraction will occur. If these functions are convex, then two "long branch repulsion" trees will be preferred over the true tree - though these two incorrect trees are expected to be tied as the preferred true. Here we extend their results, and demonstrate the existence of a tree shape (which we refer to as a "twisted Farris-zone" tree) for which a single incorrect tree topology will be guaranteed to be preferred if the corrected distance function is convex. We also report that the standard practice of treating gaps in sequence alignments as missing data is sufficient to produce non-linear corrected distance functions if the substitution process is not independent of the insertion/deletion process. Taken together, these results imply inconsistent tree inference under mild conditions. For example, if some positions in a sequence are constrained to be free of substitutions and insertion/deletion events while the remaining sites evolve with independent substitutions and insertion/deletion events, then the distances obtained by treating gaps as missing data can support an incorrect tree topology even given an unlimited amount of data. Copyright © 2015 Elsevier Inc. All rights reserved.

Trees influence preferencial flow and water uptake in tropical savanna

NASA Astrophysics Data System (ADS)

Benegas, Laura; Bargues-Tobella, Aida; Hasselquist, Niles; Malmer, Anders; Ilstedt, Ulrik

2017-04-01

To address potential competition between trees and grasses for soil water, and to disentangle the main process responsible for local soil water dynamics in pasture ecosystems, we conducted a study of the soil water content and water source partitioning of grasses and trees within a pasture in the Copan River catchment, Honduras. We used differences in the 2H/1H (δD) isotopic signature of soil water (δSW) and the local meteoric water line (LMWL; δLMWL) as a relative index of evaporation, following a recent model proposed by Hasselquist et al (under review). The model uses Lc-excess calculated as the absolute value of the difference between measured δD and that predicted by the local meteoric water line (lc-excess = ¦δDM - δDP¦). Lc-excess values close to zero indicate little difference between soil water samples and local precipitation, whereas larger values indicate a greater degree of evaporation .()...(adapted from Landwehr and Coplen, 2006). From the relation between Lc-excess and SWC, we can tease apart different processes by which trees influence local soil water dynamics, where one such processes indicate that if preferential flow, i.e quick flows through macropores that by-pass the soil matrix, is the main pathway for water movement in the soil, then the Lc-excess values of soil water at deeper depths will be closer to zero than those of the surface soil, whereas relatively higher Lc-excess values would indicate increasing dominance of matrix flow. We found that soil underneath trees was wetter than underneath grasses at the dry season and we can relate this with a lack of clear relationship between Lc-excess and SWC and with the treés apparent shift to groundwater sources for root uptake especially in the dry season. Due to the positive correlation between Lc-excess and SWC under trees and due to the lower Lc-excess values found at subsoil below trees during the dry season, we can infer that preferential flow is also facilitated by the trees enhancing its contribution to groundwater recharge. The possible water losses via interception linked with trees on the soil water dynamic was counterbalanced by the positive contribution of trees to preferential flow and groundwater recharge.

Integration of climatic water deficit and fine-scale physiography in process-based modeling of forest landscape resilience to large-scale tree mortality

NASA Astrophysics Data System (ADS)

Yang, J.; Weisberg, P.; Dilts, T.

2016-12-01

Climate warming can lead to large-scale drought-induced tree mortality events and greatly affect forest landscape resilience. Climatic water deficit (CWD) and its physiographic variations provide a key mechanism in driving landscape dynamics in response to climate change. Although CWD has been successfully applied in niche-based species distribution models, its application in process-based forest landscape models is still scarce. Here we present a framework incorporating fine-scale influence of terrain on ecohydrology in modeling forest landscape dynamics. We integrated CWD with a forest landscape succession and disturbance model (LANDIS-II) to evaluate how tree species distribution might shift in response to different climate-fire scenarios across an elevation-aspect gradient in a semi-arid montane landscape of northeastern Nevada, USA. Our simulations indicated that drought-intolerant tree species such as quaking aspen could experience greatly reduced distributions in the more arid portions of their existing ranges due to water stress limitations under future climate warming scenarios. However, even at the most xeric portions of its range, aspen is likely to persist in certain environmental settings due to unique and often fine-scale combinations of resource availability, species interactions and disturbance regime. The modeling approach presented here allowed identification of these refugia. In addition, this approach helped quantify how the direction and magnitude of fire influences on species distribution would vary across topoclimatic gradients, as well as furthers our understanding on the role of environmental conditions, fire, and inter-specific competition in shaping potential responses of landscape resilience to climate change.

Explaining the dependence of climatic response of tree radial growth on permafrost

NASA Astrophysics Data System (ADS)

Bryukhanova, Marina; Benkova, Anna; von Arx, Georg; Fonti, Patrick; Simanko, Valentina; Kirdyanov, Alexander; Shashkin, Alexander

2015-04-01

In northern regions of Siberia it is infrequent to have long-term observations of the variability of soil features, phenological data, duration of the growing season, which can be used to infer the influence of the environment on tree growth and productivity. The best way to understand tree-growth and tree responses to environmental changes is to make use of mechanistic models, allowing to combine already available experiment/field data with other parameters based on biological principles of tree growth. The goal of our study is to estimate which tree species (deciduous, conifer deciduous or conifer evergreen) is more plastic under possible climate changes in permafrost zone. The studied object is located in the northern part of central Siberia, Russia (64°N, 100°E). The study plot was selected within a post-fire succession and representatives for 100 years old even aged mixed forest of Larix gmelinii (Rupr.) Rupr. and Betula pubescens Ehrh. with few exemplars of Spruce (Picea obovata Ledeb.). To understand physiological response of larch, birch and spruce trees to climatic changes the ecological-physiological process-based model of tree photosynthesis (Benkova and Shashkin 2003) was applied. Multiparametric tree-ring chronologies were analyzed and correlated with climatic parameters over the last 77 years. This work is supported by the Ministry of Education and Science of the Russian Federation (Grant from the President of RF for Young Scientists MK-1589.2014.4).

A study of crown development mechanisms using a shoot-based tree model and segmented terrestrial laser scanning data.

PubMed

Sievänen, Risto; Raumonen, Pasi; Perttunen, Jari; Nikinmaa, Eero; Kaitaniemi, Pekka

2018-05-24

Functional-structural plant models (FSPMs) allow simulation of tree crown development as the sum of modular (e.g. shoot-level) responses triggered by the local environmental conditions. The actual process of space filling by the crowns can be studied. Although the FSPM simulations are at organ scale, the data for their validation have usually been at more aggregated levels (whole-crown or whole-tree). Measurements made by terrestrial laser scanning (TLS) that have been segmented into elementary units (internodes) offer a phenotyping tool to validate the FSPM predictions at levels comparable with their detail. We demonstrate the testing of different formulations of crown development of Scots pine trees in the LIGNUM model using segmented TLS data. We made TLS measurements from four sample trees growing in a forest on a relatively poor soil from sapling size to mature stage. The TLS data were segmented into internodes. The segmentation also produced information on whether needles were present in the internode. We applied different formulations of crown development (flushing of buds and length of growth of new internodes) in LIGNUM. We optimized the parameter values of each formulation using genetic algorithms to observe the best fit of LIGNUM simulations to the measured trees. The fitness function in the estimation combined both tree-level characteristics (e.g. tree height and crown length) and measures of crown shape (e.g. spatial distribution of needle area). Comparison of different formulations against the data indicates that the Extended Borchert-Honda model for shoot elongation works best within LIGNUM. Control of growth by local density in the crown was important for all shoot elongation formulations. Modifying the number of lateral buds as a function of local density in the crown was the best way to accomplish density control. It was demonstrated how segmented TLS data can be used in the context of a shoot-based model to select model components.

Can Sap Flow Help Us to Better Understand Transpiration Patterns in Landscapes?

NASA Astrophysics Data System (ADS)

Hassler, S. K.; Weiler, M.; Blume, T.

2017-12-01

Transpiration is a key process in the hydrological cycle and a sound understanding and quantification of transpiration and its spatial variability is essential for management decisions and for improving the parameterisation of hydrological and soil-vegetation-atmosphere transfer models. At the tree scale, transpiration is commonly estimated by measuring sap flow. Besides evaporative demand and water availability, tree-specific characteristics such as species, size or social status, stand-specific characteristics such as basal area or stand density and site-specific characteristics such as geology, slope position or aspect control sap flow of individual trees. However, little is known about the relative importance or the dynamic interplay of these controls. We studied these influences with multiple linear regression models to explain the variability of sap velocity measurements in 61 beech and oak trees, located at 24 sites spread over a 290 km²-catchment in Luxembourg. For each of 132 consecutive days of the growing season of 2014 we applied linear models to the daily spatial pattern of sap velocity and determined the importance of the different predictors. By upscaling sap velocities to the tree level with the help of species-dependent empirical estimates for sapwood area we also examined patterns of sap flow as a more direct representation of transpiration. Results indicate that a combination of mainly tree- and site-specific factors controls sap velocity patterns in this landscape, namely tree species, tree diameter, geology and aspect. For sap flow, the site-specific predictors provided the largest contribution to the explained variance, however, in contrast to the sap velocity analysis, geology was more important than aspect. Spatial variability of atmospheric demand and soil moisture explained only a small fraction of the variance. However, the temporal dynamics of the explanatory power of the tree-specific characteristics, especially species, were correlated to the temporal dynamics of potential evaporation. We conclude that spatial representation of transpiration in models could benefit from including patterns according to tree and site characteristics.

The ratio of NPP to GPP: evidence of change over the course of stand development.

PubMed

Mäkelä, A; Valentine, H T

2001-09-01

Using Scots pine (Pinus sylvestris L.) in Fenno-Scandia as a case study, we investigate whether net primary production (NPP) and maintenance respiration are constant fractions of gross primary production (GPP) as even-aged mono-specific stands progress from initiation to old age. A model of the ratio of NPP to GPP is developed based on (1) the classical model of respiration, which divides total respiration into construction and maintenance components, and (2) a process-based model, which derives respiration from processes including construction, nitrate uptake and reduction, ion uptake, phloem loading and maintenance. Published estimates of specific respiration and production rates, and some recent measurements of components of dry matter in stands of different ages, are used to quantify the two approaches over the course of stand development in an average environment. Both approaches give similar results, showing a decrease in the NPP/GPP ratio with increasing tree height. In addition, we show that stand-growth models fitted under three different sets of assumptions-(i) annual specific rates of maintenance respiration of sapwood (mW) and photosynthesis (sC) are constant; (ii) m(W) is constant, but sC decreases with increasing tree height; and (iii) total maintenance respiration is a constant fraction of GPP and s(C) decreases with increasing tree height-can lead to nearly identical model projections that agree with empirical observations of NPP and stand-growth variables. Remeasurements of GPP and respiration over time in chronosequences of stands may be needed to discern which set of assumptions is correct. Total (construction + maintenance) sapwood respiration per unit mass of sapwood (kg C (kg C year)-1) decreased with increasing stand age, sapwood stock, and average tree height under all three assumptions. However, total sapwood respiration (kg C (ha year)-1) increased over the course of stand development under (i) and (ii), contributing to a downward trend in the time course of the NPP/GPP ratio after closure. A moderate decrease in mW with increasing tree height or sapwood cross-sectional area had little effect on the downward trend. On the basis of this evidence, we argue that a significant decline in the NPP/GPP ratio with tree size or age seems highly probable, although the decline may appear insignificant over some segments of stand development. We also argue that, because stand-growth models can give correct answers for the wrong reasons, statistical calibration of such models should be avoided whenever possible; instead, values of physiological parameters should come from measurements of the physiological processes themselves.

How does variation in rainfall affect simulated tropical tree mortality, functional diversity and coexistence?

NASA Astrophysics Data System (ADS)

Powell, T.; Kueppers, L. M.; Koven, C.; Johnson, D. J.; Faybishenko, B.; McDowell, N. G.; Chambers, J. Q.

2016-12-01

Land surface models that include demographic and plant hydrodynamic processes are promising tools for characterizing how different drought scenarios may affect carbon cycling of tropical forests. The Ecosystem Demography (ED2) model, now formulated with such features, was used to evaluate how different drought scenarios affect mortality patterns, functional diversity and coexistence of four plant functional types (PFTs) of tropical trees at Barro Colorado Island (BCI), Panama. The four PFTs simulated were early- versus late-successional groups subdivided into drought-tolerant versus -intolerant groups. The hydrodynamic formulation enables the four PFTs to compete mechanistically along two largely orthogonal resource gradients of water and light. The model simulations produced considerable differences in the aboveground biomass response to contrasting drying scenarios that included longer dry seasons, El Nino related droughts, and drier dry seasons. The emergent mortality dynamics reflect the physiological trade-off between water-use and carbon fixation formulated by the hydrodynamic regulation over stomatal conductance. During dry periods, the model predicts increased mortality rates of pioneer trees compared to generalists and drought-intolerant trees compared to -tolerant trees. The model also predicts that surviving cohorts in the smallest size classes of drought-intolerant trees are occasionally primed for release from competition following acute droughts. Observations at BCI showed increased mortality rates for large trees (i.e. >30 cm dbh) during the 1982 El Nino drought, but not subsequent El Nino related droughts. The causes of the elevated mortality rates are explored with the model. Coexistence of four plant functional types in the model is highly sensitive to the parameterization of stem hydraulic conductivity; but, surprisingly not very sensitive to shifts in rainfall patterns. These results demonstrate (a) that plant hydrodynamics are critical for simulating dynamic mortality patterns between drought-tolerant and -intolerant PFTs in order to increase representation of functional diversity in land surface models, and (b) that more demographic, plant hydraulic and deeper soil moisture observations are required to constrain hydrodynamic parameter selection.

Vascular system modeling in parallel environment - distributed and shared memory approaches

PubMed Central

Jurczuk, Krzysztof; Kretowski, Marek; Bezy-Wendling, Johanne

2011-01-01

The paper presents two approaches in parallel modeling of vascular system development in internal organs. In the first approach, new parts of tissue are distributed among processors and each processor is responsible for perfusing its assigned parts of tissue to all vascular trees. Communication between processors is accomplished by passing messages and therefore this algorithm is perfectly suited for distributed memory architectures. The second approach is designed for shared memory machines. It parallelizes the perfusion process during which individual processing units perform calculations concerning different vascular trees. The experimental results, performed on a computing cluster and multi-core machines, show that both algorithms provide a significant speedup. PMID:21550891

Water, Carbon, and Nutrient Cycling Following Insect-induced Tree Mortality: How Well Do Plot-scale Observations Predict Ecosystem-Scale Response?

NASA Astrophysics Data System (ADS)

Brooks, P. D.; Barnard, H. R.; Biederman, J. A.; Borkhuu, B.; Edburg, S. L.; Ewers, B. E.; Gochis, D. J.; Gutmann, E. D.; Harpold, A. A.; Hicke, J. A.; Pendall, E.; Reed, D. E.; Somor, A. J.; Troch, P. A.

2011-12-01

Widespread tree mortality caused by insect infestations and drought has impacted millions of hectares across western North America in recent years. Although previous work on post-disturbance responses (e.g. experimental manipulations, fire, and logging) provides insight into how water and biogeochemical cycles may respond to insect infestations and drought, we find that the unique nature of these drivers of tree mortality complicates extrapolation to larger scales. Building from previous work on forest disturbance, we present a conceptual model of how temporal changes in forest structure impact the individual components of energy balance, hydrologic partitioning, and biogeochemical cycling and the interactions among them. We evaluate and refine this model using integrated observations and process modeling on multiple scales including plot, stand, flux tower footprint, hillslope, and catchment to identify scaling relationships and emergent patterns in hydrological and biogeochemical responses. Our initial results suggest that changes in forest structure at point or plot scales largely have predictable effects on energy, water, and biogeochemical cycles that are well captured by land surface, hydrological, and biogeochemical models. However, observations from flux towers and nested catchments suggest that both the hydrological and biogeochemical effects observed at tree and plot scales may be attenuated or exacerbated at larger scales. Compensatory processes are associated with attenuation (e.g. as transpiration decreases, evaporation and sublimation increase), whereas both attenuation and exacerbation may result from nonlinear scaling behavior across transitions in topography and ecosystem structure that affect the redistribution of energy, water, and solutes. Consequently, the effects of widespread tree mortality on ecosystem services of water supply and carbon sequestration will likely depend on how spatial patterns in mortality severity across the landscape affect large-scale hydrological partitioning.

Light dark matter through assisted annihilation

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

Dey, Ujjal Kumar; Maity, Tarak Nath; Ray, Tirtha Sankar, E-mail: ujjal@cts.iitkgp.ernet.in, E-mail: tarak.maity.physics@gmail.com, E-mail: tirthasankar.ray@gmail.com

2017-03-01

In this paper we investigate light dark matter scenarios where annihilation to Standard Model particles at tree-level is kinematically forbidden. In such cases annihilation can be aided by massive Standard Model-like species, called assisters , in the initial state that enhances the available phase space opening up novel tree-level processes. We investigate the feasibility of such non-standard assisted annihilation processes to reproduce the observed relic density of dark matter. We present a simple scalar dark matter-scalar assister model where this is realised. We find that if the dark matter and assister are relatively degenerate the required relic density can bemore » achieved for a keV-MeV scale dark matter. We briefly discuss the cosmological constraints on such dark matter scenarios.« less

Tree phylogenetic diversity promotes host-parasitoid interactions.

PubMed

Staab, Michael; Bruelheide, Helge; Durka, Walter; Michalski, Stefan; Purschke, Oliver; Zhu, Chao-Dong; Klein, Alexandra-Maria

2016-07-13

Evidence from grassland experiments suggests that a plant community's phylogenetic diversity (PD) is a strong predictor of ecosystem processes, even stronger than species richness per se This has, however, never been extended to species-rich forests and host-parasitoid interactions. We used cavity-nesting Hymenoptera and their parasitoids collected in a subtropical forest as a model system to test whether hosts, parasitoids, and their interactions are influenced by tree PD and a comprehensive set of environmental variables, including tree species richness. Parasitism rate and parasitoid abundance were positively correlated with tree PD. All variables describing parasitoids decreased with elevation, and were, except parasitism rate, dependent on host abundance. Quantitative descriptors of host-parasitoid networks were independent of the environment. Our study indicates that host-parasitoid interactions in species-rich forests are related to the PD of the tree community, which influences parasitism rates through parasitoid abundance. We show that effects of tree community PD are much stronger than effects of tree species richness, can cascade to high trophic levels, and promote trophic interactions. As during habitat modification phylogenetic information is usually lost non-randomly, even species-rich habitats may not be able to continuously provide the ecosystem process parasitism if the evolutionarily most distinct plant lineages vanish. © 2016 The Author(s).

The algebra of the general Markov model on phylogenetic trees and networks.

PubMed

Sumner, J G; Holland, B R; Jarvis, P D

2012-04-01

It is known that the Kimura 3ST model of sequence evolution on phylogenetic trees can be extended quite naturally to arbitrary split systems. However, this extension relies heavily on mathematical peculiarities of the associated Hadamard transformation, and providing an analogous augmentation of the general Markov model has thus far been elusive. In this paper, we rectify this shortcoming by showing how to extend the general Markov model on trees to include incompatible edges; and even further to more general network models. This is achieved by exploring the algebra of the generators of the continuous-time Markov chain together with the “splitting” operator that generates the branching process on phylogenetic trees. For simplicity, we proceed by discussing the two state case and then show that our results are easily extended to more states with little complication. Intriguingly, upon restriction of the two state general Markov model to the parameter space of the binary symmetric model, our extension is indistinguishable from the Hadamard approach only on trees; as soon as any incompatible splits are introduced the two approaches give rise to differing probability distributions with disparate structure. Through exploration of a simple example, we give an argument that our extension to more general networks has desirable properties that the previous approaches do not share. In particular, our construction allows for convergent evolution of previously divergent lineages; a property that is of significant interest for biological applications.

[Advances in studies on the structure of farmland shelterbelt ecosystem].

PubMed

Li, Chunping; Guan, Wenbin; Fan, Zhiping; Su, Fanxin; Wang, Xilin

2003-11-01

The ecological function of farmland shelterbelt system is determined by its structure. The spatio-temporal structure is a key aspect in related researches, which is very necessary to study the integrity, stability and durability of shelterbelt modules. In this article, the researches on the structure of farmland shelterbelt ecosystem were reviewed from the four scales of tree structure, shelterbelt structure, shelterbelts network and landscape structure. The principles, methods and productions of each scale were summarized, and the prospects were also discussed. Dynamic simulation of tree growth process in shelterbelts could be conducted by the theory of form and quality structure of tree and by fractal graphics, which were helpful to study the mechanism of individual trees and belts based on photosynthetic and transpiration mechanism of individual trees. The mechanism model of shelterbelt porosity should be conducted, so that, the sustainable yield model of shelterbelt management could be established, and the optimized model of shelterbelt networks with multi-special and multi-hierarchical structure could also be formed. Evaluating the reasonability, stability and durability of shelterbelt landscape based on the theories and methods of landscape ecology was an important task in the future studies.

Accounting for Landscape Heterogeneity Improves Spatial Predictions of Tree Vulnerability to Drought

NASA Astrophysics Data System (ADS)

Schwantes, A. M.; Parolari, A.; Swenson, J. J.; Johnson, D. M.; Domec, J. C.; Jackson, R. B.; Pelak, N. F., III; Porporato, A. M.

2017-12-01

Globally, as climate change continues, forest vulnerability to droughts and heatwaves is increasing, but vulnerability differs regionally and locally depending on landscape position. However, most models used in forecasting forest responses to heatwaves and droughts do not incorporate relevant spatial processes. To improve predictions of spatial tree vulnerability, we employed a non-linear stochastic model of soil moisture dynamics across a landscape, accounting for spatial differences in aspect, topography, and soils. Our unique approach integrated plant hydraulics and landscape processes, incorporating effects from lateral redistribution of water using a topographic index and radiation and temperature differences attributable to aspect. Across a watershed in central Texas we modeled dynamic water stress for a dominant tree species, Juniperus ashei. We compared our results to a detailed spatial dataset of drought-impacted areas (>25% canopy loss) derived from remote sensing during the severe 2011 drought. We then projected future dynamic water stress through the 21st century using climate projections from 10 global climate models under two scenarios, and compared models with and without landscape heterogeneity. Within this watershed, 42% of J. ashei dominated systems were impacted by the 2011 drought. Modeled dynamic water stress tracked these spatial patterns of observed drought-impacted areas. Total accuracy increased from 59%, when accounting only for soil variability, to 73% when including lateral redistribution of water and radiation and temperature effects. Dynamic water stress was projected to increase through the 21st century, with only minimal buffering from the landscape. During the hotter and more severe droughts projected in the 21st century, up to 90% of the watershed crossed a dynamic water stress threshold associated with canopy loss in 2011. Favorable microsites may exist across a landscape where trees can persist; however, if future droughts are too severe, the buffering capacity of a heterogenous landscape could be overwhelmed. Incorporating spatial data will improve projections of future tree water stress and identification of potential resilient refugia.

Adventitious root formation in tree species: involvement of transcription factors.

PubMed

Legué, Valérie; Rigal, Adeline; Bhalerao, Rishikesh P

2014-06-01

Adventitious rooting is an essential step in the vegetative propagation of economically important horticultural and woody species. Populus has emerged as an experimental model for studying processes that are important in tree growth and development. It is highly useful for molecular genetic analysis of adventitious roots in trees. In this short review, we will highlight the recent progress made in the identification of transcription factors involved in the control of adventitious rooting in woody species. Their regulation will be discussed. © 2014 Scandinavian Plant Physiology Society.

Tree-, stand- and site-specific controls on landscape-scale patterns of transpiration

NASA Astrophysics Data System (ADS)

Kathrin Hassler, Sibylle; Weiler, Markus; Blume, Theresa

2018-01-01

Transpiration is a key process in the hydrological cycle, and a sound understanding and quantification of transpiration and its spatial variability is essential for management decisions as well as for improving the parameterisation and evaluation of hydrological and soil-vegetation-atmosphere transfer models. For individual trees, transpiration is commonly estimated by measuring sap flow. Besides evaporative demand and water availability, tree-specific characteristics such as species, size or social status control sap flow amounts of individual trees. Within forest stands, properties such as species composition, basal area or stand density additionally affect sap flow, for example via competition mechanisms. Finally, sap flow patterns might also be influenced by landscape-scale characteristics such as geology and soils, slope position or aspect because they affect water and energy availability; however, little is known about the dynamic interplay of these controls.We studied the relative importance of various tree-, stand- and site-specific characteristics with multiple linear regression models to explain the variability of sap velocity measurements in 61 beech and oak trees, located at 24 sites across a 290 km2 catchment in Luxembourg. For each of 132 consecutive days of the growing season of 2014 we modelled the daily sap velocity and derived sap flow patterns of these 61 trees, and we determined the importance of the different controls.Results indicate that a combination of mainly tree- and site-specific factors controls sap velocity patterns in the landscape, namely tree species, tree diameter, geology and aspect. For sap flow we included only the stand- and site-specific predictors in the models to ensure variable independence. Of those, geology and aspect were most important. Compared to these predictors, spatial variability of atmospheric demand and soil moisture explains only a small fraction of the variability in the daily datasets. However, the temporal dynamics of the explanatory power of the tree-specific characteristics, especially species, are correlated to the temporal dynamics of potential evaporation. We conclude that transpiration estimates on the landscape scale would benefit from not only consideration of hydro-meteorological drivers, but also tree, stand and site characteristics in order to improve the spatial and temporal representation of transpiration for hydrological and soil-vegetation-atmosphere transfer models.

Linking Tropical Forest Function to Hydraulic Traits in a Size-Structured and Trait-Based Model

NASA Astrophysics Data System (ADS)

Christoffersen, B. O.; Gloor, M.; Fauset, S.; Fyllas, N.; Galbraith, D.; Baker, T. R.; Rowland, L.; Fisher, R.; Binks, O.; Sevanto, S.; Xu, C.; Jansen, S.; Choat, B.; Mencuccini, M.; McDowell, N. G.; Meir, P.

2015-12-01

A major weakness of forest ecosystem models is their inability to capture the diversity of responses to changes in water availability, severely hampering efforts to predict the fate of tropical forests under climate change. Such models often prescribe moisture sensitivity using heuristic response functions that are uniform across all individuals and lack important knowledge about trade-offs in hydraulic traits. We address this weakness by implementing a process representation of plant hydraulics into an individual- and trait-based model (Trait Forest Simulator; TFS) intended for application at discrete sites where community-level distributions of stem and leaf trait spectra (wood density, leaf mass per area, leaf nitrogen and phosphorus content) are known. The model represents a trade-off in the safety and efficiency of water conduction in xylem tissue through hydraulic traits, while accounting for the counteracting effects of increasing hydraulic path length and xylem conduit taper on whole-plant hydraulic resistance with increasing tree size. Using existing trait databases and additional meta-analyses from the rich literature on tropical tree ecophysiology, we obtained all necessary hydraulic parameters associated with xylem conductivity, vulnerability curves, pressure-volume curves, and hydraulic architecture (e.g., leaf-to-sapwood area ratios) as a function of the aforementioned traits and tree size. Incorporating these relationships in the model greatly improved the diversity of tree response to seasonal changes in water availability as well as in response to drought, as determined by comparison with field observations and experiments. Importantly, this individual- and trait-based framework provides a testbed for identifying both critical processes and functional traits needed for inclusion in coarse-scale Dynamic Global Vegetation Models, which will lead to reduced uncertainty in the future state of tropical forests.

Empirical phylogenies and species abundance distributions are consistent with preequilibrium dynamics of neutral community models with gene flow.

PubMed

Bonnet-Lebrun, Anne-Sophie; Manica, Andrea; Eriksson, Anders; Rodrigues, Ana S L

2017-05-01

Community characteristics reflect past ecological and evolutionary dynamics. Here, we investigate whether it is possible to obtain realistically shaped modeled communities-that is with phylogenetic trees and species abundance distributions shaped similarly to typical empirical bird and mammal communities-from neutral community models. To test the effect of gene flow, we contrasted two spatially explicit individual-based neutral models: one with protracted speciation, delayed by gene flow, and one with point mutation speciation, unaffected by gene flow. The former produced more realistic communities (shape of phylogenetic tree and species-abundance distribution), consistent with gene flow being a key process in macro-evolutionary dynamics. Earlier models struggled to capture the empirically observed branching tempo in phylogenetic trees, as measured by the gamma statistic. We show that the low gamma values typical of empirical trees can be obtained in models with protracted speciation, in preequilibrium communities developing from an initially abundant and widespread species. This was even more so in communities sampled incompletely, particularly if the unknown species are the youngest. Overall, our results demonstrate that the characteristics of empirical communities that we have studied can, to a large extent, be explained through a purely neutral model under preequilibrium conditions. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

Extinction threshold for spatial forest dynamics with height structure.

PubMed

Garcia-Domingo, Josep L; Saldaña, Joan

2011-05-07

We present a pair-approximation model for spatial forest dynamics defined on a regular lattice. The model assumes three possible states for a lattice site: empty (gap site), occupied by an immature tree, and occupied by a mature tree, and considers three nonlinearities in the dynamics associated to the processes of light interference, gap expansion, and recruitment. We obtain an expression of the basic reproduction number R(0) which, in contrast to the one obtained under the mean-field approach, uses information about the spatial arrangement of individuals close to extinction. Moreover, we analyze the corresponding survival-extinction transition of the forest and the spatial correlations among gaps, immature and mature trees close to this critical point. Predictions of the pair-approximation model are compared with those of a cellular automaton. Copyright © 2011 Elsevier Ltd. All rights reserved.

An Examination of Drought-Induced Hydraulic Stress in Conifer Forests Using a Coupled Ecohydrologic Model.

NASA Astrophysics Data System (ADS)

Simeone, C.; Maneta, M. P.; Holden, Z. A.; Dobrowski, S.; Sala, A.

2017-12-01

Recent studies indicate that increases in drought stress due to climate change will increase forest mortality across the western U.S. Although ecohydrologic models used to study regional hydrologic stress response in forests have made rapid advances in recent years, they often incorporate simplified descriptions of the local hydrology, do not implement an explicit description of plant hydraulics, and do not permit to study the tradeoffs between frequency, intensity, and accumulation of hydrologic stress in vegetation. We use the spatially-distributed, mechanistic ecohydrologic model Ech2o, which effectively captures spatial variations in both hydrology, energy exchanges, and regional climate to simulate high-resolution tree hydraulics, estimating soil and leaf water potential, tree effective water conductance, and percent loss of conductivity in the xylem (PLC) at 250 meter resolution and sub-daily timestep across a topographically complex landscape. Tree hydraulics are simulated assuming a diffusive process in the soil-tree-atmosphere continuum. We use PLC to develop a vegetation dynamic stress index that scales plant-level processes to the landscape scale, and that takes into account the temporal accumulation of instantaneous hydraulic stress, growing season length, frequency and duration of drought periods, and plant drought tolerance. The resulting index is interpreted as the probability of drought induced tree mortality in a given location during the simulated period. We apply this index to regions of Northern Idaho and Western Montana. Results show that drought stress is highly spatially variable, sensitive to local-scale hydrologic and atmospheric conditions, and responsive to the recovery rate from individual hydraulic stress episodes.

Drought-associated tree mortality: Global patterns and insights from tree-ring studies in the southwestern U.S.A

NASA Astrophysics Data System (ADS)

Macalady, Alison Kelly

Forests play an important role in the earth system, regulating climate, maintaining biodiversity, and provisioning human communities with water, food and fuel. Interactions between climate and forest dynamics are not well constrained, and high uncertainty characterizes projections of global warming impacts on forests and associated ecosystem services. Recently observed tree mortality and forest die-off forewarn an acceleration of forest change with rising temperature and increased drought. However, the processes leading to tree death during drought are poorly understood, limiting our ability to anticipate future forest dynamics. The objective of this dissertation was to improve understanding of drought-associated tree mortality through literature synthesis and tree-ring studies on trees that survived and died during droughts in the southwestern USA. Specifically, this dissertation 1) documented global tree mortality patterns and identified emerging trends and research gaps; 2) quantified relationships between growth, climate, competition and mortality of pinon pine during droughts in New Mexico; 3) investigated tree defense anatomy as a potentially key element in pinon avoidance of death; and, 4) characterized the climate sensitivity of pinon resin ducts in order to gain insight into potential trends in tree defenses with climate variability and change. There has been an increase in studies reporting tree mortality linked to drought, heat, and the associated activity of insects and pathogens. Cases span the forested continents and occurred in water, light and temperature-limited forests. We hypothesized that increased tree mortality may be an emerging global phenomenon related to rising temperatures and drought (Appendix A). Recent radial growth was 53% higher on average in pinon that survived versus died during two episodes of drought-associated mortality, and statistical models of mortality risk based on average growth, growth variability, and abrupt growth changes correctly classified the status of ˜70% of trees. Climate responses and competitive interactions partly explained growth differences between dying and surviving trees, with muted response to wet/cool conditions and enhanced sensitivity to competition from congeners linked to growth patterns associated with death. Discrimination and validation of models of mortality risk varied widely across sites and drought events, indicating shifting growth-mortality relationships and differences in mortality processes across space and time (Appendix B). Pre-formed defense anatomy is strongly associated with pinon survivorship over a range of sites and stand conditions. Models of mortality risk that account for both growth and resin duct attributes had ≈10 19 more support than models that contained only growth. The greatest improvement in classification was among trees from the 2000s drought, suggesting an enhanced role for tree defense allocation and/or bark beetle activity during recent warm versus historic cool drought. Accounting for defense characteristics and growth-defense allocation is likely to be important for improving representation of drought-associated mortality (Appendix C). Pinon resin duct chronologies contain climate responses that are coherent and distinct from those of radial growth. Growth responds positively and strongly to previous fall and current winter precipitation, and negatively to late spring and early summer temperature. A relatively equal positive resin duct response to winter precipitation and positive response to mid-to-late summer drought suggests that changes in climate will affect tree defense anatomy in complex ways, with the outcome determined by seasonal changes in precipitation and temperature (Appendix D).

Functional model of biological neural networks.

PubMed

Lo, James Ting-Ho

2010-12-01

A functional model of biological neural networks, called temporal hierarchical probabilistic associative memory (THPAM), is proposed in this paper. THPAM comprises functional models of dendritic trees for encoding inputs to neurons, a first type of neuron for generating spike trains, a second type of neuron for generating graded signals to modulate neurons of the first type, supervised and unsupervised Hebbian learning mechanisms for easy learning and retrieving, an arrangement of dendritic trees for maximizing generalization, hardwiring for rotation-translation-scaling invariance, and feedback connections with different delay durations for neurons to make full use of present and past informations generated by neurons in the same and higher layers. These functional models and their processing operations have many functions of biological neural networks that have not been achieved by other models in the open literature and provide logically coherent answers to many long-standing neuroscientific questions. However, biological justifications of these functional models and their processing operations are required for THPAM to qualify as a macroscopic model (or low-order approximate) of biological neural networks.

Simulating stand climate, phenology, and photosynthesis of a forest stand with a process-based growth model.

PubMed

Rötzer, Thomas; Leuchner, Michael; Nunn, Angela J

2010-07-01

In the face of climate change and accompanying risks, forest management in Europe is becoming increasingly important. Model simulations can help to understand the reactions and feedbacks of a changing environment on tree growth. In order to simulate forest growth based on future climate change scenarios, we tested the basic processes underlying the growth model BALANCE, simulating stand climate (air temperature, photosynthetically active radiation (PAR) and precipitation), tree phenology, and photosynthesis. A mixed stand of 53- to 60-year-old Norway spruce (Picea abies) and European beech (Fagus sylvatica) in Southern Germany was used as a reference. The results show that BALANCE is able to realistically simulate air temperature gradients in a forest stand using air temperature measurements above the canopy and PAR regimes at different heights for single trees inside the canopy. Interception as a central variable for water balance of a forest stand was also estimated. Tree phenology, i.e. bud burst and leaf coloring, could be reproduced convincingly. Simulated photosynthesis rates were in accordance with measured values for beech both in the sun and the shade crown. For spruce, however, some discrepancies in the rates were obvious, probably due to changed environmental conditions after bud break. Overall, BALANCE has shown to respond to scenario simulations of a changing environment (e.g., climate change, change of forest stand structure).

Error analysis of leaf area estimates made from allometric regression models

NASA Technical Reports Server (NTRS)

Feiveson, A. H.; Chhikara, R. S.

1986-01-01

Biological net productivity, measured in terms of the change in biomass with time, affects global productivity and the quality of life through biochemical and hydrological cycles and by its effect on the overall energy balance. Estimating leaf area for large ecosystems is one of the more important means of monitoring this productivity. For a particular forest plot, the leaf area is often estimated by a two-stage process. In the first stage, known as dimension analysis, a small number of trees are felled so that their areas can be measured as accurately as possible. These leaf areas are then related to non-destructive, easily-measured features such as bole diameter and tree height, by using a regression model. In the second stage, the non-destructive features are measured for all or for a sample of trees in the plots and then used as input into the regression model to estimate the total leaf area. Because both stages of the estimation process are subject to error, it is difficult to evaluate the accuracy of the final plot leaf area estimates. This paper illustrates how a complete error analysis can be made, using an example from a study made on aspen trees in northern Minnesota. The study was a joint effort by NASA and the University of California at Santa Barbara known as COVER (Characterization of Vegetation with Remote Sensing).

Rooting phylogenetic trees under the coalescent model using site pattern probabilities.

PubMed

Tian, Yuan; Kubatko, Laura

2017-12-19

Phylogenetic tree inference is a fundamental tool to estimate ancestor-descendant relationships among different species. In phylogenetic studies, identification of the root - the most recent common ancestor of all sampled organisms - is essential for complete understanding of the evolutionary relationships. Rooted trees benefit most downstream application of phylogenies such as species classification or study of adaptation. Often, trees can be rooted by using outgroups, which are species that are known to be more distantly related to the sampled organisms than any other species in the phylogeny. However, outgroups are not always available in evolutionary research. In this study, we develop a new method for rooting species tree under the coalescent model, by developing a series of hypothesis tests for rooting quartet phylogenies using site pattern probabilities. The power of this method is examined by simulation studies and by application to an empirical North American rattlesnake data set. The method shows high accuracy across the simulation conditions considered, and performs well for the rattlesnake data. Thus, it provides a computationally efficient way to accurately root species-level phylogenies that incorporates the coalescent process. The method is robust to variation in substitution model, but is sensitive to the assumption of a molecular clock. Our study establishes a computationally practical method for rooting species trees that is more efficient than traditional methods. The method will benefit numerous evolutionary studies that require rooting a phylogenetic tree without having to specify outgroups.

Vulnerability of Amazon forests to storm-driven tree mortality

NASA Astrophysics Data System (ADS)

Negrón-Juárez, Robinson I.; Holm, Jennifer A.; Magnabosco Marra, Daniel; Rifai, Sami W.; Riley, William J.; Chambers, Jeffrey Q.; Koven, Charles D.; Knox, Ryan G.; McGroddy, Megan E.; Di Vittorio, Alan V.; Urquiza-Muñoz, Jose; Tello-Espinoza, Rodil; Alegria Muñoz, Waldemar; Ribeiro, Gabriel H. P. M.; Higuchi, Niro

2018-05-01

Tree mortality is a key driver of forest community composition and carbon dynamics. Strong winds associated with severe convective storms are dominant natural drivers of tree mortality in the Amazon. Why forests vary with respect to their vulnerability to wind events and how the predicted increase in storm events might affect forest ecosystems within the Amazon are not well understood. We found that windthrows are common in the Amazon region extending from northwest (Peru, Colombia, Venezuela, and west Brazil) to central Brazil, with the highest occurrence of windthrows in the northwest Amazon. More frequent winds, produced by more frequent severe convective systems, in combination with well-known processes that limit the anchoring of trees in the soil, help to explain the higher vulnerability of the northwest Amazon forests to winds. Projected increases in the frequency and intensity of convective storms in the Amazon have the potential to increase wind-related tree mortality. A forest demographic model calibrated for the northwestern and the central Amazon showed that northwestern forests are more resilient to increased wind-related tree mortality than forests in the central Amazon. Our study emphasizes the importance of including wind-related tree mortality in model simulations for reliable predictions of the future of tropical forests and their effects on the Earth’ system.

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

PubMed

Franklin, Oskar; Palmroth, Sari; Näsholm, Torgny

2014-11-01

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

VHF/UHF imagery and RCS measurements of ground targets in forested terrain

NASA Astrophysics Data System (ADS)

Gatesman, Andrew J.; Beaudoin, Christopher J.; Giles, Robert H.; Waldman, Jerry; Nixon, William E.

2002-08-01

The monostatic VV and HH-polarized radar signatures of several targets and trees have been measured at foliage penetration frequencies (VHF/UHF) by using 1/35th scale models and an indoor radar range operating at X-band. An array of high-fidelity scale model ground vehicles and test objects as well as scaled ground terrain and trees have been fabricated for the study. Radar measurement accuracy has been confirmed by comparing the signature of a test object with a method of moments radar cross section prediction code. In addition to acquiring signatures of targets located on a smooth, dielectric ground plane, data have also been acquired with targets located in simulated wooded terrain that included scaled tree trunks and tree branches. In order to assure the correct backscattering behavior, all dielectric properties of live tree wood and moist soil were scaled properly to match the complex dielectric constant of the full-scale materials. The impact of the surrounding tree clutter on the VHF/UHF radar signatures of ground vehicles was accessed. Data were processed into high-resolution, polar-formatted ISAR imagery and signature comparisons are made between targets in open-field and forested scenarios.

Modeling the Emergent Impacts of Harvesting Acadian Forests over 100+ Years

NASA Astrophysics Data System (ADS)

Luus, K. A.; Plug, L. J.

2007-12-01

Harvesting strategies and policies for Acadian forest in Nova Scotia, Canada, presently are set using Decision Support Models (DSMs) that aim to maximize the long-term (>100y) value of forests through decisions implemented over short time horizons (5-80 years). However, DSMs typically are aspatial, lack ecological processes and do not treat erosion, so the long-term (>100y) emergent impacts of the prescribed forestry decisions on erosion and vegetation in Acadian forests remain poorly known. To better understand these impacts, we created an equation-based model that simulates the evolution of a ≥4 km2 forest in time steps of 1 y and at a spatial resolution of 3 m2, the footprint of a single mature tree. The model combines 1) ecological processes of recruitment, competition, and mortality; 2) geomorphic processes of hillslope erosion; 3) anthropic processes of tree harvesting, replanting, and road construction under constraints imposed by regulations and cost/benefit ratio. The model uses digital elevation models, parameters (where available), and calibration (where measurements are not available) for conditions presently found in central Cape Breton, Nova Scotia. The model is unique because it 1) deals with the impacts of harvesting on an Acadian forest; and 2) vegetation and erosion are coupled. The model was tested by comparing the species-specific biomass of long-term (40 y) forest plot data to simulated results. At the spatial scale of individual 1 ha plots, model predictions presently account for approximately 50% of observed biomass changes through time, but predictions are hampered by the effects of serendipitous "random" events such as single tree windfall. Harvesting increases the cumulative erosion over 3000 years by 240% when compared to an old growth forest and significantly suppresses the growth of Balsam Fir and Sugar Maple. We discuss further tests of the model, and how it might be used to investigate the long-term sustainability of the recommendations made by DSMs and to better understand the relationship between vegetation, erosion, and forest management strategies.

[A process of aquatic ecological function regionalization: The dual tree framework and conceptual model].

PubMed

Guo, Shu Hai; Wu, Bo

2017-12-01

Aquatic ecological regionalization and aquatic ecological function regionalization are the basis of water environmental management of a river basin and rational utilization of an aquatic ecosystem, and have been studied in China for more than ten years. Regarding the common problems in this field, the relationship between aquatic ecological regionalization and aquatic ecological function regionalization was discussed in this study by systematic analysis of the aquatic ecological zoning and the types of aquatic ecological function. Based on the dual tree structure, we put forward the RFCH process and the diamond conceptual model. Taking Liaohe River basin as an example and referring to the results of existing regionalization studies, we classified the aquatic ecological function regions based on three-class aquatic ecological regionalization. This study provided a process framework for aquatic ecological function regionalization of a river basin.

Design of Software for Design of Finite Element for Structural Analysis. Ph.D. Thesis - Stuttgart Univ., 22 Nov. 1983

NASA Technical Reports Server (NTRS)

Helfrich, Reinhard

1987-01-01

The concepts of software engineering which allow a user of the finite element method to describe a model, to collect and to check the model data in a data base as well as to form the matrices required for a finite element calculation are examined. Next the components of the model description are conceived including the mesh tree, the topology, the configuration, the kinematic boundary conditions, the data for each element, and the loads. The possibilities for description and review of the data are considered. The concept of the segments for the modularization of the programs follows the components of the model description. The significance of the mesh tree as a globular guiding structure will be understood in view of the principle of the unity of the model, the mesh tree, and the data base. The user-friendly aspects of the software system will be summarized: the principle of language communication, the data generators, error processing, and data security.

Biogeochemical modelling vs. tree-ring data - comparison of forest ecosystem productivity estimates

NASA Astrophysics Data System (ADS)

Zorana Ostrogović Sever, Maša; Barcza, Zoltán; Hidy, Dóra; Paladinić, Elvis; Kern, Anikó; Marjanović, Hrvoje

2017-04-01

Forest ecosystems are sensitive to environmental changes as well as human-induce disturbances, therefore process-based models with integrated management modules represent valuable tool for estimating and forecasting forest ecosystem productivity under changing conditions. Biogeochemical model Biome-BGC simulates carbon, nitrogen and water fluxes, and it is widely used for different terrestrial ecosystems. It was modified and parameterised by many researchers in the past to meet the specific local conditions. In this research, we used recently published improved version of the model Biome-BGCMuSo (BBGCMuSo), with multilayer soil module and integrated management module. The aim of our research is to validate modelling results of forest ecosystem productivity (NPP) from BBGCMuSo model with observed productivity estimated from an extensive dataset of tree-rings. The research was conducted in two distinct forest complexes of managed Pedunculate oak in SE Europe (Croatia), namely Pokupsko basin and Spačva basin. First, we parameterized BBGCMuSo model at a local level using eddy-covariance (EC) data from Jastrebarsko EC site. Parameterized model was used for the assessment of productivity on a larger scale. Results of NPP assessment with BBGCMuSo are compared with NPP estimated from tree ring data taken from trees on over 100 plots in both forest complexes. Keywords: Biome-BGCMuSo, forest productivity, model parameterization, NPP, Pedunculate oak

Individual tree detection from Unmanned Aerial Vehicle (UAV) derived canopy height model in an open canopy mixed conifer forest

Treesearch

Midhun Mohan; Carlos Alberto Silva; Carine Klauberg; Prahlad Jat; Glenn Catts; Adrian Cardil; Andrew Thomas Hudak; Mahendra Dia

2017-01-01

Advances in Unmanned Aerial Vehicle (UAV) technology and data processing capabilities have made it feasible to obtain high-resolution imagery and three dimensional (3D) data which can be used for forest monitoring and assessing tree attributes. This study evaluates the applicability of low consumer grade cameras attached to UAVs and structure-from-motion (SfM)...

[Health assessment of individual trees in natural Larix gmelinii forest in Great Xing' an Mountains of China].

PubMed

Zhu, Yu; Liu, Zhao-Gang; Jin, Guang-Ze

2013-05-01

To integrate the health assessment results of individual trees into the health assessment of subcompartment (or stand) scale could improve the accuracy of subcompartment (or stand) scale health assessment, and realize the coupling process between the individual tree scale and the subcompartment (or stand) scale, providing a theoretical basis for the realization of forest health management. Taking the natural Larix gmelinii forest in Great Xing' an Mountains as the object, a health assessment indicators system of individual trees was established, which included root state, canopy defoliation degree, crown transparency, crown overlap, crown dieback ratio, live crown ratio, crown skewness, and vertical competition index. The principal component analysis (PCA) was employed to eliminate the correlations, the entropy value method was adopted to confirm the weight of each indicator, and the health status of individual L. gmelinii was assessed by fuzzy synthetic evaluation (FSE) method. Based on the health assessment results, a prediction model of the individual tree health was established by discriminant analysis (DA) method. The results showed that the trees in sub-healthy gradation were up to 36.7%, and those in healthy gradation only reached 12.9%. The proportion of the trees in unhealthy gradation exceeded that of the trees in healthy gradation, occupying 21.1% of the total. The prediction accuracy of the established model was 86.3%. More rational and effective management measures should be taken to improve the tree health grade.

Evolutionarily stable strategy of carbon and nitrogen investments in forest leaves and its application in vegetation dynamic modeling

NASA Astrophysics Data System (ADS)

Weng, E.; Farrior, C.; Dybzinski, R.; Pacala, S. W.

2015-12-01

Leaf mass per area (LMA) and leaf lifespan (LL) are two highly correlated plant traits that are key to plant physiological and ecological properties. Usually, low LMA means short LL, high nitrogen (N) content per unit mass, and fast turnover rates of nutrients; high LMA leads to long LL, low N content, and slow turnover rates. Deciduous trees with low LMA and short lifespan leaves have low carbon cost but high nitrogen demand; and evergreen trees, with high LMA and long lifespan leaves, have high carbon cost but low nitrogen demand. These relationships lead to: 1) evergreen trees have higher leaf area index than deciduous trees; 2) evergreen trees' carbon use efficiency is lower than the deciduous trees' because of their thick leaves and therefore high maintenance respiration; 3) the advantage of evergreens trees brought by their extra leaves over deciduous trees diminishes with increase N in ecosystem. These facts determine who will win when trees compete with each other in a N-limited ecosystem. In this study, we formulate a mathematical model according to the relationships between LMA, LL, leaf nitrogen, and leaf building and maintenance cost, where LMA is the fundamental variable determining the other three. We analyze the evolutionarily stable strategies (ESSs) of LMA with this mathematical model by examining the benefits of carbon and nitrogen investments to leaves in ecosystems with different N. The model shows the ESS converges to low LMA at high N and high LMA at low N. At intermediate N, there are two ESSs at low and high ends of LMA, respectively. The ESS also leads to low forest productivity by outcompeting the possible high productive strategies. We design a simulation scheme in an individual-based competition model (LM3-PPA) to simulate forest dynamics as results of the competition between deciduous and evergreen trees in three different biomes, which are temperate deciduous forest, deciduous-evergreen mixed forest, and boreal evergreen forest. The simulated results are consistent with the actual forests. Our model and simulated results indicate the distribution of evergreen and deciduous forests can be explained by one single leaf trait (i.e., LMA) and associated physiological and biogeochemical processes.

Hybrid model of arm for analysis of regional blood oxygenation in non-invasive optical diagnostics

NASA Astrophysics Data System (ADS)

Nowocień, Sylwester; Mroczka, Janusz

2017-06-01

The paper presents a new comprehensive approach to modeling and analysis of processes occurring during the blood flow in the arm's small vessels as well as non-invasive measurement method of mixed venous oxygen saturation. During the work, a meta-analysis of available physiological data was performed and based on its result a hybrid model of forearm vascular tree was proposed. The model, in its structure, takes into account a classical nonlinear hydro-electric analogy in conjunction with light-tissue interaction. Several geometries of arm vascular tree obtained from magnetic resonance angiography (MRA) image were analyzed which allowed to proposed the structure of electrical analog network. Proposed model allows to simulate the behavior of forearm blood flow from the vascular tree mechanics point of view, as well as effects of the impact of cuff and vessel wall mechanics on the recorded photoplethysmographic signals. In particular, it allows to analyze the reaction and anatomical effects in small vessels and microcirculation caused by occlusive maneuver in selected techniques, what was of particular interest to authors and motivation to undertake research in this area. Preliminary studies using proposed model showed that inappropriate selection of occlusion maneuver parameters (e.g. occlusion time, cuff pressure etc.), cause dangerous turbulence of blood flow in the venous section of the vascular tree.

How trees allocate carbon for optimal growth: insight from a game-theoretic model.

PubMed

Fu, Liyong; Sun, Lidan; Han, Hao; Jiang, Libo; Zhu, Sheng; Ye, Meixia; Tang, Shouzheng; Huang, Minren; Wu, Rongling

2017-02-01

How trees allocate photosynthetic products to primary height growth and secondary radial growth reflects their capacity to best use environmental resources. Despite substantial efforts to explore tree height-diameter relationship empirically and through theoretical modeling, our understanding of the biological mechanisms that govern this phenomenon is still limited. By thinking of stem woody biomass production as an ecological system of apical and lateral growth components, we implement game theory to model and discern how these two components cooperate symbiotically with each other or compete for resources to determine the size of a tree stem. This resulting allometry game theory is further embedded within a genetic mapping and association paradigm, allowing the genetic loci mediating the carbon allocation of stemwood growth to be characterized and mapped throughout the genome. Allometry game theory was validated by analyzing a mapping data of stem height and diameter growth over perennial seasons in a poplar tree. Several key quantitative trait loci were found to interpret the process and pattern of stemwood growth through regulating the ecological interactions of stem apical and lateral growth. The application of allometry game theory enables the prediction of the situations in which the cooperation, competition or altruism is an optimal decision of a tree to fully use the environmental resources it owns. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Fast simulation of reconstructed phylogenies under global time-dependent birth-death processes.

PubMed

Höhna, Sebastian

2013-06-01

Diversification rates and patterns may be inferred from reconstructed phylogenies. Both the time-dependent and the diversity-dependent birth-death process can produce the same observed patterns of diversity over time. To develop and test new models describing the macro-evolutionary process of diversification, generic and fast algorithms to simulate under these models are necessary. Simulations are not only important for testing and developing models but play an influential role in the assessment of model fit. In the present article, I consider as the model a global time-dependent birth-death process where each species has the same rates but rates may vary over time. For this model, I derive the likelihood of the speciation times from a reconstructed phylogenetic tree and show that each speciation event is independent and identically distributed. This fact can be used to simulate efficiently reconstructed phylogenetic trees when conditioning on the number of species, the time of the process or both. I show the usability of the simulation by approximating the posterior predictive distribution of a birth-death process with decreasing diversification rates applied on a published bird phylogeny (family Cettiidae). The methods described in this manuscript are implemented in the R package TESS, available from the repository CRAN (http://cran.r-project.org/web/packages/TESS/). Supplementary data are available at Bioinformatics online.

The structure of tropical forests and sphere packings

PubMed Central

Jahn, Markus Wilhelm; Dobner, Hans-Jürgen; Wiegand, Thorsten; Huth, Andreas

2015-01-01

The search for simple principles underlying the complex architecture of ecological communities such as forests still challenges ecological theorists. We use tree diameter distributions—fundamental for deriving other forest attributes—to describe the structure of tropical forests. Here we argue that tree diameter distributions of natural tropical forests can be explained by stochastic packing of tree crowns representing a forest crown packing system: a method usually used in physics or chemistry. We demonstrate that tree diameter distributions emerge accurately from a surprisingly simple set of principles that include site-specific tree allometries, random placement of trees, competition for space, and mortality. The simple static model also successfully predicted the canopy structure, revealing that most trees in our two studied forests grow up to 30–50 m in height and that the highest packing density of about 60% is reached between the 25- and 40-m height layer. Our approach is an important step toward identifying a minimal set of processes responsible for generating the spatial structure of tropical forests. PMID:26598678

Can phenological models predict tree phenology accurately under climate change conditions?

NASA Astrophysics Data System (ADS)

Chuine, Isabelle; Bonhomme, Marc; Legave, Jean Michel; García de Cortázar-Atauri, Inaki; Charrier, Guillaume; Lacointe, André; Améglio, Thierry

2014-05-01

The onset of the growing season of trees has been globally earlier by 2.3 days/decade during the last 50 years because of global warming and this trend is predicted to continue according to climate forecast. The effect of temperature on plant phenology is however not linear because temperature has a dual effect on bud development. On one hand, low temperatures are necessary to break bud dormancy, and on the other hand higher temperatures are necessary to promote bud cells growth afterwards. Increasing phenological changes in temperate woody species have strong impacts on forest trees distribution and productivity, as well as crops cultivation areas. Accurate predictions of trees phenology are therefore a prerequisite to understand and foresee the impacts of climate change on forests and agrosystems. Different process-based models have been developed in the last two decades to predict the date of budburst or flowering of woody species. They are two main families: (1) one-phase models which consider only the ecodormancy phase and make the assumption that endodormancy is always broken before adequate climatic conditions for cell growth occur; and (2) two-phase models which consider both the endodormancy and ecodormancy phases and predict a date of dormancy break which varies from year to year. So far, one-phase models have been able to predict accurately tree bud break and flowering under historical climate. However, because they do not consider what happens prior to ecodormancy, and especially the possible negative effect of winter temperature warming on dormancy break, it seems unlikely that they can provide accurate predictions in future climate conditions. It is indeed well known that a lack of low temperature results in abnormal pattern of bud break and development in temperate fruit trees. An accurate modelling of the dormancy break date has thus become a major issue in phenology modelling. Two-phases phenological models predict that global warming should delay or compromise dormancy break at the species equatorward range limits leading to a delay or even impossibility to flower or set new leaves. These models are classically parameterized with flowering or budburst dates only, with no information on the dormancy break date because this information is very scarce. We evaluated the efficiency of a set of process-based phenological models to accurately predict the dormancy break dates of four fruit trees. Our results show that models calibrated solely with flowering or budburst dates do not accurately predict the dormancy break date. Providing dormancy break date for the model parameterization results in much more accurate simulation of this latter, with however a higher error than that on flowering or bud break dates. But most importantly, we show also that models not calibrated with dormancy break dates can generate significant differences in forecasted flowering or bud break dates when using climate scenarios. Our results claim for the urgent need of massive measurements of dormancy break dates in forest and fruit trees to yield more robust projections of phenological changes in a near future.

Generalization of Faustmann's Formula for Stochastic Forest Growth and Prices with Markov Decision Process Models

Treesearch

Joseph Buongiorno

2001-01-01

Faustmann's formula gives the land value, or the forest value of land with trees, under deterministic assumptions regarding future stand growth and prices, over an infinite horizon. Markov decision process (MDP) models generalize Faustmann's approach by recognizing that future stand states and prices are known only as probabilistic distributions. The...

Combining Genome-Wide Information with a Functional Structural Plant Model to Simulate 1-Year-Old Apple Tree Architecture.

PubMed

Migault, Vincent; Pallas, Benoît; Costes, Evelyne

2016-01-01

In crops, optimizing target traits in breeding programs can be fostered by selecting appropriate combinations of architectural traits which determine light interception and carbon acquisition. In apple tree, architectural traits were observed to be under genetic control. However, architectural traits also result from many organogenetic and morphological processes interacting with the environment. The present study aimed at combining a FSPM built for apple tree, MAppleT, with genetic determinisms of architectural traits, previously described in a bi-parental population. We focused on parameters related to organogenesis (phyllochron and immediate branching) and morphogenesis processes (internode length and leaf area) during the first year of tree growth. Two independent datasets collected in 2004 and 2007 on 116 genotypes, issued from a 'Starkrimson' × 'Granny Smith' cross, were used. The phyllochron was estimated as a function of thermal time and sylleptic branching was modeled subsequently depending on phyllochron. From a genetic map built with SNPs, marker effects were estimated on four MAppleT parameters with rrBLUP, using 2007 data. These effects were then considered in MAppleT to simulate tree development in the two climatic conditions. The genome wide prediction model gave consistent estimations of parameter values with correlation coefficients between observed values and estimated values from SNP markers ranging from 0.79 to 0.96. However, the accuracy of the prediction model following cross validation schemas was lower. Three integrative traits (the number of leaves, trunk length, and number of sylleptic laterals) were considered for validating MAppleT simulations. In 2007 climatic conditions, simulated values were close to observations, highlighting the correct simulation of genetic variability. However, in 2004 conditions which were not used for model calibration, the simulations differed from observations. This study demonstrates the possibility of integrating genome-based information in a FSPM for a perennial fruit tree. It also showed that further improvements are required for improving the prediction ability. Especially temperature effect should be extended and other factors taken into account for modeling GxE interactions. Improvements could also be expected by considering larger populations and by testing other genome wide prediction models. Despite these limitations, this study opens new possibilities for supporting plant breeding by in silico evaluations of the impact of genotypic polymorphisms on plant integrative phenotypes.

Monitoring the Urban Tree Cover for Urban Ecosystem Services - The Case of Leipzig, Germany

NASA Astrophysics Data System (ADS)

Banzhaf, E.; Kollai, H.

2015-04-01

Urban dynamics such as (extreme) growth and shrinkage bring about fundamental challenges for urban land use and related changes. In order to achieve a sustainable urban development, it is crucial to monitor urban green infrastructure at microscale level as it provides various urban ecosystem services in neighbourhoods, supporting quality of life and environmental health. We monitor urban trees by means of a multiple data set to get a detailed knowledge on its distribution and change over a decade for the entire city. We have digital orthophotos, a digital elevation model and a digital surface model. The refined knowledge on the absolute height above ground helps to differentiate tree tops. Grounded on an object-based image analysis scheme a detailed mapping of trees in an urbanized environment is processed. Results show high accuracy of tree detection and avoidance of misclassification due to shadows. The study area is the City of Leipzig, Germany. One of the leading German cities, it is home to contiguous community allotments that characterize the configuration of the city. Leipzig has one of the most well-preserved floodplain forests in Europe.

Tropical rain forest tree growth and atmospheric carbon dynamics linked to interannual temperature variation during 1984–2000

PubMed Central

Clark, D. A.; Piper, S. C.; Keeling, C. D.; Clark, D. B.

2003-01-01

During 1984–2000, canopy tree growth in old-growth tropical rain forest at La Selva, Costa Rica, varied >2-fold among years. The trees' annual diameter increments in this 16-yr period were negatively correlated with annual means of daily minimum temperatures. The tree growth variations also negatively covaried with the net carbon exchange of the terrestrial tropics as a whole, as inferred from nearly pole-to-pole measurements of atmospheric carbon dioxide (CO2) interpreted by an inverse tracer–transport model. Strong reductions in tree growth and large inferred tropical releases of CO2 to the atmosphere occurred during the record-hot 1997–1998 El Niño. These and other recent findings are consistent with decreased net primary production in tropical forests in the warmer years of the last two decades. As has been projected by recent process model studies, such a sensitivity of tropical forest productivity to on-going climate change would accelerate the rate of atmospheric CO2 accumulation. PMID:12719545

Optimisation of biomass productivity of black locust (Robinia pseudoacacia L.) on marginal lands - a case study in Lower Lusatia, NE Germany

NASA Astrophysics Data System (ADS)

Seserman, Diana-Maria; Veste, Maik; Freese, Dirk

2017-04-01

The profitability of reclaiming post-mining areas depends on the tree biomass productivity and the restoration of ecosystem functions, such as improving soil and water quality. Agroforestry systems, regarded as combined land-use systems of trees and crops, have the ability to facilitate soil development while reducing wind speed, soil erosion and evaporation. Achieving the maximum biomass productivity of the tree stands depends on the corresponding soil conditions and water availability, but is also influenced by stand structure and the competition between individual trees. For this purpose, black locust (Robinia pseudoacacia L.) trees were planted in a Nelder design in 2010, on a reclaimed post-mining site of the open-cast lignite mining in Welzow Süd (Brandenburg, Germany). Black locust is regarded as a drought-adapted tree species and commonly used for the reclamation of former lignite mining sites in Lower Lusatia, Germany. The Nelder design encompasses angles of arc of equal measure and with the same origin traversed by successive circumferences set at a predefined radial distance. Accordingly, a total of 1071 trees were planted in Welzow Süd at the intersection between 63 spokes and 17 circumferences and at densities ranging from 0.4 to 8.0 m2, with the aim of examining the influence of stand density on the tree growth in a timeframe of six years. In order to evaluate the biomass production of the trees and to determine an optimal planting density on a marginal land, various scenarios were assessed with the help of the Yield-SAFE model, a parameter-sparse process-based agroforestry model. The study revealed the consequences of choosing different tree densities on the tree biomass productivity and water use of trees in relation to the competition for light and water. References Keesman KJ, van der Werf W, van Keulen H, 2007. Production ecology of agroforestry systems: A minimal mechanistic model and analytical derivation of the land equivalent ratio. Mathematical Biosciences, vol. 209, pp. 608-623. Mantovani D, Veste M, Böhm C, Vignudelli M, Freese D, 2015. Drought impact on the spatial and temporal variation of growth performance and plant water status of black locust (Robinia pseudoacacia L.) in agroforestry systems in Lower Lusatia (Germany). iForest 8, 743-757. Mantovani D, Veste M, Freese D, 2014. Black locust (Robinia pseudoacacia L.) ecophysiological and morphological adaptations to drought and their consequence on biomass production and water use efficiency. New Zealand Journal of Forestry 44, 29. van der Werf W, Keesman K, Burgess PJ, Graves AR, Pilbeam D, Incoll LD, Metselaar K, Mayus M, Stappers R, van Keulen H, Palma JHN, Dupraz C, 2007. Yield-SAFE: a parameter-sparse process-based dynamic model for predicting resource capture, growth and production in agroforestry systems. Ecological Engineering, vol. 29, pp. 419-433.

Past and ongoing shifts in Joshua tree distribution support future modeled range contraction

USGS Publications Warehouse

Cole, Kenneth L.; Ironside, Kirsten; Eischeid, Jon K.; Garfin, Gregg; Duffy, Phil; Toney, Chris

2011-01-01

The future distribution of the Joshua tree (Yucca brevifolia) is projected by combining a geostatistical analysis of 20th-century climates over its current range, future modeled climates, and paleoecological data showing its response to a past similar climate change. As climate rapidly warmed ;11 700 years ago, the range of Joshua tree contracted, leaving only the populations near what had been its northernmost limit. Its ability to spread northward into new suitable habitats after this time may have been inhibited by the somewhat earlier extinction of megafaunal dispersers, especially the Shasta ground sloth. We applied a model of climate suitability for Joshua tree, developed from its 20th-century range and climates, to future climates modeled through a set of six individual general circulation models (GCM) and one suite of 22 models for the late 21st century. All distribution data, observed climate data, and future GCM results were scaled to spatial grids of ;1 km and ;4 km in order to facilitate application within this topographically complex region. All of the models project the future elimination of Joshua tree throughout most of the southern portions of its current range. Although estimates of future monthly precipitation differ between the models, these changes are outweighed by large increases in temperature common to all the models. Only a few populations within the current range are predicted to be sustainable. Several models project significant potential future expansion into new areas beyond the current range, but the species' Historical and current rates of dispersal would seem to prevent natural expansion into these new areas. Several areas are predicted to be potential sites for relocation/ assisted migration. This project demonstrates how information from paleoecology and modern ecology can be integrated in order to understand ongoing processes and future distributions.

Fuzzy tree automata and syntactic pattern recognition.

PubMed

Lee, E T

1982-04-01

An approach of representing patterns by trees and processing these trees by fuzzy tree automata is described. Fuzzy tree automata are defined and investigated. The results include that the class of fuzzy root-to-frontier recognizable ¿-trees is closed under intersection, union, and complementation. Thus, the class of fuzzy root-to-frontier recognizable ¿-trees forms a Boolean algebra. Fuzzy tree automata are applied to processing fuzzy tree representation of patterns based on syntactic pattern recognition. The grade of acceptance is defined and investigated. Quantitative measures of ``approximate isosceles triangle,'' ``approximate elongated isosceles triangle,'' ``approximate rectangle,'' and ``approximate cross'' are defined and used in the illustrative examples of this approach. By using these quantitative measures, a house, a house with high roof, and a church are also presented as illustrative examples. In addition, three fuzzy tree automata are constructed which have the capability of processing the fuzzy tree representations of ``fuzzy houses,'' ``houses with high roofs,'' and ``fuzzy churches,'' respectively. The results may have useful applications in pattern recognition, image processing, artificial intelligence, pattern database design and processing, image science, and pictorial information systems.

Distinguishing Between Convergent Evolution and Violation of the Molecular Clock for Three Taxa.

PubMed

Mitchell, Jonathan D; Sumner, Jeremy G; Holland, Barbara R

2018-05-18

We give a non-technical introduction to convergence-divergence models, a new modeling approach for phylogenetic data that allows for the usual divergence of lineages after lineage-splitting but also allows for taxa to converge, i.e. become more similar over time. By examining the 3-taxon case in some detail we illustrate that phylogeneticists have been "spoiled" in the sense of not having to think about the structural parameters in their models by virtue of the strong assumption that evolution is tree-like. We show that there are not always good statistical reasons to prefer the usual class of tree-like models over more general convergence-divergence models. Specifically we show many 3-taxon data sets can be equally well explained by supposing violation of the molecular clock due to change in the rate of evolution along different edges, or by keeping the assumption of a constant rate of evolution but instead assuming that evolution is not a purely divergent process. Given the abundance of evidence that evolution is not strictly tree-like, our discussion is an illustration that as phylogeneticists we need to think clearly about the structural form of the models we use. For cases with four taxa we show that there will be far greater ability to distinguish models with convergence from non-clock-like tree models.

Statistical Methods in Ai: Rare Event Learning Using Associative Rules and Higher-Order Statistics

NASA Astrophysics Data System (ADS)

Iyer, V.; Shetty, S.; Iyengar, S. S.

2015-07-01

Rare event learning has not been actively researched since lately due to the unavailability of algorithms which deal with big samples. The research addresses spatio-temporal streams from multi-resolution sensors to find actionable items from a perspective of real-time algorithms. This computing framework is independent of the number of input samples, application domain, labelled or label-less streams. A sampling overlap algorithm such as Brooks-Iyengar is used for dealing with noisy sensor streams. We extend the existing noise pre-processing algorithms using Data-Cleaning trees. Pre-processing using ensemble of trees using bagging and multi-target regression showed robustness to random noise and missing data. As spatio-temporal streams are highly statistically correlated, we prove that a temporal window based sampling from sensor data streams converges after n samples using Hoeffding bounds. Which can be used for fast prediction of new samples in real-time. The Data-cleaning tree model uses a nonparametric node splitting technique, which can be learned in an iterative way which scales linearly in memory consumption for any size input stream. The improved task based ensemble extraction is compared with non-linear computation models using various SVM kernels for speed and accuracy. We show using empirical datasets the explicit rule learning computation is linear in time and is only dependent on the number of leafs present in the tree ensemble. The use of unpruned trees (t) in our proposed ensemble always yields minimum number (m) of leafs keeping pre-processing computation to n × t log m compared to N2 for Gram Matrix. We also show that the task based feature induction yields higher Qualify of Data (QoD) in the feature space compared to kernel methods using Gram Matrix.

DG TO FT - AUTOMATIC TRANSLATION OF DIGRAPH TO FAULT TREE MODELS

NASA Technical Reports Server (NTRS)

Iverson, D. L.

1994-01-01

Fault tree and digraph models are frequently used for system failure analysis. Both types of models represent a failure space view of the system using AND and OR nodes in a directed graph structure. Each model has its advantages. While digraphs can be derived in a fairly straightforward manner from system schematics and knowledge about component failure modes and system design, fault tree structure allows for fast processing using efficient techniques developed for tree data structures. The similarities between digraphs and fault trees permits the information encoded in the digraph to be translated into a logically equivalent fault tree. The DG TO FT translation tool will automatically translate digraph models, including those with loops or cycles, into fault tree models that have the same minimum cut set solutions as the input digraph. This tool could be useful, for example, if some parts of a system have been modeled using digraphs and others using fault trees. The digraphs could be translated and incorporated into the fault trees, allowing them to be analyzed using a number of powerful fault tree processing codes, such as cut set and quantitative solution codes. A cut set for a given node is a group of failure events that will cause the failure of the node. A minimum cut set for a node is any cut set that, if any of the failures in the set were to be removed, the occurrence of the other failures in the set will not cause the failure of the event represented by the node. Cut sets calculations can be used to find dependencies, weak links, and vital system components whose failures would cause serious systems failure. The DG TO FT translation system reads in a digraph with each node listed as a separate object in the input file. The user specifies a terminal node for the digraph that will be used as the top node of the resulting fault tree. A fault tree basic event node representing the failure of that digraph node is created and becomes a child of the terminal root node. A subtree is created for each of the inputs to the digraph terminal node and the root of those subtrees are added as children of the top node of the fault tree. Every node in the digraph upstream of the terminal node will be visited and converted. During the conversion process, the algorithm keeps track of the path from the digraph terminal node to the current digraph node. If a node is visited twice, then the program has found a cycle in the digraph. This cycle is broken by finding the minimal cut sets of the twice visited digraph node and forming those cut sets into subtrees. Another implementation of the algorithm resolves loops by building a subtree based on the digraph minimal cut sets calculation. It does not reduce the subtree to minimal cut set form. This second implementation produces larger fault trees, but runs much faster than the version using minimal cut sets since it does not spend time reducing the subtrees to minimal cut sets. The fault trees produced by DG TO FT will contain OR gates, AND gates, Basic Event nodes, and NOP gates. The results of a translation can be output as a text object description of the fault tree similar to the text digraph input format. The translator can also output a LISP language formatted file and an augmented LISP file which can be used by the FTDS (ARC-13019) diagnosis system, available from COSMIC, which performs diagnostic reasoning using the fault tree as a knowledge base. DG TO FT is written in C-language to be machine independent. It has been successfully implemented on a Sun running SunOS, a DECstation running ULTRIX, a Macintosh running System 7, and a DEC VAX running VMS. The RAM requirement varies with the size of the models. DG TO FT is available in UNIX tar format on a .25 inch streaming magnetic tape cartridge (standard distribution) or on a 3.5 inch diskette. It is also available on a 3.5 inch Macintosh format diskette or on a 9-track 1600 BPI magnetic tape in DEC VAX FILES-11 format. Sample input and sample output are provided on the distribution medium. An electronic copy of the documentation in Macintosh Microsoft Word format is provided on the distribution medium. DG TO FT was developed in 1992. Sun, and SunOS are trademarks of Sun Microsystems, Inc. DECstation, ULTRIX, VAX, and VMS are trademarks of Digital Equipment Corporation. UNIX is a registered trademark of AT&T Bell Laboratories. Macintosh is a registered trademark of Apple Computer, Inc. System 7 is a trademark of Apple Computers Inc. Microsoft Word is a trademark of Microsoft Corporation.

Comparing nonparametric Bayesian tree priors for clonal reconstruction of tumors.

PubMed

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

2015-01-01

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

Comparison of water-use efficiency estimates based on tree-ring carbon isotopes with simulations of a dynamic vegetation model

NASA Astrophysics Data System (ADS)

Saurer, Matthias; Renato, Spahni; Fortunat, Joos; David, Frank; Kerstin, Treydte; Rolf, Siegwolf

2015-04-01

Tree-ring d13C-based estimates of intrinsic water-use efficiency (iWUE, reflecting the ratio of assimilation A to stomatal conductance gs) generally show a strong increase during the industrial period, likely associated with the increase in atmospheric CO2. However, it is not clear, first, if tree-ring d13C-derived iWUE-values indeed reflect actual plant and ecosystem-scale variability in fluxes and, second, what physiological changes were the drivers of the observed iWUE increase, changes in A or gs or both. To address these questions, we used a complex dynamic vegetation model (LPX) that combines process-based vegetation dynamics with land-atmosphere carbon and water exchange. The analysis was conducted for three functional types, representing conifers, oaks, larch, and various sites in Europe, where tree-ring isotope data are available. The increase in iWUE over the 20th century was comparable in LPX-simulations as in tree-ring-estimates, strengthening confidence in these results. Furthermore, the results from the LPX model suggest that the cause of the iWUE increase was reduced stomatal conductance during recent decades rather than increased assimilation. High-frequency variation reflects the influence of climate, like for example the 1976 summer drought, resulting in strongly reduced A and g in the model, particularly for oak.

SimPhy: Phylogenomic Simulation of Gene, Locus, and Species Trees

PubMed Central

Mallo, Diego; De Oliveira Martins, Leonardo; Posada, David

2016-01-01

We present a fast and flexible software package—SimPhy—for the simulation of multiple gene families evolving under incomplete lineage sorting, gene duplication and loss, horizontal gene transfer—all three potentially leading to species tree/gene tree discordance—and gene conversion. SimPhy implements a hierarchical phylogenetic model in which the evolution of species, locus, and gene trees is governed by global and local parameters (e.g., genome-wide, species-specific, locus-specific), that can be fixed or be sampled from a priori statistical distributions. SimPhy also incorporates comprehensive models of substitution rate variation among lineages (uncorrelated relaxed clocks) and the capability of simulating partitioned nucleotide, codon, and protein multilocus sequence alignments under a plethora of substitution models using the program INDELible. We validate SimPhy's output using theoretical expectations and other programs, and show that it scales extremely well with complex models and/or large trees, being an order of magnitude faster than the most similar program (DLCoal-Sim). In addition, we demonstrate how SimPhy can be useful to understand interactions among different evolutionary processes, conducting a simulation study to characterize the systematic overestimation of the duplication time when using standard reconciliation methods. SimPhy is available at https://github.com/adamallo/SimPhy, where users can find the source code, precompiled executables, a detailed manual and example cases. PMID:26526427

Tree-Level Hydrodynamic Approach for Improved Stomatal Conductance Parameterization

NASA Astrophysics Data System (ADS)

Mirfenderesgi, G.; Bohrer, G.; Matheny, A. M.; Ivanov, V. Y.

2014-12-01

The land-surface models do not mechanistically resolve hydrodynamic processes within the tree. The Finite-Elements Tree-Crown Hydrodynamics model version 2 (FETCH2) is based on the pervious FETCH model approach, but with finite difference numerics, and simplified single-beam conduit system. FETCH2 simulates water flow through the tree as a simplified system of porous media conduits. It explicitly resolves spatiotemporal hydraulic stresses throughout the tree's vertical extent that cannot be easily represented using other stomatal-conductance models. Empirical equations relate water potential at the stem to stomata conductance at leaves connected to the stem (through unresolved branches) at that height. While highly simplified, this approach bring some realism to the simulation of stomata conductance because the stomata can respond to stem water potential, rather than an assumed direct relationship with soil moisture, as is currently the case in almost all models. By enabling mechanistic simulation of hydrological traits, such as xylem conductivity, conductive area per DBH, vertical distribution of leaf area and maximal and minimal water content in the xylem, and their effect of the dynamics of water flow in the tree system, the FETCH2 modeling system enhanced our understanding of the role of hydraulic limitations on an experimental forest plot short-term water stresses that lead to tradeoffs between water and light availability for transpiring leaves in forest ecosystems. FETCH2 is particularly suitable to resolve the effects of structural differences between tree and species and size groups, and the consequences of differences in hydraulic strategies of different species. We leverage on a large dataset of sap flow from 60 trees of 4 species at our experimental plot at the University of Michigan Biological Station. Comparison of the sap flow and transpiration patterns in this site and an undisturbed control site shows significant difference in hydraulic strategies between species which affect their response to the disturbance. We used FETCH2 to conduct a sensitivity analysis of the total stand-level transpiration to the inter-specific differences in hydraulic strategies and used the results to reflect on the future trajectory of the forest, in terms of species composition and transpiration.

Below-ground biotic interactions moderated the postglacial range dynamics of trees.

PubMed

Pither, Jason; Pickles, Brian J; Simard, Suzanne W; Ordonez, Alejandro; Williams, John W

2018-05-17

Tree range shifts during geohistorical global change events provide a useful real-world model for how future changes in forest biomes may proceed. In North America, during the last deglaciation, the distributions of tree taxa varied significantly as regards the rate and direction of their responses for reasons that remain unclear. Local-scale processes such as establishment, growth, and resilience to environmental stress ultimately influence range dynamics. Despite the fact that interactions between trees and soil biota are known to influence local-scale processes profoundly, evidence linking below-ground interactions to distribution dynamics remains scarce. We evaluated climate velocity and plant traits related to dispersal, environmental tolerance and below-ground symbioses, as potential predictors of the geohistorical rates of expansion and contraction of the core distributions of tree genera between 16 and 7 ka bp. The receptivity of host genera towards ectomycorrhizal fungi was strongly supported as a positive predictor of poleward rates of distribution expansion, and seed mass was supported as a negative predictor. Climate velocity gained support as a positive predictor of rates of distribution contraction, but not expansion. Our findings indicate that understanding how tree distributions, and thus forest ecosystems, respond to climate change requires the simultaneous consideration of traits, biotic interactions and abiotic forcing. © 2018 The Authors. New Phytologist © 2018 New Phytologist Trust.

Challenges and approaches to projecting changes in forest distributions in complex mountain landscape

NASA Astrophysics Data System (ADS)

Kueppers, L. M.; Molotch, N. P.; Meromy, L.; Moyes, A. B.; Conlisk, E.; Castanha, C.

2015-12-01

The extent and density of forest trees in mountain landscapes is a first order control on watershed function, affecting patterns of snow accumulation, timing of snowmelt, and amount and quality of run-off, through alterations of surface energy and water fluxes and wind. Climate change is increasingly affecting the density and distribution of mature forests through changes to disturbance regimes, increases in physiological stress and increases in mortality due to warmer temperatures. In addition, climate change is likely altering patterns of regeneration and driving establishment of trees in high elevation meadows and alpine tundra. Though hard to detect in current forestry datasets, changes in tree establishment are critical to the future of forests. Experimental approaches, such as our climate warming experiment in the Colorado Front Range, can provide valuable data regarding seedling sensitivity to climate variability and change across important landscape positions. We've found that warming enhances negative effects of water stress across forest, treeline and alpine sites, reducing recruitment in the absence of additional summer moisture. At the lowest elevation, reductions with warming have reduced Engelmann spruce recruitment to zero. Species differ in their responses to warming in the alpine, but together confirm the importance of seed dispersal to upward forest shifts. The presence of trees or other vegetation can facilitate tree establishment by modifying microclimates, especially at and above treeline. Ultimately, these ecological and demographic processes govern the timescales of tree and forest responses to climate variability and change. For the long-lived species that dominate high elevation watersheds, these processes can take decades or centuries to play out, meaning many tree populations are and will continue to be out of equilibrium with a rapidly changing climate. Projecting changes in tree distributions and abundances across mountain landscapes requires integration of changes in hydroclimatic conditions across diverse topoclimatic settings; the sensitivity of recruitment, growth and mortality to climate; and feedbacks between trees and microclimate into modeling tools that represent time-explicit ecological and demographic processes.

Modelling Single Tree Structure with Terrestrial Laser Scanner

NASA Astrophysics Data System (ADS)

Yurtseven, H.; Akgül, M.; Gülci, S.

2017-11-01

Recent technological developments, which has reliable accuracy and quality for all engineering works, such as remote sensing tools have wide range use in forestry applications. Last decade, sustainable use and management opportunities of forest resources are favorite topics. Thus, precision of obtained data plays an important role in evaluation of current status of forests' value. The use of aerial and terrestrial laser technology has more reliable and effective models to advance the appropriate natural resource management. This study investigates the use of terrestrial laser scanner (TLS) technology in forestry, and also the methodological data processing stages for tree volume extraction is explained. Z+F Imager 5010C TLS system was used for measure single tree information such as tree height, diameter of breast height, branch volume and canopy closure. In this context more detailed and accurate data can be obtained than conventional inventory sampling in forestry by using TLS systems. However the accuracy of obtained data is up to the experiences of TLS operator in the field. Number of scan stations and its positions are other important factors to reduce noise effect and accurate 3D modelling. The results indicated that the use of point cloud data to extract tree information for forestry applications are promising methodology for precision forestry.

Interim reliability evaluation program, Browns Ferry fault trees

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

Stewart, M.E.

1981-01-01

An abbreviated fault tree method is used to evaluate and model Browns Ferry systems in the Interim Reliability Evaluation programs, simplifying the recording and displaying of events, yet maintaining the system of identifying faults. The level of investigation is not changed. The analytical thought process inherent in the conventional method is not compromised. But the abbreviated method takes less time, and the fault modes are much more visible.

Vehicle Modeling for use in the CAFE model: Process description and modeling assumptions

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

Moawad, Ayman; Kim, Namdoo; Rousseau, Aymeric

2016-06-01

The objective of this project is to develop and demonstrate a process that, at a minimum, provides more robust information that can be used to calibrate inputs applicable under the CAFE model’s existing structure. The project will be more fully successful if a process can be developed that minimizes the need for decision trees and replaces the synergy factors by inputs provided directly from a vehicle simulation tool. The report provides a description of the process that was developed by Argonne National Laboratory and implemented in Autonomie.

Integrating ecosystem services analysis into scenario planning practice: accounting for street tree benefits with i-Tree valuation in Central Texas.

PubMed

Hilde, Thomas; Paterson, Robert

2014-12-15

Scenario planning continues to gain momentum in the United States as an effective process for building consensus on long-range community plans and creating regional visions for the future. However, efforts to integrate more sophisticated information into the analytical framework to help identify important ecosystem services have lagged in practice. This is problematic because understanding the tradeoffs of land consumption patterns on ecological integrity is central to mitigating the environmental degradation caused by land use change and new development. In this paper we describe how an ecosystem services valuation model, i-Tree, was integrated into a mainstream scenario planning software tool, Envision Tomorrow, to assess the benefits of public street trees for alternative future development scenarios. The tool is then applied to development scenarios from the City of Hutto, TX, a Central Texas Sustainable Places Project demonstration community. The integrated tool represents a methodological improvement for scenario planning practice, offers a way to incorporate ecosystem services analysis into mainstream planning processes, and serves as an example of how open source software tools can expand the range of issues available for community and regional planning consideration, even in cases where community resources are limited. The tool also offers room for future improvements; feasible options include canopy analysis of various future land use typologies, as well as a generalized street tree model for broader U.S. application. Copyright © 2014 Elsevier Ltd. All rights reserved.

The Creation and Statistical Evaluation of a Deterministic Model of the Human Bronchial Tree from HRCT Images.

PubMed

Montesantos, Spyridon; Katz, Ira; Pichelin, Marine; Caillibotte, Georges

2016-01-01

A quantitative description of the morphology of lung structure is essential prior to any form of predictive modeling of ventilation or aerosol deposition implemented within the lung. The human lung is a very complex organ, with airway structures that span two orders of magnitude and having a multitude of interfaces between air, tissue and blood. As such, current medical imaging protocols cannot provide medical practitioners and researchers with in-vivo knowledge of deeper lung structures. In this work a detailed algorithm for the generation of an individualized 3D deterministic model of the conducting part of the human tracheo-bronchial tree is described. Distinct initial conditions were obtained from the high-resolution computed tomography (HRCT) images of seven healthy volunteers. The algorithm developed is fractal in nature and is implemented as a self-similar space sub-division procedure. The expansion process utilizes physiologically realistic relationships and thresholds to produce an anatomically consistent human airway tree. The model was validated through extensive statistical analysis of the results and comparison of the most common morphological features with previously published morphometric studies and other equivalent models. The resulting trees were shown to be in good agreement with published human lung geometric characteristics and can be used to study, among other things, structure-function relationships in simulation studies.

Epidemic Reconstruction in a Phylogenetics Framework: Transmission Trees as Partitions of the Node Set

PubMed Central

Hall, Matthew; Woolhouse, Mark; Rambaut, Andrew

2015-01-01

The use of genetic data to reconstruct the transmission tree of infectious disease epidemics and outbreaks has been the subject of an increasing number of studies, but previous approaches have usually either made assumptions that are not fully compatible with phylogenetic inference, or, where they have based inference on a phylogeny, have employed a procedure that requires this tree to be fixed. At the same time, the coalescent-based models of the pathogen population that are employed in the methods usually used for time-resolved phylogeny reconstruction are a considerable simplification of epidemic process, as they assume that pathogen lineages mix freely. Here, we contribute a new method that is simultaneously a phylogeny reconstruction method for isolates taken from an epidemic, and a procedure for transmission tree reconstruction. We observe that, if one or more samples is taken from each host in an epidemic or outbreak and these are used to build a phylogeny, a transmission tree is equivalent to a partition of the set of nodes of this phylogeny, such that each partition element is a set of nodes that is connected in the full tree and contains all the tips corresponding to samples taken from one and only one host. We then implement a Monte Carlo Markov Chain (MCMC) procedure for simultaneous sampling from the spaces of both trees, utilising a newly-designed set of phylogenetic tree proposals that also respect node partitions. We calculate the posterior probability of these partitioned trees based on a model that acknowledges the population structure of an epidemic by employing an individual-based disease transmission model and a coalescent process taking place within each host. We demonstrate our method, first using simulated data, and then with sequences taken from the H7N7 avian influenza outbreak that occurred in the Netherlands in 2003. We show that it is superior to established coalescent methods for reconstructing the topology and node heights of the phylogeny and performs well for transmission tree reconstruction when the phylogeny is well-resolved by the genetic data, but caution that this will often not be the case in practice and that existing genetic and epidemiological data should be used to configure such analyses whenever possible. This method is available for use by the research community as part of BEAST, one of the most widely-used packages for reconstruction of dated phylogenies. PMID:26717515

Moderate forest disturbance as a stringent test for gap and big-leaf models

NASA Astrophysics Data System (ADS)

Bond-Lamberty, B.; Fisk, J.; Holm, J. A.; Bailey, V.; Gough, C. M.

2014-07-01

Disturbance-induced tree mortality is a key factor regulating the carbon balance of a forest, but tree mortality and its subsequent effects are poorly represented processes in terrestrial ecosystem models. In particular, it is unclear whether models can robustly simulate moderate (non-catastrophic) disturbances, which tend to increase biological and structural complexity and are increasingly common in aging US forests. We tested whether three forest ecosystem models - Biome-BGC, a classic big-leaf model, and the ED and ZELIG gap-oriented models - could reproduce the resilience to moderate disturbance observed in an experimentally manipulated forest (the Forest Accelerated Succession Experiment in northern Michigan, USA, in which 38% of canopy dominants were stem girdled and compared to control plots). Each model was parameterized, spun up, and disturbed following similar protocols, and run for 5 years post-disturbance. The models replicated observed declines in aboveground biomass well. Biome-BGC captured the timing and rebound of observed leaf area index (LAI), while ED and ZELIG correctly estimated the magnitude of LAI decline. None of the models fully captured the observed post-disturbance C fluxes. Biome-BGC net primary production (NPP) was correctly resilient, but for the wrong reasons, while ED and ZELIG exhibited large, unobserved drops in NPP and net ecosystem production. The biological mechanisms proposed to explain the observed rapid resilience of the C cycle are typically not incorporated by these or other models. As a result we expect that most ecosystem models, developed to simulate processes following stand-replacing disturbances, will not simulate well the gradual and less extensive tree mortality characteristic of moderate disturbances.

The Quantification of Consistent Subjective Logic Tree Branch Weights for PSHA

NASA Astrophysics Data System (ADS)

Runge, A. K.; Scherbaum, F.

2012-04-01

The development of quantitative models for the rate of exceedance of seismically generated ground motion parameters is the target of probabilistic seismic hazard analysis (PSHA). In regions of low to moderate seismicity, the selection and evaluation of source- and/or ground-motion models is often a major challenge to hazard analysts and affected by large epistemic uncertainties. In PSHA this type of uncertainties is commonly treated within a logic tree framework in which the branch weights express the degree-of-belief values of an expert in the corresponding set of models. For the calculation of the distribution of hazard curves, these branch weights are subsequently used as subjective probabilities. However the quality of the results depends strongly on the "quality" of the expert knowledge. A major challenge for experts in this context is to provide weight estimates which are logically consistent (in the sense of Kolmogorov's axioms) and to be aware of and to deal with the multitude of heuristics and biases which affect human judgment under uncertainty. For example, people tend to give smaller weights to each branch of a logic tree the more branches it has, starting with equal weights for all branches and then adjusting this uniform distribution based on his/her beliefs about how the branches differ. This effect is known as pruning bias.¹ A similar unwanted effect, which may even wrongly suggest robustness of the corresponding hazard estimates, will appear in cases where all models are first judged according to some numerical quality measure approach and the resulting weights are subsequently normalized to sum up to one.2 To address these problems, we have developed interactive graphical tools for the determination of logic tree branch weights in form of logically consistent subjective probabilities, based on the concepts suggested in Curtis and Wood (2004).3 Instead of determining the set of weights for all the models in a single step, the computer driven elicitation process is performed as a sequence of evaluations of relative weights for small subsets of models which are presented to the analyst. From these, the distribution of logic tree weights for the whole model set is determined as solution of an optimization problem. The model subset presented to the analyst in each step is designed to maximize the expected information. The result of this process is a set of logically consistent weights together with a measure of confidence determined from the amount of conflicting information which is provided by the expert during the relative weighting process.

A Root water uptake model to compensate disease stress in citrus trees

NASA Astrophysics Data System (ADS)

Peddinti, S. R.; Kambhammettu, B. P.; Lad, R. S.; Suradhaniwar, S.

2017-12-01

Plant root water uptake (RWU) controls a number of hydrologic fluxes in simulating unsaturated flow and transport processes. Variable saturated models that simulate soil-water-plant interactions within the rizhosphere do not account for the health of the tree. This makes them difficult to analyse RWU patterns for diseased trees. Improper irrigation management activities on diseased (Phytopthora spp. affected) citrus trees of central India has resulted in a significant reduction in crop yield accompanied by disease escalation. This research aims at developing a quantitative RWU model that accounts for the reduction in water stress as a function of plant disease level (hereafter called as disease stress). A total of four research plots with varying disease severity were considered for our field experimentation. A three-dimensional electrical resistivity tomography (ERT) was performed to understand spatio-temporal distribution in soil moisture following irrigation. Evaporation and transpiration were monitored daily using micro lysimeter and sap flow meters respectively. Disease intensity was quantified (on 0 to 9 scale) using pathological analysis on soil samples. Pedo-physocal and pedo-electric relations were established under controlled laboratory conditions. A non-linear disease stress response function for citrus trees was derived considering phonological, hydrological, and pathological parameters. Results of numerical simulations conclude that the propagation of error in RWU estimates by ignoring the health condition of the tree is significant. The developed disease stress function was then validated in the presence of deficit water and nutrient stress conditions. Results of numerical analysis showed a good agreement with experimental data, corroborating the need for alternate management practices for disease citrus trees.

Long-term scenarios of the invasive black cherry in pine-oak forest: Impact of regeneration success

NASA Astrophysics Data System (ADS)

Vanhellemont, Margot; Baeten, Lander; Verbeeck, Hans; Hermy, Martin; Verheyen, Kris

2011-05-01

The spread of invasive tree species in forests can be slow because of their long life span and the lag phases that may occur during the invasion process. Models of forest succession are a useful tool to explore how these invasive species might affect long-term forest development. We used the spatially explicit individual tree model SORTIE-ND to gain insight into the long-term development of a gap-dependent invasive tree species, Prunus serotina, in a pine-oak forest on sandy soil, the forest type in which P. serotina occurs most often in its introduced range. Forest inventory data, tree ring data, and photographs of the tree crowns were collected in a forest reserve in the Netherlands, characterized by high game densities. The collected data were then combined with data from literature to parameterize the model. We ran the model for two different scenarios in order to evaluate the impact of differences in the regeneration success of the native Quercus robur and the invasive P. serotina. The outcome of the simulations shows two differing courses of forest development. The invasive P. serotina became the dominant species when the regeneration of Q. robur was hindered, e.g., because of high herbivore densities. When both Q. robur and P. serotina were able to regenerate, Q. robur became the most abundant species in the long-term. We hypothesize that the relatively short life span of P. serotina may preclude its dominance if other long-lived tree species are present and able to regenerate.

Modelling Sensory Limitation: The Role of Tree Selection, Memory and Information Transfer in Bats’ Roost Searching Strategies

PubMed Central

Ruczyński, Ireneusz; Bartoń, Kamil A.

2012-01-01

Sensory limitation plays an important role in the evolution of animal behaviour. Animals have to find objects of interest (e.g. food, shelters, predators). When sensory abilities are strongly limited, animals adjust their behaviour to maximize chances for success. Bats are nocturnal, live in complex environments, are capable of flight and must confront numerous perceptual challenges (e.g. limited sensory range, interfering clutter echoes). This makes them an excellent model for studying the role of compensating behaviours to decrease costs of finding resources. Cavity roosting bats are especially interesting because the availability of tree cavities is often limited, and their quality is vital for bats during the breeding season. From a bat’s sensory point of view, cavities are difficult to detect and finding them requires time and energy. However, tree cavities are also long lasting, allowing information transfer among conspecifics. Here, we use a simple simulation model to explore the benefits of tree selection, memory and eavesdropping (compensation behaviours) to searches for tree cavities by bats with short and long perception range. Our model suggests that memory and correct discrimination of tree suitability are the basic strategies decreasing the cost of roost finding, whereas perceptual range plays a minor role in this process. Additionally, eavesdropping constitutes a buffer that reduces the costs of finding new resources (such as roosts), especially when they occur in low density. We conclude that natural selection may promote different strategies of roost finding in relation to habitat conditions and cognitive skills of animals. PMID:23028666

A matter of phylogenetic scale: Distinguishing incomplete lineage sorting from lateral gene transfer as the cause of gene tree discord in recent versus deep diversification histories.

PubMed

Knowles, L Lacey; Huang, Huateng; Sukumaran, Jeet; Smith, Stephen A

2018-03-01

Discordant gene trees are commonly encountered when sequences from thousands of loci are applied to estimate phylogenetic relationships. Several processes contribute to this discord. Yet, we have no methods that jointly model different sources of conflict when estimating phylogenies. An alternative to analyzing entire genomes or all the sequenced loci is to identify a subset of loci for phylogenetic analysis. If we can identify data partitions that are most likely to reflect descent from a common ancestor (i.e., discordant loci that indeed reflect incomplete lineage sorting [ILS], as opposed to some other process, such as lateral gene transfer [LGT]), we can analyze this subset using powerful coalescent-based species-tree approaches. Test data sets were simulated where discord among loci could arise from ILS and LGT. Data sets where analyzed using the newly developed program CLASSIPHY (Huang et al., ) to assess whether our ability to distinguish the cause of discord among loci varied when ILS and LGT occurred in the recent versus deep past and whether the accuracy of these inferences were affected by the mutational process. We show that accuracy of probabilistic classification of individual loci by the cause of discord differed when ILS and LGT events occurred more recently compared with the distant past and that the signal-to-noise ratio arising from the mutational process contributes to difficulties in inferring LGT data partitions. We discuss our findings in terms of the promise and limitations of identifying subsets of loci for species-tree inference that will not violate the underlying coalescent model (i.e., data partitions in which ILS, and not LGT, contributes to discord). We also discuss the empirical implications of our work given the many recalcitrant nodes in the tree of life (e.g., origins of angiosperms, amniotes, or Neoaves), and recent arguments for concatenating loci. © 2018 Botanical Society of America.

Models for estimation and simulation of crown and canopy cover

Treesearch

John D. Shaw

2005-01-01

Crown width measurements collected during Forest Inventory and Analysis and Forest Health Monitoring surveys are being used to develop individual tree crown width models and plot-level canopy cover models for species and forest types in the Intermountain West. Several model applications are considered in the development process, including remote sensing of plot...

Using an Integrated Hydrologic Model to Assess the Ecohydrological Impacts of Change on a Mountain Headwaters Critical Zone

NASA Astrophysics Data System (ADS)

Collins, C.; Maxwell, R. M.; Visser, A.

2016-12-01

The critical zone is the region of the Earth's crust where hydrogeology, ecology, and climate interact. As many critical zone processes are fundamental, the significance of studying critical zone processes goes beyond understanding the local ecohydrological setting. Therefore studying critical zone governing processes requires an interdisciplinary approach that integrates simulation and observation. In this study, a high-resolution integrated hydrologic model, ParFlow-CLM, was developed for the Providence Creek watershed. Providence Creek is a highly instrumented critical zone observatory (CZO) located in the southern Sierra Nevada Mountains, a region currently experiencing a range of short-term responses (i.e. tree mortality) to a severe four-year drought. Sources of plant water use, pathways and residence times of water through the subsurface are identified using a suite of isotopic signatures and numerical particle tracking. Implications of using a fully coupled integrated hydrologic model accompanied by tracer analysis include better understanding of water partitioning and water storage in the regolith and vegetation water use during drought time conditions. The importance of subsurface storage, plant available water and lateral flow during the 2012-2015 drought to mitigate vegetation stress are addressed and verified against observed tree mortality. The stream flow response to tree mortality in the aftermath of the drought, analogous to the Colorado Mountain Pine Beetle case, provides insight into the potential effects of proposed forest management practices.

Terrestrial laser scanning for biomass assessment and tree reconstruction: improved processing efficiency

NASA Astrophysics Data System (ADS)

Alboabidallah, Ahmed; Martin, John; Lavender, Samantha; Abbott, Victor

2017-09-01

Terrestrial Laser Scanning (TLS) processing for biomass mapping involves large data volumes, and often includes relatively slow 3D object fitting steps that increase the processing time. This study aimed to test new features that can speed up the overall processing time. A new type of 3D voxel is used, where the horizontal layers are parallel to the Digital Terrain Model. This voxel type allows procedures to extract tree diameters using just one layer, but still gives direct tree-height estimations. Layer intersection is used to emphasize the trunks as upright standing objects, which are detected in the spatially segmented intersection of the breast-height voxels and then extended upwards and downwards. The diameters were calculated by fitting elliptical cylinders to the laser points in the detected trunk segments. Non-trunk segments, used in sub-tree- structures, were found using the parent-child relationships between successive layers. The branches were reconstructed by skeletonizing each sub-tree branch, and the biomass was distributed statistically amongst the weighted skeletons. The procedure was applied to nine plots within the UK. The average correlation coefficients between reconstructed and directly measured tree diameters, heights and branches were R2 = 0.92, 0.97 and 0.59 compared to 0.91, 0.95, and 0.63 when cylindrical fitting was used. The average time to apply the method reduced from 5hrs:18mins per plot, for the conventional methods, to 2hrs:24mins when the same hardware and software libraries were used with the 3D voxels. These results indicate that this 3D voxel method can produce, much more quickly, results of a similar accuracy that would improve efficiency if applied to projects with large volume TLS datasets.

Functional trait differences influence neighbourhood interactions in a hyperdiverse Amazonian forest.

PubMed

Fortunel, Claire; Valencia, Renato; Wright, S Joseph; Garwood, Nancy C; Kraft, Nathan J B

2016-09-01

As distinct community assembly processes can produce similar community patterns, assessing the ecological mechanisms promoting coexistence in hyperdiverse rainforests remains a considerable challenge. We use spatially explicit neighbourhood models of tree growth to quantify how functional trait and phylogenetic similarities predict variation in growth and crowding effects for the 315 most abundant tree species in a 25-ha lowland rainforest plot in Ecuador. We find that functional trait differences reflect variation in (1) species maximum potential growth, (2) the intensity of interspecific interactions for some species, and (3) species sensitivity to neighbours. We find that neighbours influenced tree growth in 28% of the 315 focal tree species. Neighbourhood effects are not detected in the remaining 72%, which may reflect the low statistical power to model rare taxa and/or species insensitivity to neighbours. Our results highlight the spectrum of ways in which functional trait differences can shape community dynamics in highly diverse rainforests. © 2016 John Wiley & Sons Ltd/CNRS.

A mathematical framework for modelling cambial surface evolution using a level set method

PubMed Central

Sellier, Damien; Plank, Michael J.; Harrington, Jonathan J.

2011-01-01

Background and Aims During their lifetime, tree stems take a series of successive nested shapes. Individual tree growth models traditionally focus on apical growth and architecture. However, cambial growth, which is distributed over a surface layer wrapping the whole organism, equally contributes to plant form and function. This study aims at providing a framework to simulate how organism shape evolves as a result of a secondary growth process that occurs at the cellular scale. Methods The development of the vascular cambium is modelled as an expanding surface using the level set method. The surface consists of multiple compartments following distinct expansion rules. Growth behaviour can be formulated as a mathematical function of surface state variables and independent variables to describe biological processes. Key Results The model was coupled to an architectural model and to a forest stand model to simulate cambium dynamics and wood formation at the scale of the organism. The model is able to simulate competition between cambia, surface irregularities and local features. Predicting the shapes associated with arbitrarily complex growth functions does not add complexity to the numerical method itself. Conclusions Despite their slenderness, it is sometimes useful to conceive of trees as expanding surfaces. The proposed mathematical framework provides a way to integrate through time and space the biological and physical mechanisms underlying cambium activity. It can be used either to test growth hypotheses or to generate detailed maps of wood internal structure. PMID:21470972

Numerical experiments to explain multiscale hydrological responses to mountain pine beetle tree mortality in a headwater watershed

USGS Publications Warehouse

Penn, Colin A.; Bearup, Lindsay A.; Maxwell, Reed M.; Clow, David W.

2016-01-01

The effects of mountain pine beetle (MPB)-induced tree mortality on a headwater hydrologic system were investigated using an integrated physical modeling framework with a high-resolution computational grid. Simulations of MPB-affected and unaffected conditions, each with identical atmospheric forcing for a normal water year, were compared at multiple scales to evaluate the effects of scale on MPB-affected hydrologic systems. Individual locations within the larger model were shown to maintain hillslope-scale processes affecting snowpack dynamics, total evapotranspiration, and soil moisture that are comparable to several field-based studies and previous modeling work. Hillslope-scale analyses also highlight the influence of compensating changes in evapotranspiration and snow processes. Reduced transpiration in the Grey Phase of MPB-induced tree mortality was offset by increased late-summer evaporation, while overall snowpack dynamics were more dependent on elevation effects than MPB-induced tree mortality. At the watershed scale, unaffected areas obscured the magnitude of MPB effects. Annual water yield from the watershed increased during Grey Phase simulations by 11 percent; a difference that would be difficult to diagnose with long-term gage observations that are complicated by inter-annual climate variability. The effects on hydrology observed and simulated at the hillslope scale can be further damped at the watershed scale, which spans more life zones and a broader range of landscape properties. These scaling effects may change under extreme conditions, e.g., increased total MPB-affected area or a water year with above average snowpack.

Airborne measurements of isoprene and monoterpene emissions from southeastern U.S. forests.

PubMed

Yu, Haofei; Guenther, Alex; Gu, Dasa; Warneke, Carsten; Geron, Chris; Goldstein, Allen; Graus, Martin; Karl, Thomas; Kaser, Lisa; Misztal, Pawel; Yuan, Bin

2017-10-01

Isoprene and monoterpene emission rates are essential inputs for atmospheric chemistry models that simulate atmospheric oxidant and particle distributions. Process studies of the biochemical and physiological mechanisms controlling these emissions are advancing our understanding and the accuracy of model predictions but efforts to quantify regional emissions have been limited by a lack of constraints on regional distributions of ecosystem emission capacities. We used an airborne wavelet-based eddy covariance measurement technique to characterize isoprene and monoterpene fluxes with high spatial resolution during the 2013 SAS (Southeast Atmosphere Study) in the southeastern United States. The fluxes measured by direct eddy covariance were comparable to emissions independently estimated using an indirect inverse modeling approach. Isoprene emission factors based on the aircraft wavelet flux estimates for high isoprene chemotypes (e.g., oaks) were similar to the MEGAN2.1 biogenic emission model estimates for landscapes dominated by oaks. Aircraft flux measurement estimates for landscapes with fewer isoprene emitting trees (e.g., pine plantations), were about a factor of two lower than MEGAN2.1 model estimates. The tendency for high isoprene emitters in these landscapes to occur in the shaded understory, where light dependent isoprene emissions are diminished, may explain the lower than expected emissions. This result demonstrates the importance of accurately representing the vertical profile of isoprene emitting biomass in biogenic emission models. Airborne measurement-based emission factors for high monoterpene chemotypes agreed with MEGAN2.1 in landscapes dominated by pine (high monoterpene chemotype) trees but were more than a factor of three higher than model estimates for landscapes dominated by oak (relatively low monoterpene emitting) trees. This results suggests that unaccounted processes, such as floral emissions or light dependent monoterpene emissions, or vegetation other than high monoterpene emitting trees may be an important source of monoterpene emissions in those landscapes and should be identified and included in biogenic emission models. Copyright © 2017 Elsevier B.V. All rights reserved.

Airborne measurements of isoprene and monoterpene emissions from southeastern U.S. forests

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

Yu, Haofei; Guenther, Alex; Gu, Dasa

Isoprene and monoterpene emission rates are essential inputs for atmospheric chemistry models that simulate atmospheric oxidant and particle distributions. Process studies of the biochemical and physiological mechanisms controlling these emissions are advancing our understanding and the accuracy of model predictions but efforts to quantify regional emissions have been limited by a lack of constraints on regional distributions of ecosystem emission capacities. We used an airborne wavelet-based eddy covariance measurement technique to characterize isoprene and monoterpene fluxes with high spatial resolution during the 2013 SAS (Southeast Atmosphere Study) in the southeastern United States. The fluxes measured by direct eddy covariance weremore » comparable to emissions independently estimated using an indirect inverse modeling approach. Isoprene emission factors based on the aircraft wavelet flux estimates for high isoprene chemotypes (e.g., oaks) were similar to the MEGAN2.1 biogenic emission model estimates for landscapes dominated by oaks. Aircraft flux measurement estimates for landscapes with fewer isoprene emitting trees (e.g., pine plantations), were about a factor of two lower than MEGAN2.1 model estimates. The tendency for high isoprene emitters in these landscapes to occur in the shaded understory, where light dependent isoprene emissions are diminished, may explain the lower than expected emissions. This result demonstrates the importance of accurately representing the vertical profile of isoprene emitting biomass in biogenic emission models. Airborne measurement-based emission factors for high monoterpene chemotypes agreed with MEGAN2.1 in landscapes dominated by pine (high monoterpene chemotype) trees but were more than a factor of three higher than model estimates for landscapes dominated by oak (relatively low monoterpene emitting) trees. This results suggests that unaccounted processes, such as floral emissions or light dependent monoterpene emissions, or vegetation other than high monoterpene emitting trees may be an important source of monoterpene emissions in those landscapes and should be identified and included in biogenic emission models.« less

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

Interspecific variation in growth responses to climate and competition of five eastern tree species.

PubMed

Rollinson, Christine R; Kaye, Margot W; Canham, Charles D

2016-04-01

Climate and competition are often presented from two opposing views of the dominant driver of individual tree growth and species distribution in temperate forests, such as those in the eastern United States. Previous studies have provided abundant evidence indicating that both factors influence tree growth, and we argue that these effects are not independent of one another and rather that interactions between climate, competition, and size best describe tree growth. To illustrate this point, we describe the growth responses of five common eastern tree species to interacting effects of temperature, precipitation, competition, and individual size using maximum likelihood estimation. Models that explicitly include interactions among these four factors explained over half of the variance in annual growth for four out of five species using annual climate. Expanding temperature and precipitation analyses to include seasonal interactions resulted in slightly improved models with a mean R2 of 0.61 (SD 0.10). Growth responses to individual factors as well their interactions varied greatly among species. For example, growth sensitivity to temperature for Quercus rubra increased with maximum annual precipitation, but other species showed no change in sensitivity or slightly reduced annual growth. Our results also indicate that three-way interactions among individual stem size, competition, and temperature may determine which of the five co-occurring species in our study could have the highest growth rate in a given year. Continued consideration and quantification of interactions among climate, competition, and individual-based characteristics are likely to increase understanding of key biological processes such as tree growth. Greater parameterization of interactions between traditionally segregated factors such as climate and competition may also help build a framework to reconcile drivers of individual-based processes such as growth with larger-scale patterns of species distribution.

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

The relationship between tree growth patterns and likelihood of mortality: A study of two tree species in the Sierra Nevada

USGS Publications Warehouse

Das, A.J.; Battles, J.J.; Stephenson, N.L.; van Mantgem, P.J.

2007-01-01

We examined mortality of Abies concolor (Gord. & Glend.) Lindl. (white fir) and Pinus lambertiana Dougl. (sugar pine) by developing logistic models using three growth indices obtained from tree rings: average growth, growth trend, and count of abrupt growth declines. For P. lambertiana, models with average growth, growth trend, and count of abrupt declines improved overall prediction (78.6% dead trees correctly classified, 83.7% live trees correctly classified) compared with a model with average recent growth alone (69.6% dead trees correctly classified, 67.3% live trees correctly classified). For A. concolor, counts of abrupt declines and longer time intervals improved overall classification (trees with DBH ???20 cm: 78.9% dead trees correctly classified and 76.7% live trees correctly classified vs. 64.9% dead trees correctly classified and 77.9% live trees correctly classified; trees with DBH <20 cm: 71.6% dead trees correctly classified and 71.0% live trees correctly classified vs. 67.2% dead trees correctly classified and 66.7% live trees correctly classified). In general, count of abrupt declines improved live-tree classification. External validation of A. concolor models showed that they functioned well at stands not used in model development, and the development of size-specific models demonstrated important differences in mortality risk between understory and canopy trees. Population-level mortality-risk models were developed for A. concolor and generated realistic mortality rates at two sites. Our results support the contention that a more comprehensive use of the growth record yields a more robust assessment of mortality risk. ?? 2007 NRC.

Global tree network for computing structures enabling global processing operations

DOEpatents

Blumrich; Matthias A.; Chen, Dong; Coteus, Paul W.; Gara, Alan G.; Giampapa, Mark E.; Heidelberger, Philip; Hoenicke, Dirk; Steinmacher-Burow, Burkhard D.; Takken, Todd E.; Vranas, Pavlos M.

2010-01-19

A system and method for enabling high-speed, low-latency global tree network communications among processing nodes interconnected according to a tree network structure. The global tree network enables collective reduction operations to be performed during parallel algorithm operations executing in a computer structure having a plurality of the interconnected processing nodes. Router devices are included that interconnect the nodes of the tree via links to facilitate performance of low-latency global processing operations at nodes of the virtual tree and sub-tree structures. The global operations performed include one or more of: broadcast operations downstream from a root node to leaf nodes of a virtual tree, reduction operations upstream from leaf nodes to the root node in the virtual tree, and point-to-point message passing from any node to the root node. The global tree network is configurable to provide global barrier and interrupt functionality in asynchronous or synchronized manner, and, is physically and logically partitionable.

Assessing forest vulnerability to climate warming using a process-based model of tree growth: bad prospects for rear-edges.

PubMed

Sánchez-Salguero, Raúl; Camarero, Jesus Julio; Gutiérrez, Emilia; González Rouco, Fidel; Gazol, Antonio; Sangüesa-Barreda, Gabriel; Andreu-Hayles, Laia; Linares, Juan Carlos; Seftigen, Kristina

2017-07-01

Growth models can be used to assess forest vulnerability to climate warming. If global warming amplifies water deficit in drought-prone areas, tree populations located at the driest and southernmost distribution limits (rear-edges) should be particularly threatened. Here, we address these statements by analyzing and projecting growth responses to climate of three major tree species (silver fir, Abies alba; Scots pine, Pinus sylvestris; and mountain pine, Pinus uncinata) in mountainous areas of NE Spain. This region is subjected to Mediterranean continental conditions, it encompasses wide climatic, topographic and environmental gradients, and, more importantly, it includes rear-edges of the continuous distributions of these tree species. We used tree-ring width data from a network of 110 forests in combination with the process-based Vaganov-Shashkin-Lite growth model and climate-growth analyses to forecast changes in tree growth during the 21st century. Climatic projections were based on four ensembles CO 2 emission scenarios. Warm and dry conditions during the growing season constrain silver fir and Scots pine growth, particularly at the species rear-edge. By contrast, growth of high-elevation mountain pine forests is enhanced by climate warming. The emission scenario (RCP 8.5) corresponding to the most pronounced warming (+1.4 to 4.8 °C) forecasted mean growth reductions of -10.7% and -16.4% in silver fir and Scots pine, respectively, after 2050. This indicates that rising temperatures could amplify drought stress and thus constrain the growth of silver fir and Scots pine rear-edge populations growing at xeric sites. Contrastingly, mountain pine growth is expected to increase by +12.5% due to a longer and warmer growing season. The projections of growth reduction in silver fir and Scots pine portend dieback and a contraction of their species distribution areas through potential local extinctions of the most vulnerable driest rear-edge stands. Our modeling approach provides accessible tools to evaluate forest vulnerability to warmer conditions. © 2016 John Wiley & Sons Ltd.

LANDIS PRO: a landscape model that predicts forest composition and structure changes at regional scales

Treesearch

Wen J. Wang; Hong S. He; Jacob S. Fraser; Frank R. Thompson; Stephen R. Shifley; Martin A. Spetich

2014-01-01

LANDIS PRO predicts forest composition and structure changes incorporating species-, stand-, and landscape-scales processes at regional scales. Species-scale processes include tree growth, establishment, and mortality. Stand-scale processes contain density- and size-related resource competition that regulates self-thinning and seedling establishment. Landscapescale...

Potential effects of tree-to-shrub type conversion on streamflow in California's Sierra Nevada

NASA Astrophysics Data System (ADS)

Baguskas, S. A.; Bart, R.; Molinari, N.; Tague, C.; Moritz, M.

2014-12-01

There is widespread concern that changes in climate and fire regime may lead to vegetation change across California, which in turn may influence watershed hydrology. Although plant cover is known to affect numerous hydrological processes, sensitivities to vegetation type and spatial arrangement of species within watersheds are not well understood. The primary objective of our research was to generate mechanistically-based projections of how potential type conversion from forested to shrub dominated systems may affect streamflow. During the 2014 growing season, we measured ecophysiological responses (plant water status and leaf gas exchange rates) of two dominant tree and shrub species to changes in seasonal water availability at two sites within the southern Sierra Nevada Critical Zone Observatory. Plant physiological observations were used to parameterize a process-based eco-hydrological model, RHESSys. This model was used to evaluate the impact of changes in seasonal water availability and vegetation type-conversion on streamflow. Based on our field observations, shrubs and trees had similar access to water through the early part of the growing season (April-early June); however, by late July, available water to shrubs was twice that of trees (shrubs, -0.55 ± 0.08 MPa; trees, -1.07 ± 0.08 MPa, p<0.05). Likewise, maximum transpiration (E) and carbon assimilation (A) rates per unit leaf area were twice as high for shrubs then trees in July (shrubs, A= 21 ± 2.3 μmol m-2 s-1, E=6.6 ± 1.8 mmol m-2 s-1; trees, A=8.2 ± 1.9 μmol m-2 s-1, E=2.4 ± 0.3 mmol m-2 s-1). Preliminary modeled changes in streamflow following simulated vegetation conversion were found to affect both the timing and amount of discharge. Controls on pre vs. post-conversion streamflow included changes in interception, rooting depth, energy balance, and plant response to changes in seasonal water availability. Our research demonstrates how linking strategic field data collection and mechanistic ecohydrologic models can be used as a robust tool for assessing the potential impact of vegetation change on the water balance of an ecosystem. This is an increasingly valuable approach to inform management decisions focused on adapting strategies based on projected changes in climate.

Functional outcomes of fungal community shifts driven by tree genotype and spatial-temporal factors in Mediterranean pine forests.

PubMed

Pérez-Izquierdo, Leticia; Zabal-Aguirre, Mario; Flores-Rentería, Dulce; González-Martínez, Santiago C; Buée, Marc; Rincón, Ana

2017-04-01

Fungi provide relevant ecosystem services contributing to primary productivity and the cycling of nutrients in forests. These fungal inputs can be decisive for the resilience of Mediterranean forests under global change scenarios, making necessary an in-deep knowledge about how fungal communities operate in these ecosystems. By using high-throughput sequencing and enzymatic approaches, we studied the fungal communities associated with three genotypic variants of Pinus pinaster trees, in 45-year-old common garden plantations. We aimed to determine the impact of biotic (i.e., tree genotype) and abiotic (i.e., season, site) factors on the fungal community structure, and to explore whether structural shifts triggered functional responses affecting relevant ecosystem processes. Tree genotype and spatial-temporal factors were pivotal structuring fungal communities, mainly by influencing their assemblage and selecting certain fungi. Diversity variations of total fungal community and of that of specific fungal guilds, together with edaphic properties and tree's productivity, explained relevant ecosystem services such as processes involved in carbon turnover and phosphorous mobilization. A mechanistic model integrating relations of these variables and ecosystem functional outcomes is provided. Our results highlight the importance of structural shifts in fungal communities because they may have functional consequences for key ecosystem processes in Mediterranean forests. © 2017 Society for Applied Microbiology and John Wiley and Sons Ltd.

On incomplete sampling under birth-death models and connections to the sampling-based coalescent.

PubMed

Stadler, Tanja

2009-11-07

The constant rate birth-death process is used as a stochastic model for many biological systems, for example phylogenies or disease transmission. As the biological data are usually not fully available, it is crucial to understand the effect of incomplete sampling. In this paper, we analyze the constant rate birth-death process with incomplete sampling. We derive the density of the bifurcation events for trees on n leaves which evolved under this birth-death-sampling process. This density is used for calculating prior distributions in Bayesian inference programs and for efficiently simulating trees. We show that the birth-death-sampling process can be interpreted as a birth-death process with reduced rates and complete sampling. This shows that joint inference of birth rate, death rate and sampling probability is not possible. The birth-death-sampling process is compared to the sampling-based population genetics model, the coalescent. It is shown that despite many similarities between these two models, the distribution of bifurcation times remains different even in the case of very large population sizes. We illustrate these findings on an Hepatitis C virus dataset from Egypt. We show that the transmission times estimates are significantly different-the widely used Gamma statistic even changes its sign from negative to positive when switching from the coalescent to the birth-death process.

Resolving Evolutionary Relationships in Closely Related Species with Whole-Genome Sequencing Data

PubMed Central

Nater, Alexander; Burri, Reto; Kawakami, Takeshi; Smeds, Linnéa; Ellegren, Hans

2015-01-01

Using genetic data to resolve the evolutionary relationships of species is of major interest in evolutionary and systematic biology. However, reconstructing the sequence of speciation events, the so-called species tree, in closely related and potentially hybridizing species is very challenging. Processes such as incomplete lineage sorting and interspecific gene flow result in local gene genealogies that differ in their topology from the species tree, and analyses of few loci with a single sequence per species are likely to produce conflicting or even misleading results. To study these phenomena on a full phylogenomic scale, we use whole-genome sequence data from 200 individuals of four black-and-white flycatcher species with so far unresolved phylogenetic relationships to infer gene tree topologies and visualize genome-wide patterns of gene tree incongruence. Using phylogenetic analysis in nonoverlapping 10-kb windows, we show that gene tree topologies are extremely diverse and change on a very small physical scale. Moreover, we find strong evidence for gene flow among flycatcher species, with distinct patterns of reduced introgression on the Z chromosome. To resolve species relationships on the background of widespread gene tree incongruence, we used four complementary coalescent-based methods for species tree reconstruction, including complex modeling approaches that incorporate post-divergence gene flow among species. This allowed us to infer the most likely species tree with high confidence. Based on this finding, we show that regions of reduced effective population size, which have been suggested as particularly useful for species tree inference, can produce positively misleading species tree topologies. Our findings disclose the pitfalls of using loci potentially under selection as phylogenetic markers and highlight the potential of modeling approaches to disentangle species relationships in systems with large effective population sizes and post-divergence gene flow. PMID:26187295

Probing leptophilic dark sectors with hadronic processes

NASA Astrophysics Data System (ADS)

D'Eramo, Francesco; Kavanagh, Bradley J.; Panci, Paolo

2017-08-01

We study vector portal dark matter models where the mediator couples only to leptons. In spite of the lack of tree-level couplings to colored states, radiative effects generate interactions with quark fields that could give rise to a signal in current and future experiments. We identify such experimental signatures: scattering of nuclei in dark matter direct detection; resonant production of lepton-antilepton pairs at the Large Hadron Collider; and hadronic final states in dark matter indirect searches. Furthermore, radiative effects also generate an irreducible mass mixing between the vector mediator and the Z boson, severely bounded by ElectroWeak Precision Tests. We use current experimental results to put bounds on this class of models, accounting for both radiatively induced and tree-level processes. Remarkably, the former often overwhelm the latter.

Probing leptophilic dark sectors with hadronic processes

DOE PAGES

D'Eramo, Francesco; Kavanagh, Bradley J.; Panci, Paolo

2017-05-29

We study vector portal dark matter models where the mediator couples only to leptons. In spite of the lack of tree-level couplings to colored states, radiative effects generate interactions with quark fields that could give rise to a signal in current and future experiments. We identify such experimental signatures: scattering of nuclei in dark matter direct detection; resonant production of lepton–antilepton pairs at the Large Hadron Collider; and hadronic final states in dark matter indirect searches. Furthermore, radiative effects also generate an irreducible mass mixing between the vector mediator and the Z boson, severely bounded by ElectroWeak Precision Tests. Wemore » use current experimental results to put bounds on this class of models, accounting for both radiatively induced and tree-level processes. Remarkably, the former often overwhelm the latter.« less

CellTree: an R/bioconductor package to infer the hierarchical structure of cell populations from single-cell RNA-seq data.

PubMed

duVerle, David A; Yotsukura, Sohiya; Nomura, Seitaro; Aburatani, Hiroyuki; Tsuda, Koji

2016-09-13

Single-cell RNA sequencing is fast becoming one the standard method for gene expression measurement, providing unique insights into cellular processes. A number of methods, based on general dimensionality reduction techniques, have been suggested to help infer and visualise the underlying structure of cell populations from single-cell expression levels, yet their models generally lack proper biological grounding and struggle at identifying complex differentiation paths. Here we introduce cellTree: an R/Bioconductor package that uses a novel statistical approach, based on document analysis techniques, to produce tree structures outlining the hierarchical relationship between single-cell samples, while identifying latent groups of genes that can provide biological insights. With cellTree, we provide experimentalists with an easy-to-use tool, based on statistically and biologically-sound algorithms, to efficiently explore and visualise single-cell RNA data. The cellTree package is publicly available in the online Bionconductor repository at: http://bioconductor.org/packages/cellTree/ .

Balancing the risks of hydraulic failure and carbon starvation: a twig scale analysis in declining Scots pine

PubMed Central

Torres‐Ruiz, José M.; Poyatos, Rafael; Martinez‐Vilalta, Jordi; Meir, Patrick; Cochard, Hervé; Mencuccini, Maurizio

2015-01-01

Abstract Understanding physiological processes involved in drought‐induced mortality is important for predicting the future of forests and for modelling the carbon and water cycles. Recent research has highlighted the variable risks of carbon starvation and hydraulic failure in drought‐exposed trees. However, little is known about the specific responses of leaves and supporting twigs, despite their critical role in balancing carbon acquisition and water loss. Comparing healthy (non‐defoliated) and unhealthy (defoliated) Scots pine at the same site, we measured the physiological variables involved in regulating carbon and water resources. Defoliated trees showed different responses to summer drought compared with non‐defoliated trees. Defoliated trees maintained gas exchange while non‐defoliated trees reduced photosynthesis and transpiration during the drought period. At the branch scale, very few differences were observed in non‐structural carbohydrate concentrations between health classes. However, defoliated trees tended to have lower water potentials and smaller hydraulic safety margins. While non‐defoliated trees showed a typical response to drought for an isohydric species, the physiology appears to be driven in defoliated trees by the need to maintain carbon resources in twigs. These responses put defoliated trees at higher risk of branch hydraulic failure and help explain the interaction between carbon starvation and hydraulic failure in dying trees. PMID:25997464

MEqTrees Telescope and Radio-sky Simulations and CPU Benchmarking

NASA Astrophysics Data System (ADS)

Shanmugha Sundaram, G. A.

2009-09-01

MEqTrees is a Python-based implementation of the classical Measurement Equation, wherein the various 2×2 Jones matrices are parametrized representations in the spatial and sky domains for any generic radio telescope. Customized simulations of radio-source sky models and corrupt Jones terms are demonstrated based on a policy framework, with performance estimates derived for array configurations, ``dirty''-map residuals and processing power requirements for such computations on conventional platforms.

Modelling tree dynamics to assess the implementation of EU policies related to afforestation in SW Spain rangelands

NASA Astrophysics Data System (ADS)

Herguido, Estela; Pulido, Manuel; Francisco Lavado Contador, Joaquín; Schnabel, Susanne

2017-04-01

In Iberian dehesas and montados, the lack of tree recruitment compromises its long-term sustainability. However, in marginal areas of dehesas shrub encroachment facilitates tree recruitment while altering the distinctive physiognomic and cultural characteristics of the system. These are ongoing processes that should be considered when designing afforestation measures and policies. Based on spatial variables, we modeled the proneness of a piece of land to undergo tree recruitment and the results were related with the afforestation measures carried out under the UE First Afforestation Agricultural Land Program between 1992 and 2008. We analyzed the temporal tree population dynamics in 800 randomly selected plots of 100 m radius (2,510 ha in total) in dehesas and treeless pasturelands of Extremadura (hereafter rangelands). Tree changes were revealed by comparing aerial images taken in 1956 with orthophotographs and infrared ones from 2012. Spatial models that predict the areas prone either to lack tree recruitment or with recruitment were developed and based on three data mining algorithms: MARS (Multivariate Adaptive Regression Splines), Random Forest (RF) and Stochastic Gradient Boosting (Tree-Net, TN). Recruited-tree locations (1) vs. locations of places with no recruitment (0) (randomly selected from the study areas) were used as the binary dependent variable. A 5% of the data were used as test data set. As candidate explanatory variables we used 51 different topographic, climatic, bioclimatic, land cover-related and edaphic ones. The statistical models developed were extrapolated to the spatial context of the afforested areas in the region and also to the whole Extremenian rangelands, and the percentage of area modelled as prone to tree recruitment was calculated for each case. A total of 46,674.63 ha were afforested with holm oak (Quercus ilex) or cork oak (Quercus suber) in the studied rangelands under the UE First Afforestation Agricultural Land Program. In the sampled plots, 16,747 trees were detected as recruited, while 47,058 and 12,803 were present in both dates and lost during the studied period, respectively. Based on the Area Under the ROC Curve (AUC), all the data mining models considered showed a high fitness (MARS AUC= 0.86; TN AUC= 0.92; RF AUC= 0.95) and low misclassification rates. Correctly predicted test samples for absence and presence of tree recruitment accounted respectively to 78.3% and 76.8% when using MARS, 90.8% and 90.8% using TN and 88.9% and 89.1% using RF. The spatial patterns of the different models were similar. However, attending only the percentage of area prone to tree recruitment, outstanding differences were observed among models considering the total surface of rangelands (36.03% in MARS, 22.88% in TN and 6.72 % in RF). Despite these differences, when comparing the results with those of the afforested surfaces (31.73% in MARS, 20.70% in TN and 5.63 % in RF) the three algorithms pointed to similar conclusions, i.e. the afforestations performed in rangelands of Extremadura under UE First Afforestation Agricultural Land Program, barely discriminate between areas with or without natural regeneration. In conclusion, data mining technics are suitable to develop high-performance spatial models of vegetation dynamics. These models could be useful for policy and decision makers aimed at assessing the implementation of afforestation measures and the selection of more adequate locations.

Moderate forest disturbance as a stringent test for gap and big-leaf models

NASA Astrophysics Data System (ADS)

Bond-Lamberty, B. P.; Fisk, J.; Holm, J. A.; Bailey, V. L.; Gough, C. M.

2014-12-01

Disturbance-induced tree mortality is a key factor regulating the carbon balance of a forest, but tree mortality and its subsequent effects are poorly represented processes in terrestrial ecosystem models. In particular, it is unclear whether models can robustly simulate moderate (non-catastrophic) disturbances, which tend to increase biological and structural complexity and are increasingly common in aging U.S. forests. We tested whether three forest ecosystem models—Biome-BGC, a classic big-leaf model, and the ED and ZELIG gap-oriented models—could reproduce the resilience to moderate disturbance observed in an experimentally manipulated forest (the Forest Accelerated Succession Experiment in northern Michigan, USA, in which 38% of canopy dominants were stem girdled and compared to control plots). Each model was parameterized, spun up, and disturbed following similar protocols, and run for 5 years post-disturbance. The models replicated observed declines in aboveground biomass well. Biome-BGC captured the timing and rebound of observed leaf area index (LAI), while ED and ZELIG correctly estimated the magnitude of LAI decline. None of the models fully captured the observed post-disturbance C fluxes. Biome-BGC net primary production (NPP) was correctly resilient, but for the wrong reasons, while ED and ZELIG exhibited large, unobserved drops in NPP and net ecosystem production. The biological mechanisms proposed to explain the observed rapid resilience of the C cycle are typically not incorporated by these or other models. As a result we expect that most ecosystem models, developed to simulate processes following stand-replacing disturbances, will not simulate well the gradual and less extensive tree mortality characteristic of moderate disturbances.

Forest Tree Species Distribution Mapping Using Landsat Satellite Imagery and Topographic Variables with the Maximum Entropy Method in Mongolia

NASA Astrophysics Data System (ADS)

Hao Chiang, Shou; Valdez, Miguel; Chen, Chi-Farn

2016-06-01

Forest is a very important ecosystem and natural resource for living things. Based on forest inventories, government is able to make decisions to converse, improve and manage forests in a sustainable way. Field work for forestry investigation is difficult and time consuming, because it needs intensive physical labor and the costs are high, especially surveying in remote mountainous regions. A reliable forest inventory can give us a more accurate and timely information to develop new and efficient approaches of forest management. The remote sensing technology has been recently used for forest investigation at a large scale. To produce an informative forest inventory, forest attributes, including tree species are unavoidably required to be considered. In this study the aim is to classify forest tree species in Erdenebulgan County, Huwsgul province in Mongolia, using Maximum Entropy method. The study area is covered by a dense forest which is almost 70% of total territorial extension of Erdenebulgan County and is located in a high mountain region in northern Mongolia. For this study, Landsat satellite imagery and a Digital Elevation Model (DEM) were acquired to perform tree species mapping. The forest tree species inventory map was collected from the Forest Division of the Mongolian Ministry of Nature and Environment as training data and also used as ground truth to perform the accuracy assessment of the tree species classification. Landsat images and DEM were processed for maximum entropy modeling, and this study applied the model with two experiments. The first one is to use Landsat surface reflectance for tree species classification; and the second experiment incorporates terrain variables in addition to the Landsat surface reflectance to perform the tree species classification. All experimental results were compared with the tree species inventory to assess the classification accuracy. Results show that the second one which uses Landsat surface reflectance coupled with terrain variables produced better result, with the higher overall accuracy and kappa coefficient than first experiment. The results indicate that the Maximum Entropy method is an applicable, and to classify tree species using satellite imagery data coupled with terrain information can improve the classification of tree species in the study area.

Street trees reduce the negative effects of urbanization on birds.

PubMed

Pena, João Carlos de Castro; Martello, Felipe; Ribeiro, Milton Cezar; Armitage, Richard A; Young, Robert J; Rodrigues, Marcos

2017-01-01

The effects of streets on biodiversity is an important aspect of urban ecology, but it has been neglected worldwide. Several vegetation attributes (e.g. street tree density and diversity) have important effects on biodiversity and ecological processes. In this study, we evaluated the influences of urban vegetation-represented by characteristics of street trees (canopy size, proportion of native tree species and tree species richness)-and characteristics of the landscape (distance to parks and vegetation quantity), and human impacts (human population size and exposure to noise) on taxonomic data and functional diversity indices of the bird community inhabiting streets. The study area was the southern region of Belo Horizonte (Minas Gerais, Brazil), a largely urbanized city in the understudied Neotropical region. Bird data were collected on 60 point count locations distributed across the streets of the landscape. We used a series of competing GLM models (using Akaike's information criterion for small sample sizes) to assess the relative contribution of the different sets of variables to explain the observed patterns. Seventy-three bird species were observed exploiting the streets: native species were the most abundant and frequent throughout this landscape. The bird community's functional richness and Rao's Quadratic Entropy presented values lower than 0.5. Therefore, this landscape was favoring few functional traits. Exposure to noise was the most limiting factor for this bird community. However, the average size of arboreal patches and, especially the characteristics of street trees, were able to reduce the negative effects of noise on the bird community. These results show the importance of adequately planning the urban afforestation process: increasing tree species richness, preserving large trees and planting more native trees species in the streets are management practices that will increase bird species richness, abundance and community functional aspects and consequently improve human wellbeing and quality of life.

Nanoparticle transport and delivery in a heterogeneous pulmonary vasculature.

PubMed

Sohrabi, Salman; Wang, Shunqiang; Tan, Jifu; Xu, Jiang; Yang, Jie; Liu, Yaling

2017-01-04

Quantitative understanding of nanoparticles delivery in a complex vascular networks is very challenging because it involves interplay of transport, hydrodynamic force, and multivalent interactions across different scales. Heterogeneous pulmonary network includes up to 16 generations of vessels in its arterial tree. Modeling the complete pulmonary vascular system in 3D is computationally unrealistic. To save computational cost, a model reconstructed from MRI scanned images is cut into an arbitrary pathway consisting of the upper 4-generations. The remaining generations are represented by an artificially rebuilt pathway. Physiological data such as branch information and connectivity matrix are used for geometry reconstruction. A lumped model is used to model the flow resistance of the branches that are cut off from the truncated pathway. Moreover, since the nanoparticle binding process is stochastic in nature, a binding probability function is used to simplify the carrier attachment and detachment processes. The stitched realistic and artificial geometries coupled with the lumped model at the unresolved outlets are used to resolve the flow field within the truncated arterial tree. Then, the biodistribution of 200nm, 700nm and 2µm particles at different vessel generations is studied. At the end, 0.2-0.5% nanocarrier deposition is predicted during one time passage of drug carriers through pulmonary vascular tree. Our truncated approach enabled us to efficiently model hemodynamics and accordingly particle distribution in a complex 3D vasculature providing a simple, yet efficient predictive tool to study drug delivery at organ level. Copyright © 2016 Elsevier Ltd. All rights reserved.

Statistical Development and Application of Cultural Consensus Theory

DTIC Science & Technology

2012-03-31

Bulletin & Review , 17, 275-286. Schmittmann, V.D., Dolan, C.V., Raijmakers, M.E.J., and Batchelder, W.H. (2010). Parameter identification in...Wu, H., Myung, J.I., and Batchelder, W.H. (2010). Minimum description length model selection of multinomial processing tree models. Psychonomic

Soil cover by natural trees in agroforestry systems

NASA Astrophysics Data System (ADS)

Diaz-Ambrona, C. G. H.; Almoguera Millán, C.; Tarquis Alfonso, A.

2009-04-01

The dehesa is common agroforestry system in the Iberian Peninsula. These open oak parklands with silvo-pastoral use cover about two million hectares. Traditionally annual pastures have been grazed by cows, sheep and also goats while acorns feed Iberian pig diet. Evergreen oak (Quercus ilex L.) has other uses as fuelwood collection and folder after tree pruning. The hypothesis of this work is that tree density and canopy depend on soil types. We using the spanish GIS called SIGPAC to download the images of dehesa in areas with different soil types. True colour images were restoring to a binary code, previously canopy colour range was selected. Soil cover by tree canopy was calculated and number of trees. Processing result was comparable to real data. With these data we have applied a dynamic simulation model Dehesa to determine evergreen oak acorn and annual pasture production. The model Dehesa is divided into five submodels: Climate, Soil, Evergreen oak, Pasture and Grazing. The first three require the inputs: (i) daily weather data (maximum and minimum temperatures, precipitation and solar radiation); (ii) the soil input parameters for three horizons (thickness, field capacity, permanent wilting point, and bulk density); and (iii) the tree characterization of the dehesa (tree density, canopy diameter and height, and diameter of the trunk). The influence of tree on pasture potential production is inversely proportional to the canopy cover. Acorn production increase with tree canopy cover until stabilizing itself, and will decrease if density becomes too high (more than 80% soil tree cover) at that point there is competition between the trees. Main driving force for dehesa productivity is soil type for pasture, and tree cover for acorn production. Highest pasture productivity was obtained on soil Dystric Planosol (Alfisol), Dystric Cambisol and Chromo-calcic-luvisol, these soils only cover 22.4% of southwest of the Iberian peninssula. Lowest productivity was obtained on Dystric Lithosol.

Implications of hidden gauged U (1 ) model for B anomalies

NASA Astrophysics Data System (ADS)

Fuyuto, Kaori; Li, Hao-Lin; Yu, Jiang-Hao

2018-06-01

We propose a hidden gauged U (1 )H Z' model to explain deviations from the standard model (SM) values in lepton flavor universality known as RK and RD anomalies. The Z' only interacts with the SM fermions via their mixing with vectorlike doublet fermions after the U (1 )H symmetry breaking, which leads to b →s μ μ transition through the Z' at tree level. Moreover, introducing an additional mediator, inert-Higgs doublet, yields b →c τ ν process via charged scalar contribution at tree level. Using flavio package, we scrutinize adequate sizes of the relevant Wilson coefficients to these two processes by taking various flavor observables into account. It is found that significant mixing between the vectorlike and the second generation leptons is needed for the RK anomaly. A possible explanation of the RD anomaly can also be simultaneously addressed in a motivated situation, where a single scalar operator plays a dominant role, by the successful model parameters for the RK anomaly.

Ensemble learning with trees and rules: supervised, semi-supervised, unsupervised

USDA-ARS?s Scientific Manuscript database

In this article, we propose several new approaches for post processing a large ensemble of conjunctive rules for supervised and semi-supervised learning problems. We show with various examples that for high dimensional regression problems the models constructed by the post processing the rules with ...

Concept Model on Topological Learning

NASA Astrophysics Data System (ADS)

Ae, Tadashi; Kioi, Kazumasa

2010-11-01

We discuss a new model for concept based on topological learning, where the learning process on the neural network is represented by mathematical topology. The topological learning of neural networks is summarized by a quotient of input space and the hierarchical step induces a tree where each node corresponds to a quotient. In general, the concept acquisition is a difficult problem, but the emotion for a subject is represented by providing the questions to a person. Therefore, a kind of concept is captured by such data and the answer sheet can be mapped into a topology consisting of trees. In this paper, we will discuss a way of mapping the emotional concept to a topological learning model.

Development and evaluation of height diameter at breast models for native Chinese Metasequoia.

PubMed

Liu, Mu; Feng, Zhongke; Zhang, Zhixiang; Ma, Chenghui; Wang, Mingming; Lian, Bo-Ling; Sun, Renjie; Zhang, Li

2017-01-01

Accurate tree height and diameter at breast height (dbh) are important input variables for growth and yield models. A total of 5503 Chinese Metasequoia trees were used in this study. We studied 53 fitted models, of which 7 were linear models and 46 were non-linear models. These models were divided into two groups of single models and multivariate models according to the number of independent variables. The results show that the allometry equation of tree height which has diameter at breast height as independent variable can better reflect the change of tree height; in addition the prediction accuracy of the multivariate composite models is higher than that of the single variable models. Although tree age is not the most important variable in the study of the relationship between tree height and dbh, the consideration of tree age when choosing models and parameters in model selection can make the prediction of tree height more accurate. The amount of data is also an important parameter what can improve the reliability of models. Other variables such as tree height, main dbh and altitude, etc can also affect models. In this study, the method of developing the recommended models for predicting the tree height of native Metasequoias aged 50-485 years is statistically reliable and can be used for reference in predicting the growth and production of mature native Metasequoia.

Development and evaluation of height diameter at breast models for native Chinese Metasequoia

PubMed Central

Feng, Zhongke; Zhang, Zhixiang; Ma, Chenghui; Wang, Mingming; Lian, Bo-ling; Sun, Renjie; Zhang, Li

2017-01-01

Accurate tree height and diameter at breast height (dbh) are important input variables for growth and yield models. A total of 5503 Chinese Metasequoia trees were used in this study. We studied 53 fitted models, of which 7 were linear models and 46 were non-linear models. These models were divided into two groups of single models and multivariate models according to the number of independent variables. The results show that the allometry equation of tree height which has diameter at breast height as independent variable can better reflect the change of tree height; in addition the prediction accuracy of the multivariate composite models is higher than that of the single variable models. Although tree age is not the most important variable in the study of the relationship between tree height and dbh, the consideration of tree age when choosing models and parameters in model selection can make the prediction of tree height more accurate. The amount of data is also an important parameter what can improve the reliability of models. Other variables such as tree height, main dbh and altitude, etc can also affect models. In this study, the method of developing the recommended models for predicting the tree height of native Metasequoias aged 50–485 years is statistically reliable and can be used for reference in predicting the growth and production of mature native Metasequoia. PMID:28817600

Molecular and physiological responses of trees to waterlogging stress.

PubMed

Kreuzwieser, Jürgen; Rennenberg, Heinz

2014-10-01

One major effect of global climate change will be altered precipitation patterns in many regions of the world. This will cause a higher probability of long-term waterlogging in winter/spring and flash floods in summer because of extreme rainfall events. Particularly, trees not adapted at their natural site to such waterlogging stress can be impaired. Despite the enormous economic, ecological and social importance of forest ecosystems, the effect of waterlogging on trees is far less understood than the effect on many crops or the model plant Arabidopsis. There is only a handful of studies available investigating the transcriptome and metabolome of waterlogged trees. Main physiological responses of trees to waterlogging include the stimulation of fermentative pathways and an accelerated glycolytic flux. Many energy-consuming, anabolic processes are slowed down to overcome the energy crisis mediated by waterlogging. A crucial feature of waterlogging tolerance is the steady supply of glycolysis with carbohydrates, particularly in the roots; stress-sensitive trees fail to maintain sufficient carbohydrate availability resulting in the dieback of the stressed tissues. The present review summarizes physiological and molecular features of waterlogging tolerance of trees; the focus is on carbon metabolism in both, leaves and roots of trees. © 2014 John Wiley & Sons Ltd.

Research frontiers for improving our understanding of drought‐induced tree and forest mortality

USGS Publications Warehouse

Hartmann, Henrik; Moura, Catarina; Anderegg, William R. L.; Ruehr, Nadine; Salmon, Yann; Allen, Craig D.; Arndt, Stefan K.; Breshears, David D.; Davi, Hendrik; Galbraith, David; Ruthrof, Katinka X.; Wunder, Jan; Adams, Henry D.; Bloemen, Jasper; Cailleret, Maxime; Cobb, Richard; Gessler, Arthur; Grams, Thorsten E. E.; Jansen, Steven; Kautz, Markus; Lloret, Francisco; O’Brien, Michael

2018-01-01

Accumulating evidence highlights increased mortality risks for trees during severe drought, particularly under warmer temperatures and increasing vapour pressure deficit (VPD). Resulting forest die‐off events have severe consequences for ecosystem services, biophysical and biogeochemical land–atmosphere processes. Despite advances in monitoring, modelling and experimental studies of the causes and consequences of tree death from individual tree to ecosystem and global scale, a general mechanistic understanding and realistic predictions of drought mortality under future climate conditions are still lacking. We update a global tree mortality map and present a roadmap to a more holistic understanding of forest mortality across scales. We highlight priority research frontiers that promote: (1) new avenues for research on key tree ecophysiological responses to drought; (2) scaling from the tree/plot level to the ecosystem and region; (3) improvements of mortality risk predictions based on both empirical and mechanistic insights; and (4) a global monitoring network of forest mortality. In light of recent and anticipated large forest die‐off events such a research agenda is timely and needed to achieve scientific understanding for realistic predictions of drought‐induced tree mortality. The implementation of a sustainable network will require support by stakeholders and political authorities at the international level.

Post-Modeling Histogram Matching of Maps Produced Using Regression Trees

Treesearch

Andrew J. Lister; Tonya W. Lister

2006-01-01

Spatial predictive models often use statistical techniques that in some way rely on averaging of values. Estimates from linear modeling are known to be susceptible to truncation of variance when the independent (predictor) variables are measured with error. A straightforward post-processing technique (histogram matching) for attempting to mitigate this effect is...

Time-series analysis of delta13C from tree rings. I. Time trends and autocorrelation.

PubMed

Monserud, R A; Marshall, J D

2001-09-01

Univariate time-series analyses were conducted on stable carbon isotope ratios obtained from tree-ring cellulose. We looked for the presence and structure of autocorrelation. Significant autocorrelation violates the statistical independence assumption and biases hypothesis tests. Its presence would indicate the existence of lagged physiological effects that persist for longer than the current year. We analyzed data from 28 trees (60-85 years old; mean = 73 years) of western white pine (Pinus monticola Dougl.), ponderosa pine (Pinus ponderosa Laws.), and Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco var. glauca) growing in northern Idaho. Material was obtained by the stem analysis method from rings laid down in the upper portion of the crown throughout each tree's life. The sampling protocol minimized variation caused by changing light regimes within each tree. Autoregressive moving average (ARMA) models were used to describe the autocorrelation structure over time. Three time series were analyzed for each tree: the stable carbon isotope ratio (delta(13)C); discrimination (delta); and the difference between ambient and internal CO(2) concentrations (c(a) - c(i)). The effect of converting from ring cellulose to whole-leaf tissue did not affect the analysis because it was almost completely removed by the detrending that precedes time-series analysis. A simple linear or quadratic model adequately described the time trend. The residuals from the trend had a constant mean and variance, thus ensuring stationarity, a requirement for autocorrelation analysis. The trend over time for c(a) - c(i) was particularly strong (R(2) = 0.29-0.84). Autoregressive moving average analyses of the residuals from these trends indicated that two-thirds of the individual tree series contained significant autocorrelation, whereas the remaining third were random (white noise) over time. We were unable to distinguish between individuals with and without significant autocorrelation beforehand. Significant ARMA models were all of low order, with either first- or second-order (i.e., lagged 1 or 2 years, respectively) models performing well. A simple autoregressive (AR(1)), model was the most common. The most useful generalization was that the same ARMA model holds for each of the three series (delta(13)C, delta, c(a) - c(i)) for an individual tree, if the time trend has been properly removed for each series. The mean series for the two pine species were described by first-order ARMA models (1-year lags), whereas the Douglas-fir mean series were described by second-order models (2-year lags) with negligible first-order effects. Apparently, the process of constructing a mean time series for a species preserves an underlying signal related to delta(13)C while canceling some of the random individual tree variation. Furthermore, the best model for the overall mean series (e.g., for a species) cannot be inferred from a consensus of the individual tree model forms, nor can its parameters be estimated reliably from the mean of the individual tree parameters. Because two-thirds of the individual tree time series contained significant autocorrelation, the normal assumption of a random structure over time is unwarranted, even after accounting for the time trend. The residuals of an appropriate ARMA model satisfy the independence assumption, and can be used to make hypothesis tests.

Linking an ecosystem model and a landscape model to study forest species response to climate warming

Treesearch

Hong S. He; David J. Mladenoff; Thomas R. Crow

1999-01-01

No single model can address forest change from single tree to regional scales. We discuss a framework linking an ecosystem process model {LINKAGES) with a spatial landscape model (LANDIS) to examine forest species responses to climate warming for a large, heterogeneous landscape in northern Wisconsin, USA. Individual species response at the ecosystem scale was...

Anatomical modeling of the bronchial tree

NASA Astrophysics Data System (ADS)

Hentschel, Gerrit; Klinder, Tobias; Blaffert, Thomas; Bülow, Thomas; Wiemker, Rafael; Lorenz, Cristian

2010-02-01

The bronchial tree is of direct clinical importance in the context of respective diseases, such as chronic obstructive pulmonary disease (COPD). It furthermore constitutes a reference structure for object localization in the lungs and it finally provides access to lung tissue in, e.g., bronchoscope based procedures for diagnosis and therapy. This paper presents a comprehensive anatomical model for the bronchial tree, including statistics of position, relative and absolute orientation, length, and radius of 34 bronchial segments, going beyond previously published results. The model has been built from 16 manually annotated CT scans, covering several branching variants. The model is represented as a centerline/tree structure but can also be converted in a surface representation. Possible model applications are either to anatomically label extracted bronchial trees or to improve the tree extraction itself by identifying missing segments or sub-trees, e.g., if located beyond a bronchial stenosis. Bronchial tree labeling is achieved using a naïve Bayesian classifier based on the segment properties contained in the model in combination with tree matching. The tree matching step makes use of branching variations covered by the model. An evaluation of the model has been performed in a leaveone- out manner. In total, 87% of the branches resulting from preceding airway tree segmentation could be correctly labeled. The individualized model enables the detection of missing branches, allowing a targeted search, e.g., a local rerun of the tree-segmentation segmentation.

What We Talk About When We Talk About Drought: Tree-ring Perspectives on Model-Data Comparisons in Hydroclimate Research

NASA Astrophysics Data System (ADS)

Cook, B.; Anchukaitis, K. J.

2017-12-01

Comparative analyses of paleoclimate reconstructions and climate model simulations can provide valuable insights into past and future climate events. Conducting meaningful and quantitative comparisons, however, can be difficult for a variety of reasons. Here, we use tree-ring based hydroclimate reconstructions to discuss some best practices for paleoclimate-model comparisons, highlighting recent studies that have successfully used this approach. These analyses have improved our understanding of the Medieval-era megadroughts, ocean forcing of large scale drought patterns, and even climate change contributions to future drought risk. Additional work is needed, however, to better reconcile and formalize uncertainties across observed, modeled, and reconstructed variables. In this regard, process based forward models of proxy-systems will likely be a critical tool moving forward.

Writing filter processes for the SAGA editor, appendix G

NASA Technical Reports Server (NTRS)

Kirslis, Peter A.

1985-01-01

The SAGA editor provides a mechanism by which separate processes can be invoked during an editing session to traverse portions of the parse tree being edited. These processes, termed filter processes, read, analyze, and possibly transform the parse tree, returning the result to the editor. By defining new commands with the editor's user defined command facility, which invoke filter processes, authors of filter can provide complex operations as simple commands. A tree plotter, pretty printer, and Pascal tree transformation program were already written using this facility. The filter processes are introduced, parse tree structure is described and the library interface made available to the programmer. Also discussed is how to compile and run filter processes. Examples are presented to illustrate aspect of each of these areas.

Understory plant communities and the functional distinction between savanna trees, forest trees, and pines

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

Veldman, Joseph W.; Mattingly, W. Brett; Brudvig, Lars A.

Although savanna trees and forest trees are thought to represent distinct functional groups with different effects on ecosystem processes, few empirical studies have examined these effects. In particular, it remains unclear if savanna and forest trees differ in their ability to coexist with understory plants, which comprise the majority of plant diversity in most savannas. We used structural equation modeling (SEM) and data from 157 sites across three locations in the southeastern United States to understand the effects of broadleaf savanna trees, broadleaf forest trees, and pine trees on savanna understory plant communities. After accounting for underlying gradients in firemore » frequency and soil moisture, abundances (i.e., basal area and stem density) of forest trees and pines, but not savanna trees, were negatively correlated with the cover and density (i.e., local-scale species richness) of C4 graminoid species, a defining savanna understory functional group that is linked to ecosystem flammability. In analyses of the full understory community, abundances of trees from all functional groups were negatively correlated with species density and cover. For both the C4 and full communities, fire frequency promoted understory plants directly, and indirectly by limiting forest tree abundance. There was little indirect influence of fire on the understory mediated through savanna trees and pines, which are more fire tolerant than forest trees. We conclude that tree functional identity is an important factor that influences overstory tree relationships with savanna understory plant communities. In particular, distinct relationships between trees and C4 graminoids have implications for grass-tree coexistence and vegetation-fire feedbacks that maintain savanna environments and their associated understory plant diversity.« less

Beyond Tree Throw: Wind, Water, Rock and the Mechanics of Tree-Driven Bedrock Physical Weathering

NASA Astrophysics Data System (ADS)

Marshall, J. A.; Anderson, R. S.; Dawson, T. E.; Dietrich, W. E.; Minear, J. T.

2017-12-01

Tree throw is often invoked as the dominant process in converting bedrock to soil and thus helping to build the Critical Zone (CZ). In addition, observations of tree roots lifting sidewalk slabs, occupying cracks, and prying slabs of rock from cliff faces have led to a general belief in the power of plant growth forces. These common observations have led to conceptual models with trees at the center of the soil genesis process. This is despite the observation that tree throw is rare in many forested settings, and a dearth of field measurements that quantify the magnitude of growth forces. While few trees blow down, every tree grows roots, inserting many tens of percent of its mass below ground. Yet we lack data quantifying the role of trees in both damaging bedrock and detaching it (and thus producing soil). By combing force measurements at the tree-bedrock interface with precipitation, solar radiation, wind speed, and wind-driven tree sway data we quantified the magnitude and frequency of tree-driven soil-production mechanisms from two contrasting climatic and lithologic regimes (Boulder and Eel Creek CZ Observatories). Preliminary data suggests that in settings with relatively thin soils, trees can damage and detach rock due to diurnal fluctuations, wind response and rainfall events. Surprisingly, our data suggests that forces from roots and trunks growing against bedrock are insufficient to pry rock apart or damage bedrock although much more work is needed in this area. The frequency, magnitude and style of wind-driven tree forces at the bedrock interface varies considerably from one to another species. This suggests that tree properties such as mass, elasticity, stiffness and branch structure determine whether trees respond to gusts big or small, move at the same frequency as large wind gusts, or are able to self-dampen near-ground sway response to extended wind forces. Our measurements of precipitation-driven and daily fluctuations in root pressures exerted on bedrock suggest that these fluctuations may impart a cyclic stress fatigue that over the lifetime of a tree could considerably weaken the enfolding rock (104 to 106 days depending on the species). Combined, our results suggest that wind-driven root torque and water uptake may be the primary mechanisms driving bedrock erosion and soil production in thin soil settings.

Regionalization of meso-scale physically based nitrogen modeling outputs to the macro-scale by the use of regression trees

NASA Astrophysics Data System (ADS)

Künne, A.; Fink, M.; Kipka, H.; Krause, P.; Flügel, W.-A.

2012-06-01

In this paper, a method is presented to estimate excess nitrogen on large scales considering single field processes. The approach was implemented by using the physically based model J2000-S to simulate the nitrogen balance as well as the hydrological dynamics within meso-scale test catchments. The model input data, the parameterization, the results and a detailed system understanding were used to generate the regression tree models with GUIDE (Loh, 2002). For each landscape type in the federal state of Thuringia a regression tree was calibrated and validated using the model data and results of excess nitrogen from the test catchments. Hydrological parameters such as precipitation and evapotranspiration were also used to predict excess nitrogen by the regression tree model. Hence they had to be calculated and regionalized as well for the state of Thuringia. Here the model J2000g was used to simulate the water balance on the macro scale. With the regression trees the excess nitrogen was regionalized for each landscape type of Thuringia. The approach allows calculating the potential nitrogen input into the streams of the drainage area. The results show that the applied methodology was able to transfer the detailed model results of the meso-scale catchments to the entire state of Thuringia by low computing time without losing the detailed knowledge from the nitrogen transport modeling. This was validated with modeling results from Fink (2004) in a catchment lying in the regionalization area. The regionalized and modeled excess nitrogen correspond with 94%. The study was conducted within the framework of a project in collaboration with the Thuringian Environmental Ministry, whose overall aim was to assess the effect of agro-environmental measures regarding load reduction in the water bodies of Thuringia to fulfill the requirements of the European Water Framework Directive (Bäse et al., 2007; Fink, 2006; Fink et al., 2007).

Competition between trees and grasses for both soil water and mineral nitrogen in dry savannas.

PubMed

Donzelli, D; De Michele, C; Scholes, R J

2013-09-07

The co-existence of trees and grasses in savannas in general can be the result of processes involving competition for resources (e.g. water and nutrients) or differential response to disturbances such as fire, animals and human activities; or a combination of both broad mechanisms. In moist savannas, the tree-grass coexistence is mainly attributed to of disturbances, while in dry savannas, limiting resources are considered the principal mechanism of co-existence. Virtually all theoretical explorations of tree-grass dynamics in dry savannas consider only competition for soil water. Here we investigate whether coexistence could result from a balanced competition for two resources, namely soil water and mineral nitrogen. We introduce a simple dynamical resource-competition model for trees and grasses. We consider two alternative hypotheses: (1) trees are the superior competitors for nitrogen while grasses are superior competitors for water, and (2) vice-versa. We study the model properties under the two hypotheses and test each hypothesis against data from 132 dry savannas in Africa using Kendall's test of independence. We find that Hypothesis 1 gets much more support than Hypothesis 2, and more support than the null hypothesis that neither is operative. We further consider gradients of rainfall and nitrogen availability and find that the Hypothesis 1 model reproduces the observed patterns in nature. We do not consider our results to definitively show that tree-grass coexistence in dry savannas is due to balanced competition for water and nitrogen, but show that this mechanism is a possibility, which cannot be a priori excluded and should thus be considered along with the more traditional explanations. Copyright © 2013 Elsevier Ltd. All rights reserved.

Cognitive Support During High-Consequence Episodes of Care in Cardiovascular Surgery.

PubMed

Conboy, Heather M; Avrunin, George S; Clarke, Lori A; Osterweil, Leon J; Christov, Stefan C; Goldman, Julian M; Yule, Steven J; Zenati, Marco A

2017-03-01

Despite significant efforts to reduce preventable adverse events in medical processes, such events continue to occur at unacceptable rates. This paper describes a computer science approach that uses formal process modeling to provide situationally aware monitoring and management support to medical professionals performing complex processes. These process models represent both normative and non-normative situations, and are validated by rigorous automated techniques such as model checking and fault tree analysis, in addition to careful review by experts. Context-aware Smart Checklists are then generated from the models, providing cognitive support during high-consequence surgical episodes. The approach is illustrated with a case study in cardiovascular surgery.

Insights into plant water uptake from xylem-water isotope measurements in two tropical catchments with contrasting moisture conditions

USGS Publications Warehouse

Evaristo, Jaivime; McDonnell, Jeffrey J.; Scholl, Martha A.; Bruijnzeel, L. Adrian; Chun, Kwok P.

2016-01-01

Water transpired by trees has long been assumed to be sourced from the same subsurface water stocks that contribute to groundwater recharge and streamflow. However, recent investigations using dual water stable isotopes have shown an apparent ecohydrological separation between tree-transpired water and stream water. Here we present evidence for such ecohydrological separation in two tropical environments in Puerto Rico where precipitation seasonality is relatively low and where precipitation is positively correlated with primary productivity. We determined the stable isotope signature of xylem water of 30 mahogany (Swietenia spp.) trees sampled during two periods with contrasting moisture status. Our results suggest that the separation between transpiration water and groundwater recharge/streamflow water might be related less to the temporal phasing of hydrologic inputs and primary productivity, and more to the fundamental processes that drive evaporative isotopic enrichment of residual soil water within the soil matrix. The lack of an evaporative signature of both groundwater and streams in the study area suggests that these water balance components have a water source that is transported quickly to deeper subsurface storage compared to waters that trees use. A Bayesian mixing model used to partition source water proportions of xylem water showed that groundwater contribution was greater for valley-bottom, riparian trees than for ridge-top trees. Groundwater contribution was also greater at the xeric site than at the mesic–hydric site. These model results (1) underline the utility of a simple linear mixing model, implemented in a Bayesian inference framework, in quantifying source water contributions at sites with contrasting physiographic characteristics, and (2) highlight the informed judgement that should be made in interpreting mixing model results, of import particularly in surveying groundwater use patterns by vegetation from regional to global scales. 

Implementation of a Marauding Insect Module (MIM, version 1.0) in the Integrated BIosphere Simulator (IBIS, version 2.6b4) dynamic vegetation-land surface model

NASA Astrophysics Data System (ADS)

Landry, Jean-Sébastien; Price, David T.; Ramankutty, Navin; Parrott, Lael; Damon Matthews, H.

2016-04-01

Insects defoliate and kill plants in many ecosystems worldwide. The consequences of these natural processes on terrestrial ecology and nutrient cycling are well established, and their potential climatic effects resulting from modified land-atmosphere exchanges of carbon, energy, and water are increasingly being recognized. We developed a Marauding Insect Module (MIM) to quantify, in the Integrated BIosphere Simulator (IBIS), the consequences of insect activity on biogeochemical and biogeophysical fluxes, also accounting for the effects of altered vegetation dynamics. MIM can simulate damage from three different insect functional types: (1) defoliators on broadleaf deciduous trees, (2) defoliators on needleleaf evergreen trees, and (3) bark beetles on needleleaf evergreen trees, with the resulting impacts being estimated by IBIS based on the new, insect-modified state of the vegetation. MIM further accounts for the physical presence and gradual fall of insect-killed dead standing trees. The design of MIM should facilitate the addition of other insect types besides the ones already included and could guide the development of similar modules for other process-based vegetation models. After describing IBIS-MIM, we illustrate the usefulness of the model by presenting results spanning daily to centennial timescales for vegetation dynamics and cycling of carbon, energy, and water in a simplified setting and for bark beetles only. More precisely, we simulated 100 % mortality events from the mountain pine beetle for three locations in western Canada. We then show that these simulated impacts agree with many previous studies based on field measurements, satellite data, or modelling. MIM and similar tools should therefore be of great value in assessing the wide array of impacts resulting from insect-induced plant damage in the Earth system.

Modelling Mediterranean agro-ecosystems by including agricultural trees in the LPJmL model

NASA Astrophysics Data System (ADS)

Fader, M.; von Bloh, W.; Shi, S.; Bondeau, A.; Cramer, W.

2015-11-01

In the Mediterranean region, climate and land use change are expected to impact on natural and agricultural ecosystems by warming, reduced rainfall, direct degradation of ecosystems and biodiversity loss. Human population growth and socioeconomic changes, notably on the eastern and southern shores, will require increases in food production and put additional pressure on agro-ecosystems and water resources. Coping with these challenges requires informed decisions that, in turn, require assessments by means of a comprehensive agro-ecosystem and hydrological model. This study presents the inclusion of 10 Mediterranean agricultural plants, mainly perennial crops, in an agro-ecosystem model (Lund-Potsdam-Jena managed Land - LPJmL): nut trees, date palms, citrus trees, orchards, olive trees, grapes, cotton, potatoes, vegetables and fodder grasses. The model was successfully tested in three model outputs: agricultural yields, irrigation requirements and soil carbon density. With the development presented in this study, LPJmL is now able to simulate in good detail and mechanistically the functioning of Mediterranean agriculture with a comprehensive representation of ecophysiological processes for all vegetation types (natural and agricultural) and in a consistent framework that produces estimates of carbon, agricultural and hydrological variables for the entire Mediterranean basin. This development paves the way for further model extensions aiming at the representation of alternative agro-ecosystems (e.g. agroforestry), and opens the door for a large number of applications in the Mediterranean region, for example assessments of the consequences of land use transitions, the influence of management practices and climate change impacts.

Modelling Mediterranean agro-ecosystems by including agricultural trees in the LPJmL model

NASA Astrophysics Data System (ADS)

Fader, M.; von Bloh, W.; Shi, S.; Bondeau, A.; Cramer, W.

2015-06-01

Climate and land use change in the Mediterranean region is expected to affect natural and agricultural ecosystems by decreases in precipitation, increases in temperature as well as biodiversity loss and anthropogenic degradation of natural resources. Demographic growth in the Eastern and Southern shores will require increases in food production and put additional pressure on agro-ecosystems and water resources. Coping with these challenges requires informed decisions that, in turn, require assessments by means of a comprehensive agro-ecosystem and hydrological model. This study presents the inclusion of 10 Mediterranean agricultural plants, mainly perennial crops, in an agro-ecosystem model (LPJmL): nut trees, date palms, citrus trees, orchards, olive trees, grapes, cotton, potatoes, vegetables and fodder grasses. The model was successfully tested in three model outputs: agricultural yields, irrigation requirements and soil carbon density. With the development presented in this study, LPJmL is now able to simulate in good detail and mechanistically the functioning of Mediterranean agriculture with a comprehensive representation of ecophysiological processes for all vegetation types (natural and agricultural) and in a consistent framework that produces estimates of carbon, agricultural and hydrological variables for the entire Mediterranean basin. This development pave the way for further model extensions aiming at the representation of alternative agro-ecosystems (e.g. agroforestry), and opens the door for a large number of applications in the Mediterranean region, for example assessments on the consequences of land use transitions, the influence of management practices and climate change impacts.

Effects of Heterogeniety on Spatial Pattern Analysis of Wild Pistachio Trees in Zagros Woodlands, Iran

NASA Astrophysics Data System (ADS)

Erfanifard, Y.; Rezayan, F.

2014-10-01

Vegetation heterogeneity biases second-order summary statistics, e.g., Ripley's K-function, applied for spatial pattern analysis in ecology. Second-order investigation based on Ripley's K-function and related statistics (i.e., L- and pair correlation function g) is widely used in ecology to develop hypothesis on underlying processes by characterizing spatial patterns of vegetation. The aim of this study was to demonstrate effects of underlying heterogeneity of wild pistachio (Pistacia atlantica Desf.) trees on the second-order summary statistics of point pattern analysis in a part of Zagros woodlands, Iran. The spatial distribution of 431 wild pistachio trees was accurately mapped in a 40 ha stand in the Wild Pistachio & Almond Research Site, Fars province, Iran. Three commonly used second-order summary statistics (i.e., K-, L-, and g-functions) were applied to analyse their spatial pattern. The two-sample Kolmogorov-Smirnov goodness-of-fit test showed that the observed pattern significantly followed an inhomogeneous Poisson process null model in the study region. The results also showed that heterogeneous pattern of wild pistachio trees biased the homogeneous form of K-, L-, and g-functions, demonstrating a stronger aggregation of the trees at the scales of 0-50 m than actually existed and an aggregation at scales of 150-200 m, while regularly distributed. Consequently, we showed that heterogeneity of point patterns may bias the results of homogeneous second-order summary statistics and we also suggested applying inhomogeneous summary statistics with related null models for spatial pattern analysis of heterogeneous vegetations.

Coalescent Simulations Reveal Hybridization and Incomplete Lineage Sorting in Mediterranean Linaria

PubMed Central

Blanco-Pastor, José Luis; Vargas, Pablo; Pfeil, Bernard E.

2012-01-01

We examined the phylogenetic history of Linaria with special emphasis on the Mediterranean sect. Supinae (44 species). We revealed extensive highly supported incongruence among two nuclear (ITS, AGT1) and two plastid regions (rpl32-trnLUAG, trnS-trnG). Coalescent simulations, a hybrid detection test and species tree inference in *BEAST revealed that incomplete lineage sorting and hybridization may both be responsible for the incongruent pattern observed. Additionally, we present a multilabelled *BEAST species tree as an alternative approach that allows the possibility of observing multiple placements in the species tree for the same taxa. That permitted the incorporation of processes such as hybridization within the tree while not violating the assumptions of the *BEAST model. This methodology is presented as a functional tool to disclose the evolutionary history of species complexes that have experienced both hybridization and incomplete lineage sorting. The drastic climatic events that have occurred in the Mediterranean since the late Miocene, including the Quaternary-type climatic oscillations, may have made both processes highly recurrent in the Mediterranean flora. PMID:22768061

Large-Scale Mixed Temperate Forest Mapping at the Single Tree Level using Airborne Laser Scanning

NASA Astrophysics Data System (ADS)

Scholl, V.; Morsdorf, F.; Ginzler, C.; Schaepman, M. E.

2017-12-01

Monitoring vegetation on a single tree level is critical to understand and model a variety of processes, functions, and changes in forest systems. Remote sensing technologies are increasingly utilized to complement and upscale the field-based measurements of forest inventories. Airborne laser scanning (ALS) systems provide valuable information in the vertical dimension for effective vegetation structure mapping. Although many algorithms exist to extract single tree segments from forest scans, they are often tuned to perform well in homogeneous coniferous or deciduous areas and are not successful in mixed forests. Other methods are too computationally expensive to apply operationally. The aim of this study was to develop a single tree detection workflow using leaf-off ALS data for the canton of Aargau in Switzerland. Aargau covers an area of over 1,400km2 and features mixed forests with various development stages and topography. Forest type was classified using random forests to guide local parameter selection. Canopy height model-based treetop maxima were detected and maintained based on the relationship between tree height and window size, used as a proxy to crown diameter. Watershed segmentation was used to generate crown polygons surrounding each maximum. The location, height, and crown dimensions of single trees were derived from the ALS returns within each polygon. Validation was performed through comparison with field measurements and extrapolated estimates from long-term monitoring plots of the Swiss National Forest Inventory within the framework of the Swiss Federal Institute for Forest, Snow, and Landscape Research. This method shows promise for robust, large-scale single tree detection in mixed forests. The single tree data will aid ecological studies as well as forest management practices. Figure description: Height-normalized ALS point cloud data (top) and resulting single tree segments (bottom) on the Laegeren mountain in Switzerland.

Likelihood inference of non-constant diversification rates with incomplete taxon sampling.

PubMed

Höhna, Sebastian

2014-01-01

Large-scale phylogenies provide a valuable source to study background diversification rates and investigate if the rates have changed over time. Unfortunately most large-scale, dated phylogenies are sparsely sampled (fewer than 5% of the described species) and taxon sampling is not uniform. Instead, taxa are frequently sampled to obtain at least one representative per subgroup (e.g. family) and thus to maximize diversity (diversified sampling). So far, such complications have been ignored, potentially biasing the conclusions that have been reached. In this study I derive the likelihood of a birth-death process with non-constant (time-dependent) diversification rates and diversified taxon sampling. Using simulations I test if the true parameters and the sampling method can be recovered when the trees are small or medium sized (fewer than 200 taxa). The results show that the diversification rates can be inferred and the estimates are unbiased for large trees but are biased for small trees (fewer than 50 taxa). Furthermore, model selection by means of Akaike's Information Criterion favors the true model if the true rates differ sufficiently from alternative models (e.g. the birth-death model is recovered if the extinction rate is large and compared to a pure-birth model). Finally, I applied six different diversification rate models--ranging from a constant-rate pure birth process to a decreasing speciation rate birth-death process but excluding any rate shift models--on three large-scale empirical phylogenies (ants, mammals and snakes with respectively 149, 164 and 41 sampled species). All three phylogenies were constructed by diversified taxon sampling, as stated by the authors. However only the snake phylogeny supported diversified taxon sampling. Moreover, a parametric bootstrap test revealed that none of the tested models provided a good fit to the observed data. The model assumptions, such as homogeneous rates across species or no rate shifts, appear to be violated.

Genome-wide heterogeneity of nucleotide substitution model fit.

PubMed

Arbiza, Leonardo; Patricio, Mateus; Dopazo, Hernán; Posada, David

2011-01-01

At a genomic scale, the patterns that have shaped molecular evolution are believed to be largely heterogeneous. Consequently, comparative analyses should use appropriate probabilistic substitution models that capture the main features under which different genomic regions have evolved. While efforts have concentrated in the development and understanding of model selection techniques, no descriptions of overall relative substitution model fit at the genome level have been reported. Here, we provide a characterization of best-fit substitution models across three genomic data sets including coding regions from mammals, vertebrates, and Drosophila (24,000 alignments). According to the Akaike Information Criterion (AIC), 82 of 88 models considered were selected as best-fit models at least in one occasion, although with very different frequencies. Most parameter estimates also varied broadly among genes. Patterns found for vertebrates and Drosophila were quite similar and often more complex than those found in mammals. Phylogenetic trees derived from models in the 95% confidence interval set showed much less variance and were significantly closer to the tree estimated under the best-fit model than trees derived from models outside this interval. Although alternative criteria selected simpler models than the AIC, they suggested similar patterns. All together our results show that at a genomic scale, different gene alignments for the same set of taxa are best explained by a large variety of different substitution models and that model choice has implications on different parameter estimates including the inferred phylogenetic trees. After taking into account the differences related to sample size, our results suggest a noticeable diversity in the underlying evolutionary process. All together, we conclude that the use of model selection techniques is important to obtain consistent phylogenetic estimates from real data at a genomic scale.

Carbon Dynamics in Vegetation and Soils

NASA Technical Reports Server (NTRS)

Trumbore, Susan; Chambers, Jeffrey Q.; Camargo, Plinio; Martinelli, Luiz; Santos, Joaquim

2005-01-01

The overall goals of CD-08 team in Phase I were to quantify the contributions of different components of the carbon cycle to overall ecosystem carbon balance in Amazonian tropical forests and to undertake process studies at a number of sites along the eastern LBA transect to understand how and why these fluxes vary with site, season, and year. We divided this work into a number of specific tasks: (1) determining the average rate (and variability) of tree growth over the past 3 decades; (2) determining age demographics of tree populations, using radiocarbon to determine tree age; (3) assessing the rate of production and decomposition of dead wood debris; (4) determining turnover rates for organic matter in soils and the mean age of C respired from soil using radiocarbon measurements; and (5) comparing our results with models and constructing models to predict the potential of tropical forests to function as sources or sinks of C. This report summarizes the considerable progress made towards our original goals, which have led to increased understanding of the potential for central Amazon forests to act as sources or sinks of carbon with altered productivity. The overall picture of tropical forest C dynamics emerging from our Phase I studies suggests that the fraction of gross primary production allocated to growth in these forests is only 25-30%, as opposed to the 50% assumed by many ecosystem models. Consequent slow tree growth rates mean greater mean tree age for a given diameter, as reflected in our measurements and models of tree age. Radiocarbon measurements in leaf and root litter suggest that carbon stays in living tree biomass for several years up to a decade before being added to soils, where decomposition is rapid. The time lags predicted from 14C, when coupled with climate variation on similar time scales, can lead to significant interannual variation in net ecosystem C exchange.

FISHtrees 3.0: Tumor Phylogenetics Using a Ploidy Probe.

PubMed

Gertz, E Michael; Chowdhury, Salim Akhter; Lee, Woei-Jyh; Wangsa, Darawalee; Heselmeyer-Haddad, Kerstin; Ried, Thomas; Schwartz, Russell; Schäffer, Alejandro A

2016-01-01

Advances in fluorescence in situ hybridization (FISH) make it feasible to detect multiple copy-number changes in hundreds of cells of solid tumors. Studies using FISH, sequencing, and other technologies have revealed substantial intra-tumor heterogeneity. The evolution of subclones in tumors may be modeled by phylogenies. Tumors often harbor aneuploid or polyploid cell populations. Using a FISH probe to estimate changes in ploidy can guide the creation of trees that model changes in ploidy and individual gene copy-number variations. We present FISHtrees 3.0, which implements a ploidy-based tree building method based on mixed integer linear programming (MILP). The ploidy-based modeling in FISHtrees includes a new formulation of the problem of merging trees for changes of a single gene into trees modeling changes in multiple genes and the ploidy. When multiple samples are collected from each patient, varying over time or tumor regions, it is useful to evaluate similarities in tumor progression among the samples. Therefore, we further implemented in FISHtrees 3.0 a new method to build consensus graphs for multiple samples. We validate FISHtrees 3.0 on a simulated data and on FISH data from paired cases of cervical primary and metastatic tumors and on paired breast ductal carcinoma in situ (DCIS) and invasive ductal carcinoma (IDC). Tests on simulated data show improved accuracy of the ploidy-based approach relative to prior ploidyless methods. Tests on real data further demonstrate novel insights these methods offer into tumor progression processes. Trees for DCIS samples are significantly less complex than trees for paired IDC samples. Consensus graphs show substantial divergence among most paired samples from both sets. Low consensus between DCIS and IDC trees may help explain the difficulty in finding biomarkers that predict which DCIS cases are at most risk to progress to IDC. The FISHtrees software is available at ftp://ftp.ncbi.nih.gov/pub/FISHtrees.

FISHtrees 3.0: Tumor Phylogenetics Using a Ploidy Probe

PubMed Central

Chowdhury, Salim Akhter; Lee, Woei-Jyh; Wangsa, Darawalee; Heselmeyer-Haddad, Kerstin; Ried, Thomas; Schwartz, Russell; Schäffer, Alejandro A.

2016-01-01

Advances in fluorescence in situ hybridization (FISH) make it feasible to detect multiple copy-number changes in hundreds of cells of solid tumors. Studies using FISH, sequencing, and other technologies have revealed substantial intra-tumor heterogeneity. The evolution of subclones in tumors may be modeled by phylogenies. Tumors often harbor aneuploid or polyploid cell populations. Using a FISH probe to estimate changes in ploidy can guide the creation of trees that model changes in ploidy and individual gene copy-number variations. We present FISHtrees 3.0, which implements a ploidy-based tree building method based on mixed integer linear programming (MILP). The ploidy-based modeling in FISHtrees includes a new formulation of the problem of merging trees for changes of a single gene into trees modeling changes in multiple genes and the ploidy. When multiple samples are collected from each patient, varying over time or tumor regions, it is useful to evaluate similarities in tumor progression among the samples. Therefore, we further implemented in FISHtrees 3.0 a new method to build consensus graphs for multiple samples. We validate FISHtrees 3.0 on a simulated data and on FISH data from paired cases of cervical primary and metastatic tumors and on paired breast ductal carcinoma in situ (DCIS) and invasive ductal carcinoma (IDC). Tests on simulated data show improved accuracy of the ploidy-based approach relative to prior ploidyless methods. Tests on real data further demonstrate novel insights these methods offer into tumor progression processes. Trees for DCIS samples are significantly less complex than trees for paired IDC samples. Consensus graphs show substantial divergence among most paired samples from both sets. Low consensus between DCIS and IDC trees may help explain the difficulty in finding biomarkers that predict which DCIS cases are at most risk to progress to IDC. The FISHtrees software is available at ftp://ftp.ncbi.nih.gov/pub/FISHtrees. PMID:27362268

Shrinking windows of opportunity for oak seedling establishment in southern California mountains

USGS Publications Warehouse

Davis, Frank W.; Sweet, Lynn C.; Serra-Diaz, Josep M.; Franklin, Janet; McCullough, Ian M.; Flint, Alan L.; Flint, Lorraine E.; Dingman, John; Regan, Helen M.; Syphard, Alexandra D.; Hannah, Lee; Redmond, Kelly; Moritz, Max A.

2016-01-01

Seedling establishment is a critical step that may ultimately govern tree species’ distribution shifts under environmental change. Annual variation in the location of seed rain and microclimates results in transient “windows of opportunity” for tree seedling establishment across the landscape. These establishment windows vary at fine spatiotemporal scales that are not considered in most assessments of climate change impacts on tree species range dynamics and habitat displacement. We integrate field seedling establishment trials conducted in the southern Sierra Nevada and western Tehachapi Mountains of southern California with spatially downscaled grids of modeled water-year climatic water deficit (CWDwy) and mean August maximum daily temperature (Tmax) to map historical and projected future microclimates suitable for establishment windows of opportunity for Quercus douglasii, a dominant tree species of warm, dry foothill woodlands, and Q. kelloggii, a dominant of cooler, more mesic montane woodlands and forests. Based on quasi-binomial regression models, Q. douglasii seedling establishment is significantly associated with modeled CWDwy and to a lesser degree with modeled Tmax. Q. kelloggii seedling establishment is most strongly associated with Tmax and best predicted by a two-factor model including CWDwy and Tmax. Establishment niche models are applied to explore recruitment window dynamics in the western Tehachapi Mountains, where these species are currently widespread canopy dominants. Establishment windows are projected to decrease by 50–95%, shrinking locally to higher elevations and north-facing slopes by the end of this century depending on the species and climate scenario. These decreases in establishment windows suggest the potential for longer-term regional population declines of the species. While many additional processes regulate seedling establishment and growth, this study highlights the need to account for topoclimatic controls and interannual climatic variation when assessing how seedling establishment and colonization processes could be affected by climate change.

Cryptic Methane Emissions from Upland Forest Ecosystems

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

Megonigal, Patrick; Pitz, Scott

This exploratory research on Cryptic Methane Emissions from Upland Forest Ecosystems was motivated by evidence that upland ecosystems emit 36% as much methane to the atmosphere as global wetlands, yet we knew almost nothing about this source. The long-term objective was to refine Earth system models by quantifying methane emissions from upland forests, and elucidate the biogeochemical processes that govern upland methane emissions. The immediate objectives of the grant were to: (i) test the emerging paradigm that upland trees unexpectedly transpire methane, (ii) test the basic biogeochemical assumptions of an existing global model of upland methane emissions, and (iii) developmore » the suite of biogeochemical approaches that will be needed to advance research on upland methane emissions. We instrumented a temperate forest system in order to explore the processes that govern upland methane emissions. We demonstrated that methane is emitted from the stems of dominant tree species in temperate upland forests. Tree emissions occurred throughout the growing season, while soils adjacent to the trees consumed methane simultaneously, challenging the concept that forests are uniform sinks of methane. High frequency measurements revealed diurnal cycling in the rate of methane emissions, pointing to soils as the methane source and transpiration as the most likely pathway for methane transport. We propose the forests are smaller methane sinks than previously estimated due to stem emissions. Stem emissions may be particularly important in upland tropical forests characterized by high rainfall and transpiration, resolving differences between models and measurements. The methods we used can be effectively implemented in order to determine if the phenomenon is widespread.« less

In Vitro Experimental Model for the Long-Term Analysis of Cellular Dynamics During Bronchial Tree Development from Lung Epithelial Cells

PubMed Central

Maruta, Naomichi; Marumoto, Moegi

2017-01-01

Lung branching morphogenesis has been studied for decades, but the underlying developmental mechanisms are still not fully understood. Cellular movements dynamically change during the branching process, but it is difficult to observe long-term cellular dynamics by in vivo or tissue culture experiments. Therefore, developing an in vitro experimental model of bronchial tree would provide an essential tool for developmental biology, pathology, and systems biology. In this study, we succeeded in reconstructing a bronchial tree in vitro by using primary human bronchial epithelial cells. A high concentration gradient of bronchial epithelial cells was required for branching initiation, whereas homogeneously distributed endothelial cells induced the formation of successive branches. Subsequently, the branches grew in size to the order of millimeter. The developed model contains only two types of cells and it facilitates the analysis of lung branching morphogenesis. By taking advantage of our experimental model, we carried out long-term time-lapse observations, which revealed self-assembly, collective migration with leader cells, rotational motion, and spiral motion of epithelial cells in each developmental event. Mathematical simulation was also carried out to analyze the self-assembly process and it revealed simple rules that govern cellular dynamics. Our experimental model has provided many new insights into lung development and it has the potential to accelerate the study of developmental mechanisms, pattern formation, left–right asymmetry, and disease pathogenesis of the human lung. PMID:28471293

Automated morphological analysis of bone marrow cells in microscopic images for diagnosis of leukemia: nucleus-plasma separation and cell classification using a hierarchical tree model of hematopoesis

NASA Astrophysics Data System (ADS)

Krappe, Sebastian; Wittenberg, Thomas; Haferlach, Torsten; Münzenmayer, Christian

2016-03-01

The morphological differentiation of bone marrow is fundamental for the diagnosis of leukemia. Currently, the counting and classification of the different types of bone marrow cells is done manually under the use of bright field microscopy. This is a time-consuming, subjective, tedious and error-prone process. Furthermore, repeated examinations of a slide may yield intra- and inter-observer variances. For that reason a computer assisted diagnosis system for bone marrow differentiation is pursued. In this work we focus (a) on a new method for the separation of nucleus and plasma parts and (b) on a knowledge-based hierarchical tree classifier for the differentiation of bone marrow cells in 16 different classes. Classification trees are easily interpretable and understandable and provide a classification together with an explanation. Using classification trees, expert knowledge (i.e. knowledge about similar classes and cell lines in the tree model of hematopoiesis) is integrated in the structure of the tree. The proposed segmentation method is evaluated with more than 10,000 manually segmented cells. For the evaluation of the proposed hierarchical classifier more than 140,000 automatically segmented bone marrow cells are used. Future automated solutions for the morphological analysis of bone marrow smears could potentially apply such an approach for the pre-classification of bone marrow cells and thereby shortening the examination time.

Reference Canopy Stomatal Conductance Explains Spatiotemporal Patterns of Tree Transpiration

NASA Astrophysics Data System (ADS)

Loranty, M. M.; Mackay, D. S.; Ewers, B. E.; Kruger, E. L.; Traver, E.

2007-12-01

Increased heterogeneity in patterns of whole tree transpiration (EC) with increasing atmospheric vapor pressure deficit (D) suggests a dynamic response of sap flow velocity (JS) to environmental drivers. We hypothesized that differences in reference stomatal conductance (GSref), stomatal conductance at D = 1kPa, would explain the spatiotemporal dynamics of JS. Using a coupled model of plant hydraulic and biochemical processes we tested this hypothesis with sap flux data for 106 aspen ( Populus tremuloides) and 108 sugar maple ( Acer saccharum) trees collected from plots using in 2-D cyclic sampling scheme during the summer of 2005 in northern Wisconsin. Inverse modeling is used to estimate GSref for each tree. For each species, trees from across the ranges of JS and diameter distributions are compared. GSref explained temporal variability in spatial patterns of EC We explore several possible mechanistic explanations for differences in GSref among trees. Topoedaphic factors are considered to determine if location within a stand has an effect. We also consider competition with neighboring individuals as a possible explanation. Variations in GSref in aspen were explained in part by competition for light between neighboring individuals, while competition for light was not a significant factor for sugar maple. Based on simulation analysis we identify possible biochemical feedbacks as drivers of the variability in plant hydraulics. Other factors examined included micro-topography within both sites.

Compensatory mechanisms mitigate the effect of warming and drought on wood formation.

PubMed

Balducci, Lorena; Cuny, Henri E; Rathgeber, Cyrille B K; Deslauriers, Annie; Giovannelli, Alessio; Rossi, Sergio

2016-06-01

Because of global warming, high-latitude ecosystems are expected to experience increases in temperature and drought events. Wood formation will have to adjust to these new climatic constraints to maintain tree mechanical stability and long-distance water transport. The aim of this study is to understand the dynamic processes involved in wood formation under warming and drought. Xylogenesis, gas exchange, water relations and wood anatomy of black spruce [Picea mariana (Mill.) B.S.P.] saplings were monitored during a greenhouse experiment where temperature was increased during daytime or night-time (+6 °C) combined with a drought period. The kinetics of tracheid development expressed as rate and duration of the xylogenesis sub-processes were quantified using generalized additive models. Drought and warming had a strong influence on cell production, but little effect on wood anatomy. The increase in cell production rate under warmer temperatures, and especially during the night-time warming at the end of the growing season, resulted in wider tree-rings. However, the strong compensation between rates and durations of cell differentiation processes mitigates warming and drought effects on tree-ring structure. Our results allowed quantification of how wood formation kinetics is regulated when water and heat stress increase, allowing trees to adapt to future environmental conditions. © 2015 John Wiley & Sons Ltd.

Multiple Criteria Decision Analysis (MCDA) for evaluating new medicines in Health Technology Assessment and beyond: The Advance Value Framework.

PubMed

Angelis, Aris; Kanavos, Panos

2017-09-01

Escalating drug prices have catalysed the generation of numerous "value frameworks" with the aim of informing payers, clinicians and patients on the assessment and appraisal process of new medicines for the purpose of coverage and treatment selection decisions. Although this is an important step towards a more inclusive Value Based Assessment (VBA) approach, aspects of these frameworks are based on weak methodologies and could potentially result in misleading recommendations or decisions. In this paper, a Multiple Criteria Decision Analysis (MCDA) methodological process, based on Multi Attribute Value Theory (MAVT), is adopted for building a multi-criteria evaluation model. A five-stage model-building process is followed, using a top-down "value-focused thinking" approach, involving literature reviews and expert consultations. A generic value tree is structured capturing decision-makers' concerns for assessing the value of new medicines in the context of Health Technology Assessment (HTA) and in alignment with decision theory. The resulting value tree (Advance Value Tree) consists of three levels of criteria (top level criteria clusters, mid-level criteria, bottom level sub-criteria or attributes) relating to five key domains that can be explicitly measured and assessed: (a) burden of disease, (b) therapeutic impact, (c) safety profile (d) innovation level and (e) socioeconomic impact. A number of MAVT modelling techniques are introduced for operationalising (i.e. estimating) the model, for scoring the alternative treatment options, assigning relative weights of importance to the criteria, and combining scores and weights. Overall, the combination of these MCDA modelling techniques for the elicitation and construction of value preferences across the generic value tree provides a new value framework (Advance Value Framework) enabling the comprehensive measurement of value in a structured and transparent way. Given its flexibility to meet diverse requirements and become readily adaptable across different settings, the Advance Value Framework could be offered as a decision-support tool for evaluators and payers to aid coverage and reimbursement of new medicines. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Plant traits, productivity, biomass and soil properties from forest sites in the Pacific Northwest, 1999-2014.

PubMed

Berner, Logan T; Law, Beverly E

2016-01-19

Plant trait measurements are needed for evaluating ecological responses to environmental conditions and for ecosystem process model development, parameterization, and testing. We present a standardized dataset integrating measurements from projects conducted by the Terrestrial Ecosystem Research and Regional Analysis- Pacific Northwest (TERRA-PNW) research group between 1999 and 2014 across Oregon and Northern California, where measurements were collected for scaling and modeling regional terrestrial carbon processes with models such as Biome-BGC and the Community Land Model. The dataset contains measurements of specific leaf area, leaf longevity, leaf carbon and nitrogen for 35 tree and shrub species derived from more than 1,200 branch samples collected from over 200 forest plots, including several AmeriFlux sites. The dataset also contains plot-level measurements of forest composition, structure (e.g., tree biomass), and productivity, as well as measurements of soil structure (e.g., bulk density) and chemistry (e.g., carbon). Publically-archiving regional datasets of standardized, co-located, and geo-referenced plant trait measurements will advance the ability of earth system models to capture species-level climate sensitivity at regional to global scales.

Plant traits, productivity, biomass and soil properties from forest sites in the Pacific Northwest, 1999-2014

NASA Astrophysics Data System (ADS)

Berner, Logan T.; Law, Beverly E.

2016-01-01

Plant trait measurements are needed for evaluating ecological responses to environmental conditions and for ecosystem process model development, parameterization, and testing. We present a standardized dataset integrating measurements from projects conducted by the Terrestrial Ecosystem Research and Regional Analysis- Pacific Northwest (TERRA-PNW) research group between 1999 and 2014 across Oregon and Northern California, where measurements were collected for scaling and modeling regional terrestrial carbon processes with models such as Biome-BGC and the Community Land Model. The dataset contains measurements of specific leaf area, leaf longevity, leaf carbon and nitrogen for 35 tree and shrub species derived from more than 1,200 branch samples collected from over 200 forest plots, including several AmeriFlux sites. The dataset also contains plot-level measurements of forest composition, structure (e.g., tree biomass), and productivity, as well as measurements of soil structure (e.g., bulk density) and chemistry (e.g., carbon). Publically-archiving regional datasets of standardized, co-located, and geo-referenced plant trait measurements will advance the ability of earth system models to capture species-level climate sensitivity at regional to global scales.

Genealogy and gene trees.

PubMed

Rasmuson, Marianne

2008-02-01

Heredity can be followed in persons or in genes. Persons can be identified only a few generations back, but simplified models indicate that universal ancestors to all now living persons have occurred in the past. Genetic variability can be characterized as variants of DNA sequences. Data are available only from living persons, but from the pattern of variation gene trees can be inferred by means of coalescence models. The merging of lines backwards in time leads to a MRCA (most recent common ancestor). The time and place of living for this inferred person can give insights in human evolutionary history. Demographic processes are incorporated in the model, but since culture and customs are known to influence demography the models used ought to be tested against available genealogy. The Icelandic data base offers a possibility to do so and points to some discrepancies. Mitochondrial DNA and Y chromosome patterns give a rather consistent view of human evolutionary history during the latest 100 000 years but the earlier epochs of human evolution demand gene trees with longer branches. The results of such studies reveal as yet unsolved problems about the sources of our genome.

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.

Tree island pattern formation in the Florida Everglades

USGS Publications Warehouse

Carr, Joel; D'Odorico, P.; Engel, Victor C.; Redwine, Jed

2016-01-01

The Florida Everglades freshwater landscape exhibits a distribution of islands covered by woody vegetation and bordered by marshes and wet prairies. Known as “tree islands”, these ecogeomorphic features can be found in few other low gradient, nutrient limited freshwater wetlands. In the last few decades, however, a large percentage of tree islands have either shrank or disappeared in apparent response to altered water depths and other stressors associated with human impacts on the Everglades. Because the processes determining the formation and spatial organization of tree islands remain poorly understood, it is still unclear what controls the sensitivity of these landscapes to altered conditions. We hypothesize that positive feedbacks between woody plants and soil accretion are crucial to emergence and decline of tree islands. Likewise, positive feedbacks between phosphorus (P) accumulation and trees explain the P enrichment commonly observed in tree island soils. Here, we develop a spatially-explicit model of tree island formation and evolution, which accounts for these positive feedbacks (facilitation) as well as for long range competition and fire dynamics. It is found that tree island patterns form within a range of parameter values consistent with field data. Simulated impacts of reduced water levels, increased intensity of drought, and increased frequency of dry season/soil consuming fires on these feedback mechanisms result in the decline and disappearance of tree islands on the landscape.

Automatic translation of digraph to fault-tree models

NASA Technical Reports Server (NTRS)

Iverson, David L.

1992-01-01

The author presents a technique for converting digraph models, including those models containing cycles, to a fault-tree format. A computer program which automatically performs this translation using an object-oriented representation of the models has been developed. The fault-trees resulting from translations can be used for fault-tree analysis and diagnosis. Programs to calculate fault-tree and digraph cut sets and perform diagnosis with fault-tree models have also been developed. The digraph to fault-tree translation system has been successfully tested on several digraphs of varying size and complexity. Details of some representative translation problems are presented. Most of the computation performed by the program is dedicated to finding minimal cut sets for digraph nodes in order to break cycles in the digraph. Fault-trees produced by the translator have been successfully used with NASA's Fault-Tree Diagnosis System (FTDS) to produce automated diagnostic systems.

A graphical language for reliability model generation

NASA Technical Reports Server (NTRS)

Howell, Sandra V.; Bavuso, Salvatore J.; Haley, Pamela J.

1990-01-01

A graphical interface capability of the hybrid automated reliability predictor (HARP) is described. The graphics-oriented (GO) module provides the user with a graphical language for modeling system failure modes through the selection of various fault tree gates, including sequence dependency gates, or by a Markov chain. With this graphical input language, a fault tree becomes a convenient notation for describing a system. In accounting for any sequence dependencies, HARP converts the fault-tree notation to a complex stochastic process that is reduced to a Markov chain which it can then solve for system reliability. The graphics capability is available for use on an IBM-compatible PC, a Sun, and a VAX workstation. The GO module is written in the C programming language and uses the Graphical Kernel System (GKS) standard for graphics implementation. The PC, VAX, and Sun versions of the HARP GO module are currently in beta-testing.

Roles of Birds and Bats in Early Tropical-Forest Restoration

PubMed Central

de la Peña-Domene, Marinés; Martínez-Garza, Cristina; Palmas-Pérez, Sebastián; Rivas-Alonso, Edith; Howe, Henry F.

2014-01-01

Restoration of tropical forest depended in large part on seed dispersal by fruit-eating animals that transported seeds into planted forest patches. We tested effectiveness of dispersal agents as revealed by established recruits of tree and shrub species that bore seeds dispersed by birds, bats, or both. We documented restoration of dispersal processes over the first 76 months of experimental restoration in southern Mexico. Mixed-model repeated-measures randomized-block ANOVAs of seedlings recruited into experimental controls and mixed-species plantings from late-secondary and mature forest indicated that bats and birds played different roles in the first years of a restoration process. Bats dispersed pioneer tree and shrub species to slowly regenerating grassy areas, while birds mediated recruitment of later-successional species into planted stands of trees and to a lesser extent into controls. Of species of pioneer trees and shrubs established in plots, seven were primarily dispersed by birds, three by bats and four by both birds and bats. Of later-successional species recruited past the seedling stage, 13 were of species primarily dispersed by birds, and six were of species dispersed by both birds and bats. No later-successional species primarily dispersed by bats established in control or planted plots. Establishment of recruited seedlings was ten-fold higher under cover of planted trees than in grassy controls. Even pre-reproductive trees drew fruit-eating birds and the seeds that they carried from nearby forest, and provided conditions for establishment of shade-tolerant tree species. Overall, after 76 months of cattle exclusion, 94% of the recruited shrubs and trees in experimental plots were of species that we did not plant. PMID:25118608

Roles of birds and bats in early tropical-forest restoration.

PubMed

de la Peña-Domene, Marinés; Martínez-Garza, Cristina; Palmas-Pérez, Sebastián; Rivas-Alonso, Edith; Howe, Henry F

2014-01-01

Restoration of tropical forest depended in large part on seed dispersal by fruit-eating animals that transported seeds into planted forest patches. We tested effectiveness of dispersal agents as revealed by established recruits of tree and shrub species that bore seeds dispersed by birds, bats, or both. We documented restoration of dispersal processes over the first 76 months of experimental restoration in southern Mexico. Mixed-model repeated-measures randomized-block ANOVAs of seedlings recruited into experimental controls and mixed-species plantings from late-secondary and mature forest indicated that bats and birds played different roles in the first years of a restoration process. Bats dispersed pioneer tree and shrub species to slowly regenerating grassy areas, while birds mediated recruitment of later-successional species into planted stands of trees and to a lesser extent into controls. Of species of pioneer trees and shrubs established in plots, seven were primarily dispersed by birds, three by bats and four by both birds and bats. Of later-successional species recruited past the seedling stage, 13 were of species primarily dispersed by birds, and six were of species dispersed by both birds and bats. No later-successional species primarily dispersed by bats established in control or planted plots. Establishment of recruited seedlings was ten-fold higher under cover of planted trees than in grassy controls. Even pre-reproductive trees drew fruit-eating birds and the seeds that they carried from nearby forest, and provided conditions for establishment of shade-tolerant tree species. Overall, after 76 months of cattle exclusion, 94% of the recruited shrubs and trees in experimental plots were of species that we did not plant.

Post-fire Tree Mortality: Heating Increases Vulnerability to Cavitation in Longleaf Pine Branches

NASA Astrophysics Data System (ADS)

Lodge, A.; Kavanagh, K.; Dickinson, M. B.

2016-12-01

Tree mortality following wild and prescribed fires is of interest to both researchers and land managers. While some models exist that can predict mortality following fires, process-based models that incorporate physiological mechanisms of mortality are still being developed and improved. Delayed post-fire tree mortality has recently received increased attention, in part due to an increased use of prescribed fire as a restoration and management tool. One hypothesized mechanism of delayed mortality in trees is disruption of water transport in xylem due to exposure to the heat plume of a fire. This heat plume rapidly increases the vapor pressure deficit in the tree canopy, quickly increasing the tension on the water held in the xylem and leaves, potentially leading to cavitation. Cavitated xylem conduits can no longer transport water, eventually leading to tree death. We conducted a laboratory experiment examining whether heating stems increases their vulnerability to cavitation. We placed longleaf pine (Pinus palustris) branches in a water bath at sub-lethal temperatures (<60°C) and applied pressure in a cavitation chamber to simulate a range of xylem tension levels that may occur during fire. Percent loss of conductivity was measured following cavitation induced by various levels of applied pressure. When we compared the resulting vulnerability curves of heated branches to those of branches pressurized at room temperature, we observed increased vulnerability to cavitation in the heated samples especially at lower pressures. P50, or the pressure at which 50% of conductivity has been lost, decreased by 18% on branches heated to approximately 54°C. This suggests that stems heated during fires may be more vulnerable to cavitation, and provides some support for hydraulic disruption as a mechanism for post-fire tree mortality. Continued advancement in understanding of the mechanisms leading to delayed mortality will improve models predicting tree mortality.

"Growing trees backwards": Description of a stand reconstruction model (P-53)

Treesearch

Jonathan D. Bakker; Andrew J. Sanchez Meador; Peter Z. Fule; David W. Huffman; Margaret M. Moore

2008-01-01

We describe an individual-tree model that uses contemporary measurements to "grow trees backward" and reconstruct past tree diameters and stand structure in ponderosa pine dominated stands of the Southwest. Model inputs are contemporary structural measurements of all snags, logs, stumps, and living trees, and radial growth measurements, if available. Key...

"Growing trees backwards": Description of a stand reconstruction model

Treesearch

Jonathan D. Bakker; Andrew J. Sanchez Meador; Peter Z. Fule; David W. Huffman; Margaret M. Moore

2008-01-01

We describe an individual-tree model that uses contemporary measurements to "grow trees backward" and reconstruct past tree diameters and stand structure in ponderosa pine dominated stands of the Southwest. Model inputs are contemporary structural measurements of all snags, logs, stumps, and living trees, and radial growth measurements, if available. Key...

Foraging Behaviour in Magellanic Woodpeckers Is Consistent with a Multi-Scale Assessment of Tree Quality

PubMed Central

Vergara, Pablo M.; Soto, Gerardo E.; Rodewald, Amanda D.; Meneses, Luis O.; Pérez-Hernández, Christian G.

2016-01-01

Theoretical models predict that animals should make foraging decisions after assessing the quality of available habitat, but most models fail to consider the spatio-temporal scales at which animals perceive habitat availability. We tested three foraging strategies that explain how Magellanic woodpeckers (Campephilus magellanicus) assess the relative quality of trees: 1) Woodpeckers with local knowledge select trees based on the available trees in the immediate vicinity. 2) Woodpeckers lacking local knowledge select trees based on their availability at previously visited locations. 3) Woodpeckers using information from long-term memory select trees based on knowledge about trees available within the entire landscape. We observed foraging woodpeckers and used a Brownian Bridge Movement Model to identify trees available to woodpeckers along foraging routes. Woodpeckers selected trees with a later decay stage than available trees. Selection models indicated that preferences of Magellanic woodpeckers were based on clusters of trees near the most recently visited trees, thus suggesting that woodpeckers use visual cues from neighboring trees. In a second analysis, Cox’s proportional hazards models showed that woodpeckers used information consolidated across broader spatial scales to adjust tree residence times. Specifically, woodpeckers spent more time at trees with larger diameters and in a more advanced stage of decay than trees available along their routes. These results suggest that Magellanic woodpeckers make foraging decisions based on the relative quality of trees that they perceive and memorize information at different spatio-temporal scales. PMID:27416115

Foraging Behaviour in Magellanic Woodpeckers Is Consistent with a Multi-Scale Assessment of Tree Quality.

PubMed

Vergara, Pablo M; Soto, Gerardo E; Moreira-Arce, Darío; Rodewald, Amanda D; Meneses, Luis O; Pérez-Hernández, Christian G

2016-01-01

Theoretical models predict that animals should make foraging decisions after assessing the quality of available habitat, but most models fail to consider the spatio-temporal scales at which animals perceive habitat availability. We tested three foraging strategies that explain how Magellanic woodpeckers (Campephilus magellanicus) assess the relative quality of trees: 1) Woodpeckers with local knowledge select trees based on the available trees in the immediate vicinity. 2) Woodpeckers lacking local knowledge select trees based on their availability at previously visited locations. 3) Woodpeckers using information from long-term memory select trees based on knowledge about trees available within the entire landscape. We observed foraging woodpeckers and used a Brownian Bridge Movement Model to identify trees available to woodpeckers along foraging routes. Woodpeckers selected trees with a later decay stage than available trees. Selection models indicated that preferences of Magellanic woodpeckers were based on clusters of trees near the most recently visited trees, thus suggesting that woodpeckers use visual cues from neighboring trees. In a second analysis, Cox's proportional hazards models showed that woodpeckers used information consolidated across broader spatial scales to adjust tree residence times. Specifically, woodpeckers spent more time at trees with larger diameters and in a more advanced stage of decay than trees available along their routes. These results suggest that Magellanic woodpeckers make foraging decisions based on the relative quality of trees that they perceive and memorize information at different spatio-temporal scales.

Human impacts drive a global topographic signature in tree cover.

PubMed

Sandel, Brody; Svenning, Jens-Christian

2013-01-01

The Anthropocene is a geological epoch marked by major human influences on processes in the atmosphere, biosphere, hydrosphere and geosphere. One of the most dramatic features of the Anthropocene is the massive alteration of the Earth's vegetation, including forests. Here we investigate the role of topography in shaping human impacts on tree cover from local to global scales. We show that human impacts have resulted in a global tendency for tree cover to be constrained to sloped terrain and losses to be concentrated on flat terrain. This effect increases in strength with increasing human pressure and is most pronounced in countries with rapidly growing economies, limited human population stress and highly effective governments. These patterns likely reflect the relative inaccessibility of sloped topography and have important implications for conservation and modelling of future tree cover.

Tree biomass in the Swiss landscape: nationwide modelling for improved accounting for forest and non-forest trees.

PubMed

Price, B; Gomez, A; Mathys, L; Gardi, O; Schellenberger, A; Ginzler, C; Thürig, E

2017-03-01

Trees outside forest (TOF) can perform a variety of social, economic and ecological functions including carbon sequestration. However, detailed quantification of tree biomass is usually limited to forest areas. Taking advantage of structural information available from stereo aerial imagery and airborne laser scanning (ALS), this research models tree biomass using national forest inventory data and linear least-square regression and applies the model both inside and outside of forest to create a nationwide model for tree biomass (above ground and below ground). Validation of the tree biomass model against TOF data within settlement areas shows relatively low model performance (R 2 of 0.44) but still a considerable improvement on current biomass estimates used for greenhouse gas inventory and carbon accounting. We demonstrate an efficient and easily implementable approach to modelling tree biomass across a large heterogeneous nationwide area. The model offers significant opportunity for improved estimates on land use combination categories (CC) where tree biomass has either not been included or only roughly estimated until now. The ALS biomass model also offers the advantage of providing greater spatial resolution and greater within CC spatial variability compared to the current nationwide estimates.

[Sectional structure of a tree. Model analysis of the vertical biomass distribution].

PubMed

Galitskiĭ, V V

2010-01-01

A model has been proposed for the architecture of a tree in which virtual trees appear rhythmically on the treetop. Each consecutive virtual tree is a part of the previous tree. The difference between two adjacent virtual trees is a section--an element of the real tree structure. In case of a spruce, the section represents a verticil of a stem with the corresponding internode. Dynamics of a photosynthesizing part of the physiologically active biomass of each section differ from the corresponding dynamics of the virtual trees and the whole real tree. If the tree biomass dynamics has a sigma-shaped form, then the section dynamics have to be bell-shaped. It means that the lower stem should accordingly become bare, which is typically observed in nature. Model analysis reveals the limiting, in the age, form of trees to be an "umbrella". It can be observed in nature and is an outcome of physical limitation of the tree height combined with the sigma-shaped form of the tree biomass dynamics. Variation of model parameters provides for various forms of the tree biomass distribution along the height, which can be associated with certain biological species of trees.

Structural modeling and analysis of an effluent treatment process for electroplating--a graph theoretic approach.

PubMed

Kumar, Abhishek; Clement, Shibu; Agrawal, V P

2010-07-15

An attempt is made to address a few ecological and environment issues by developing different structural models for effluent treatment system for electroplating. The effluent treatment system is defined with the help of different subsystems contributing to waste minimization. Hierarchical tree and block diagram showing all possible interactions among subsystems are proposed. These non-mathematical diagrams are converted into mathematical models for design improvement, analysis, comparison, storage retrieval and commercially off-the-shelf purchases of different subsystems. This is achieved by developing graph theoretic model, matrix models and variable permanent function model. Analysis is carried out by permanent function, hierarchical tree and block diagram methods. Storage and retrieval is done using matrix models. The methodology is illustrated with the help of an example. Benefits to the electroplaters/end user are identified. 2010 Elsevier B.V. All rights reserved.

The Detection and Characterization of Urbanization, Industrialization, and Longwall Mining Impacts on Forest Ecosystems Through the Use of GiS and Remote Sensing Techniques

NASA Astrophysics Data System (ADS)

Pfeil-McCullough, Erin Kathleen

Urbanization has far reaching and significant effects on forest ecosystems, directly through urban development and indirectly through supportive processes such as coal mining and agriculture. Urban processes modify the landscape leading to altered hillslope hydrology, increased disturbance, and the introduction of non-native forest pathogens. This dissertation addresses several challenges in our ability to detect these urbanization impacts on forests via geospatial analyses. The role of forests in urban hydrological processes has been extensively studied, but the impacts of urbanized hydrology on forests remain poorly examined. This dissertation documented impacts to hydrology and forests at variety of temporal and spatial scales: 1) A geospatial comparison of the historic and contemporary forests of Allegheny County, Pennsylvania revealed substantial shifts in tree species, but less change in the species soil moisture preference. These results document additional evidence that increased heterogeneity in urban soil moisture alters forest structure. 2) To examine soil moisture changes, impacts of longwall mine subsidence were assessed by using a Landsat based canopy moisture index and hot spot analysis tools at the forest patch scale. Declines in forest canopy moisture were detected over longwall mines as mining progressed through time, and results contradicted assumptions that the hydrological impacts overlying LMS recover within 4-5 years following subsidence of undermined land. 3) Utilizing a landslide susceptibility model (SINMAP), increases in landslide susceptibility were predicted in Pittsburgh, PA based on several scenarios of ash tree loss to the emerald ash borer (EAB), a bark beetle that rapidly kills ash trees. This model provides a tool to predict changes in landslide susceptibility following tree loss, increasing the understanding of urban forest function and its role in slope stability. Detecting how urbanized hydrology impacts forest health, function, and development is fundamental to sustaining the services forests provide. Results from this dissertation will ultimately allow improvements in the management and protection of both trees and water resources in urban systems and beyond.

An overview of natural hazard impacts to railways and urban transportation systems

NASA Astrophysics Data System (ADS)

Bíl, Michal; Nezval, Vojtěch; Bílová, Martina; Andrášik, Richard; Kubeček, Jan

2017-04-01

We present an overview and two case studies of natural hazard impacts on rail transportation systems in the Czech Republic. Flooding, landsliding, heavy snowfall, windstorms and glaze (black ice) are the most common natural processes which occur in this region. Whereas flooding and landsliding usually cause direct damage to the transportation infrastructure, other hazards predominantly cause indirect losses. Railway and urban tramline networks are almost fully dependent on electricity which is provided by a system of overhead lines (electric lines above the tracks). These lines are extremely susceptible to formation of glaze which blocks conduction of electric current. A December 2014 glaze event caused significant indirect losses in the largest Czech cities and railways due to the above-mentioned process. Details of this event will be provided during the presentation. Windstorms usually cause tree falls which can affect overhead lines and physically block railway tracks. Approximately 30 % of the Czech railway network is closer than 50 m from the nearest forest. This presents significant potential for transport interruption due to falling trees. Complicated legal relations among the owners of the plots of land along railways, the environment (full-grown trees and related habitat), and the railway administrator are behind many traffic interruptions due to falling trees. We have registered 2040 tree falls between 2012 and 2015 on the railway network. A model of the fallen tree hazard was created for the entire Czech railway network. Both above-mentioned case studies provide illustrative examples of the increased fragility of the modern transportation systems which fully rely on electricity. Natural processes with a low destructive power are thereby able to cause network wide service cut-offs.

Gap-free segmentation of vascular networks with automatic image processing pipeline.

PubMed

Hsu, Chih-Yang; Ghaffari, Mahsa; Alaraj, Ali; Flannery, Michael; Zhou, Xiaohong Joe; Linninger, Andreas

2017-03-01

Current image processing techniques capture large vessels reliably but often fail to preserve connectivity in bifurcations and small vessels. Imaging artifacts and noise can create gaps and discontinuity of intensity that hinders segmentation of vascular trees. However, topological analysis of vascular trees require proper connectivity without gaps, loops or dangling segments. Proper tree connectivity is also important for high quality rendering of surface meshes for scientific visualization or 3D printing. We present a fully automated vessel enhancement pipeline with automated parameter settings for vessel enhancement of tree-like structures from customary imaging sources, including 3D rotational angiography, magnetic resonance angiography, magnetic resonance venography, and computed tomography angiography. The output of the filter pipeline is a vessel-enhanced image which is ideal for generating anatomical consistent network representations of the cerebral angioarchitecture for further topological or statistical analysis. The filter pipeline combined with computational modeling can potentially improve computer-aided diagnosis of cerebrovascular diseases by delivering biometrics and anatomy of the vasculature. It may serve as the first step in fully automatic epidemiological analysis of large clinical datasets. The automatic analysis would enable rigorous statistical comparison of biometrics in subject-specific vascular trees. The robust and accurate image segmentation using a validated filter pipeline would also eliminate operator dependency that has been observed in manual segmentation. Moreover, manual segmentation is time prohibitive given that vascular trees have more than thousands of segments and bifurcations so that interactive segmentation consumes excessive human resources. Subject-specific trees are a first step toward patient-specific hemodynamic simulations for assessing treatment outcomes. Copyright © 2017 Elsevier Ltd. All rights reserved.

Preservation of hippocampal neuron numbers and hippocampal subfield volumes in behaviorally characterized aged tree shrews.

PubMed

Keuker, Jeanine I H; de Biurrun, Gabriel; Luiten, Paul G M; Fuchs, Eberhard

2004-01-19

Aging is associated with a decreased ability to store and retrieve information. The hippocampal formation plays a critical role in such memory processes, and its integrity is affected during normal aging. We used tree shrews (Tupaia belangeri) as an animal model of aging, because in many characteristics, tree shrews are closer to primates than they are to rodents. Young and aged male tree shrews performed a holeboard spatial memory task, which permits assessment of reference and working memory. Upon completion of the behavioral measurements, we carried out modified stereological analyses of neuronal numbers in various subdivisions of the hippocampus and used the Cavalieri method to calculate the volumes of these subfields. Results showed that the working memory of aged tree shrews was significantly impaired compared with that of young animals, whereas the hippocampus-dependent reference memory remained unchanged by aging. Estimation of the number of neurons revealed preserved neuron numbers in the subiculum, in the subregions CA1, CA2, CA3, and in the hilus of the dentate gyrus. Volume measurements showed no aging-related changes in the volume of any of these hippocampal subregions, or in the molecular and granule cell layers of the dentate gyrus of tree shrews. We conclude that the observed changes in memory performance in aging tree shrews are not accompanied by observable reductions of hippocampal neuron numbers or hippocampal volume, rather, the changes in memory performance are more likely the result of modified subcellular mechanisms that are affected by the aging process. Copyright 2003 Wiley-Liss, Inc.

Carbon Sequestration Estimation of Street Trees Based on Point Cloud from Vehicle-Borne Laser Scanning System

NASA Astrophysics Data System (ADS)

Zhao, Y.; Hu, Q.

2017-09-01

Continuous development of urban road traffic system requests higher standards of road ecological environment. Ecological benefits of street trees are getting more attention. Carbon sequestration of street trees refers to the carbon stocks of street trees, which can be a measurement for ecological benefits of street trees. Estimating carbon sequestration in a traditional way is costly and inefficient. In order to solve above problems, a carbon sequestration estimation approach for street trees based on 3D point cloud from vehicle-borne laser scanning system is proposed in this paper. The method can measure the geometric parameters of a street tree, including tree height, crown width, diameter at breast height (DBH), by processing and analyzing point cloud data of an individual tree. Four Chinese scholartree trees and four camphor trees are selected for experiment. The root mean square error (RMSE) of tree height is 0.11m for Chinese scholartree and 0.02m for camphor. Crown widths in X direction and Y direction, as well as the average crown width are calculated. And the RMSE of average crown width is 0.22m for Chinese scholartree and 0.10m for camphor. The last calculated parameter is DBH, the RMSE of DBH is 0.5cm for both Chinese scholartree and camphor. Combining the measured geometric parameters and an appropriate carbon sequestration calculation model, the individual tree's carbon sequestration will be estimated. The proposed method can help enlarge application range of vehicle-borne laser point cloud data, improve the efficiency of estimating carbon sequestration, construct urban ecological environment and manage landscape.

Biophysical modelling of intra-ring variations in tracheid features and wood density of Pinus pinaster trees exposed to seasonal droughts.

PubMed

Wilkinson, Sarah; Ogée, Jérôme; Domec, Jean-Christophe; Rayment, Mark; Wingate, Lisa

2015-03-01

Process-based models that link seasonally varying environmental signals to morphological features within tree rings are essential tools to predict tree growth response and commercially important wood quality traits under future climate scenarios. This study evaluated model portrayal of radial growth and wood anatomy observations within a mature maritime pine (Pinus pinaster (L.) Aït.) stand exposed to seasonal droughts. Intra-annual variations in tracheid anatomy and wood density were identified through image analysis and X-ray densitometry on stem cores covering the growth period 1999-2010. A cambial growth model was integrated with modelled plant water status and sugar availability from the soil-plant-atmosphere transfer model MuSICA to generate estimates of cell number, cell volume, cell mass and wood density on a weekly time step. The model successfully predicted inter-annual variations in cell number, ring width and maximum wood density. The model was also able to predict the occurrence of special anatomical features such as intra-annual density fluctuations (IADFs) in growth rings. Since cell wall thickness remained surprisingly constant within and between growth rings, variations in wood density were primarily the result of variations in lumen diameter, both in the model and anatomical data. In the model, changes in plant water status were identified as the main driver of the IADFs through a direct effect on cell volume. The anatomy data also revealed that a trade-off existed between hydraulic safety and hydraulic efficiency. Although a simplified description of cambial physiology is presented, this integrated modelling approach shows potential value for identifying universal patterns of tree-ring growth and anatomical features over a broad climatic gradient. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Explanatory Power of Multi-scale Physical Descriptors in Modeling Benthic Indices Across Nested Ecoregions of the Pacific Northwest

NASA Astrophysics Data System (ADS)

Holburn, E. R.; Bledsoe, B. P.; Poff, N. L.; Cuhaciyan, C. O.

2005-05-01

Using over 300 R/EMAP sites in OR and WA, we examine the relative explanatory power of watershed, valley, and reach scale descriptors in modeling variation in benthic macroinvertebrate indices. Innovative metrics describing flow regime, geomorphic processes, and hydrologic-distance weighted watershed and valley characteristics are used in multiple regression and regression tree modeling to predict EPT richness, % EPT, EPT/C, and % Plecoptera. A nested design using seven ecoregions is employed to evaluate the influence of geographic scale and environmental heterogeneity on the explanatory power of individual and combined scales. Regression tree models are constructed to explain variability while identifying threshold responses and interactions. Cross-validated models demonstrate differences in the explanatory power associated with single-scale and multi-scale models as environmental heterogeneity is varied. Models explaining the greatest variability in biological indices result from multi-scale combinations of physical descriptors. Results also indicate that substantial variation in benthic macroinvertebrate response can be explained with process-based watershed and valley scale metrics derived exclusively from common geospatial data. This study outlines a general framework for identifying key processes driving macroinvertebrate assemblages across a range of scales and establishing the geographic extent at which various levels of physical description best explain biological variability. Such information can guide process-based stratification to avoid spurious comparison of dissimilar stream types in bioassessments and ensure that key environmental gradients are adequately represented in sampling designs.

Logic flowgraph methodology - A tool for modeling embedded systems

NASA Technical Reports Server (NTRS)

Muthukumar, C. T.; Guarro, S. B.; Apostolakis, G. E.

1991-01-01

The logic flowgraph methodology (LFM), a method for modeling hardware in terms of its process parameters, has been extended to form an analytical tool for the analysis of integrated (hardware/software) embedded systems. In the software part of a given embedded system model, timing and the control flow among different software components are modeled by augmenting LFM with modified Petrinet structures. The objective of the use of such an augmented LFM model is to uncover possible errors and the potential for unanticipated software/hardware interactions. This is done by backtracking through the augmented LFM mode according to established procedures which allow the semiautomated construction of fault trees for any chosen state of the embedded system (top event). These fault trees, in turn, produce the possible combinations of lower-level states (events) that may lead to the top event.

An application of locally linear model tree algorithm with combination of feature selection in credit scoring

NASA Astrophysics Data System (ADS)

Siami, Mohammad; Gholamian, Mohammad Reza; Basiri, Javad

2014-10-01

Nowadays, credit scoring is one of the most important topics in the banking sector. Credit scoring models have been widely used to facilitate the process of credit assessing. In this paper, an application of the locally linear model tree algorithm (LOLIMOT) was experimented to evaluate the superiority of its performance to predict the customer's credit status. The algorithm is improved with an aim of adjustment by credit scoring domain by means of data fusion and feature selection techniques. Two real world credit data sets - Australian and German - from UCI machine learning database were selected to demonstrate the performance of our new classifier. The analytical results indicate that the improved LOLIMOT significantly increase the prediction accuracy.

Trees wanted--dead or alive! Host selection and population dynamics in tree-killing bark beetles.

PubMed

Kausrud, Kyrre L; Grégoire, Jean-Claude; Skarpaas, Olav; Erbilgin, Nadir; Gilbert, Marius; Økland, Bjørn; Stenseth, Nils Chr

2011-01-01

Bark beetles (Coleoptera: Curculionidae, Scolytinae) feed and breed in dead or severely weakened host trees. When their population densities are high, some species aggregate on healthy host trees so that their defences may be exhausted and the inner bark successfully colonized, killing the tree in the process. Here we investigate under what conditions participating with unrelated conspecifics in risky mass attacks on living trees is an adaptive strategy, and what this can tell us about bark beetle outbreak dynamics. We find that the outcome of individual host selection may deviate from the ideal free distribution in a way that facilitates the emergence of tree-killing (aggressive) behavior, and that any heritability on traits governing aggressiveness seems likely to exist in a state of flux or cycles consistent with variability observed in natural populations. This may have implications for how economically and ecologically important species respond to environmental changes in climate and landscape (forest) structure. The population dynamics emerging from individual behavior are complex, capable of switching between "endemic" and "epidemic" regimes spontaneously or following changes in host availability or resistance. Model predictions are compared to empirical observations, and we identify some factors determining the occurrence and self-limitation of epidemics.

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.

Using LiDAR to Estimate Total Aboveground Biomass of Redwood Stands in the Jackson Demonstration State Forest, Mendocino, California

NASA Astrophysics Data System (ADS)

Rao, M.; Vuong, H.

2013-12-01

The overall objective of this study is to develop a method for estimating total aboveground biomass of redwood stands in Jackson Demonstration State Forest, Mendocino, California using airborne LiDAR data. LiDAR data owing to its vertical and horizontal accuracy are increasingly being used to characterize landscape features including ground surface elevation and canopy height. These LiDAR-derived metrics involving structural signatures at higher precision and accuracy can help better understand ecological processes at various spatial scales. Our study is focused on two major species of the forest: redwood (Sequoia semperirens [D.Don] Engl.) and Douglas-fir (Pseudotsuga mensiezii [Mirb.] Franco). Specifically, the objectives included linear regression models fitting tree diameter at breast height (dbh) to LiDAR derived height for each species. From 23 random points on the study area, field measurement (dbh and tree coordinate) were collected for more than 500 trees of Redwood and Douglas-fir over 0.2 ha- plots. The USFS-FUSION application software along with its LiDAR Data Viewer (LDV) were used to to extract Canopy Height Model (CHM) from which tree heights would be derived. Based on the LiDAR derived height and ground based dbh, a linear regression model was developed to predict dbh. The predicted dbh was used to estimate the biomass at the single tree level using Jenkin's formula (Jenkin et al 2003). The linear regression models were able to explain 65% of the variability associated with Redwood's dbh and 80% of that associated with Douglas-fir's dbh.

[Research on identification of species of fruit trees by spectral analysis].

PubMed

Xing, Dong-Xing; Chang, Qing-Rui

2009-07-01

Using the spectral reflectance data (R2) of canopies, the present paper identifies seven species of fruit trees bearing fruit in the fruit mature period. Firstly, it compares the fruit tree species identification capability of six kinds of satellite sensors and four kinds of vegetation index through re-sampling the spectral data with six kinds of pre-defined filter function and the related data processing of calculating vegetation indexes. Then, it structures a BP neural network model for identifying seven species of fruit trees on the basis of choosing the best transformation of R(lambda) and optimizing the model parameters. The main conclusions are: (1) the order of the identification capability of the six kinds of satellite sensors from strong to weak is: MODIS, ASTER, ETM+, HRG, QUICKBIRD and IKONOS; (2) among the four kinds of vegetation indexes, the identification capability of RVI is the most powerful, the next is NDVI, while the identification capability of SAVI or DVI is relatively weak; (3) The identification capability of RVI and NDVI calculated with the reflectance of near-infrared and red channels of ETM+ or MODIS sensor is relatively powerful; (4) Among R(lambda) and its 22 kinds of transformation data, d1 [log(1/R(lambda))](derivative gap is set 9 nm) is the best transformation for structuring BP neural network model; (5) The paper structures a 3-layer BP neural network model for identifying seven species of fruit trees using the best transformation of R(lambda) which is d1 [log(1/R(lambda))](derivative gap is set 9 nm).

Differential controls on soil carbon density and mineralization among contrasting forest types in a temperate forest ecosystem.

PubMed

You, Ye-Ming; Wang, Juan; Sun, Xiao-Lu; Tang, Zuo-Xin; Zhou, Zhi-Yong; Sun, Osbert Jianxin

2016-03-01

Understanding the controls on soil carbon dynamics is crucial for modeling responses of ecosystem carbon balance to global change, yet few studies provide explicit knowledge on the direct and indirect effects of forest stands on soil carbon via microbial processes. We investigated tree species, soil, and site factors in relation to soil carbon density and mineralization in a temperate forest of central China. We found that soil microbial biomass and community structure, extracellular enzyme activities, and most of the site factors studied varied significantly across contrasting forest types, and that the associations between activities of soil extracellular enzymes and microbial community structure appeared to be weak and inconsistent across forest types, implicating complex mechanisms in the microbial regulation of soil carbon metabolism in relation to tree species. Overall, variations in soil carbon density and mineralization are predominantly accounted for by shared effects of tree species, soil, microclimate, and microbial traits rather than the individual effects of the four categories of factors. Our findings point to differential controls on soil carbon density and mineralization among contrasting forest types and highlight the challenge to incorporate microbial processes for constraining soil carbon dynamics in global carbon cycle models.

Differential controls on soil carbon density and mineralization among contrasting forest types in a temperate forest ecosystem

PubMed Central

You, Ye-Ming; Wang, Juan; Sun, Xiao-Lu; Tang, Zuo-Xin; Zhou, Zhi-Yong; Sun, Osbert Jianxin

2016-01-01

Understanding the controls on soil carbon dynamics is crucial for modeling responses of ecosystem carbon balance to global change, yet few studies provide explicit knowledge on the direct and indirect effects of forest stands on soil carbon via microbial processes. We investigated tree species, soil, and site factors in relation to soil carbon density and mineralization in a temperate forest of central China. We found that soil microbial biomass and community structure, extracellular enzyme activities, and most of the site factors studied varied significantly across contrasting forest types, and that the associations between activities of soil extracellular enzymes and microbial community structure appeared to be weak and inconsistent across forest types, implicating complex mechanisms in the microbial regulation of soil carbon metabolism in relation to tree species. Overall, variations in soil carbon density and mineralization are predominantly accounted for by shared effects of tree species, soil, microclimate, and microbial traits rather than the individual effects of the four categories of factors. Our findings point to differential controls on soil carbon density and mineralization among contrasting forest types and highlight the challenge to incorporate microbial processes for constraining soil carbon dynamics in global carbon cycle models. PMID:26925871

Understanding the temporal dimension of the red-edge spectral region for forest decline detection using high-resolution hyperspectral and Sentinel-2a imagery

NASA Astrophysics Data System (ADS)

Zarco-Tejada, P. J.; Hornero, A.; Hernández-Clemente, R.; Beck, P. S. A.

2018-03-01

The operational monitoring of forest decline requires the development of remote sensing methods that are sensitive to the spatiotemporal variations of pigment degradation and canopy defoliation. In this context, the red-edge spectral region (RESR) was proposed in the past due to its combined sensitivity to chlorophyll content and leaf area variation. In this study, the temporal dimension of the RESR was evaluated as a function of forest decline using a radiative transfer method with the PROSPECT and 3D FLIGHT models. These models were used to generate synthetic pine stands simulating decline and recovery processes over time and explore the temporal rate of change of the red-edge chlorophyll index (CI) as compared to the trajectories obtained for the structure-related Normalized Difference Vegetation Index (NDVI). The temporal trend method proposed here consisted of using synthetic spectra to calculate the theoretical boundaries of the subspace for healthy and declining pine trees in the temporal domain, defined by CItime=n/CItime=n+1 vs. NDVItime=n/NDVItime=n+1. Within these boundaries, trees undergoing decline and recovery processes showed different trajectories through this subspace. The method was then validated using three high-resolution airborne hyperspectral images acquired at 40 cm resolution and 260 spectral bands of 6.5 nm full-width half-maximum (FWHM) over a forest with widespread tree decline, along with field-based monitoring of chlorosis and defoliation (i.e., 'decline' status) in 663 trees between the years 2015 and 2016. The temporal rate of change of chlorophyll vs. structural indices, based on reflectance spectra extracted from the hyperspectral images, was different for trees undergoing decline, and aligned towards the decline baseline established using the radiative transfer models. By contrast, healthy trees over time aligned towards the theoretically obtained healthy baseline. The applicability of this temporal trend method to the red-edge bands of the MultiSpectral Imager (MSI) instrument on board Sentinel-2a for operational forest status monitoring was also explored by comparing the temporal rate of change of the Sentinel-2-derived CI over areas with declining and healthy trees. Results demonstrated that the Sentinel-2a red-edge region was sensitive to the temporal dimension of forest condition, as the relationships obtained for pixels in healthy condition deviated from those of pixels undergoing decline.

Decision trees in epidemiological research.

PubMed

Venkatasubramaniam, Ashwini; Wolfson, Julian; Mitchell, Nathan; Barnes, Timothy; JaKa, Meghan; French, Simone

2017-01-01

In many studies, it is of interest to identify population subgroups that are relatively homogeneous with respect to an outcome. The nature of these subgroups can provide insight into effect mechanisms and suggest targets for tailored interventions. However, identifying relevant subgroups can be challenging with standard statistical methods. We review the literature on decision trees, a family of techniques for partitioning the population, on the basis of covariates, into distinct subgroups who share similar values of an outcome variable. We compare two decision tree methods, the popular Classification and Regression tree (CART) technique and the newer Conditional Inference tree (CTree) technique, assessing their performance in a simulation study and using data from the Box Lunch Study, a randomized controlled trial of a portion size intervention. Both CART and CTree identify homogeneous population subgroups and offer improved prediction accuracy relative to regression-based approaches when subgroups are truly present in the data. An important distinction between CART and CTree is that the latter uses a formal statistical hypothesis testing framework in building decision trees, which simplifies the process of identifying and interpreting the final tree model. We also introduce a novel way to visualize the subgroups defined by decision trees. Our novel graphical visualization provides a more scientifically meaningful characterization of the subgroups identified by decision trees. Decision trees are a useful tool for identifying homogeneous subgroups defined by combinations of individual characteristics. While all decision tree techniques generate subgroups, we advocate the use of the newer CTree technique due to its simplicity and ease of interpretation.

Modeling individual tree survial

Treesearch

Quang V. Cao

2016-01-01

Information provided by growth and yield models is the basis for forest managers to make decisions on how to manage their forests. Among different types of growth models, whole-stand models offer predictions at stand level, whereas individual-tree models give detailed information at tree level. The well-known logistic regression is commonly used to predict tree...

Leaf aging of Amazonian canopy trees as revealed by spectral and physiochemical measurements.

PubMed

Chavana-Bryant, Cecilia; Malhi, Yadvinder; Wu, Jin; Asner, Gregory P; Anastasiou, Athanasios; Enquist, Brian J; Cosio Caravasi, Eric G; Doughty, Christopher E; Saleska, Scott R; Martin, Roberta E; Gerard, France F

2017-05-01

Leaf aging is a fundamental driver of changes in leaf traits, thereby regulating ecosystem processes and remotely sensed canopy dynamics. We explore leaf reflectance as a tool to monitor leaf age and develop a spectra-based partial least squares regression (PLSR) model to predict age using data from a phenological study of 1099 leaves from 12 lowland Amazonian canopy trees in southern Peru. Results demonstrated monotonic decreases in leaf water (LWC) and phosphorus (P mass ) contents and an increase in leaf mass per unit area (LMA) with age across trees; leaf nitrogen (N mass ) and carbon (C mass ) contents showed monotonic but tree-specific age responses. We observed large age-related variation in leaf spectra across trees. A spectra-based model was more accurate in predicting leaf age (R 2  = 0.86; percent root mean square error (%RMSE) = 33) compared with trait-based models using single (R 2  = 0.07-0.73; %RMSE = 7-38) and multiple (R 2  = 0.76; %RMSE = 28) predictors. Spectra- and trait-based models established a physiochemical basis for the spectral age model. Vegetation indices (VIs) including the normalized difference vegetation index (NDVI), enhanced vegetation index 2 (EVI2), normalized difference water index (NDWI) and photosynthetic reflectance index (PRI) were all age-dependent. This study highlights the importance of leaf age as a mediator of leaf traits, provides evidence of age-related leaf reflectance changes that have important impacts on VIs used to monitor canopy dynamics and productivity and proposes a new approach to predicting and monitoring leaf age with important implications for remote sensing. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

Operational Tree Species Mapping in a Diverse Tropical Forest with Airborne Imaging Spectroscopy.

PubMed

Baldeck, Claire A; Asner, Gregory P; Martin, Robin E; Anderson, Christopher B; Knapp, David E; Kellner, James R; Wright, S Joseph

2015-01-01

Remote identification and mapping of canopy tree species can contribute valuable information towards our understanding of ecosystem biodiversity and function over large spatial scales. However, the extreme challenges posed by highly diverse, closed-canopy tropical forests have prevented automated remote species mapping of non-flowering tree crowns in these ecosystems. We set out to identify individuals of three focal canopy tree species amongst a diverse background of tree and liana species on Barro Colorado Island, Panama, using airborne imaging spectroscopy data. First, we compared two leading single-class classification methods--binary support vector machine (SVM) and biased SVM--for their performance in identifying pixels of a single focal species. From this comparison we determined that biased SVM was more precise and created a multi-species classification model by combining the three biased SVM models. This model was applied to the imagery to identify pixels belonging to the three focal species and the prediction results were then processed to create a map of focal species crown objects. Crown-level cross-validation of the training data indicated that the multi-species classification model had pixel-level producer's accuracies of 94-97% for the three focal species, and field validation of the predicted crown objects indicated that these had user's accuracies of 94-100%. Our results demonstrate the ability of high spatial and spectral resolution remote sensing to accurately detect non-flowering crowns of focal species within a diverse tropical forest. We attribute the success of our model to recent classification and mapping techniques adapted to species detection in diverse closed-canopy forests, which can pave the way for remote species mapping in a wider variety of ecosystems.

Operational Tree Species Mapping in a Diverse Tropical Forest with Airborne Imaging Spectroscopy

PubMed Central

Baldeck, Claire A.; Asner, Gregory P.; Martin, Robin E.; Anderson, Christopher B.; Knapp, David E.; Kellner, James R.; Wright, S. Joseph

2015-01-01

Remote identification and mapping of canopy tree species can contribute valuable information towards our understanding of ecosystem biodiversity and function over large spatial scales. However, the extreme challenges posed by highly diverse, closed-canopy tropical forests have prevented automated remote species mapping of non-flowering tree crowns in these ecosystems. We set out to identify individuals of three focal canopy tree species amongst a diverse background of tree and liana species on Barro Colorado Island, Panama, using airborne imaging spectroscopy data. First, we compared two leading single-class classification methods—binary support vector machine (SVM) and biased SVM—for their performance in identifying pixels of a single focal species. From this comparison we determined that biased SVM was more precise and created a multi-species classification model by combining the three biased SVM models. This model was applied to the imagery to identify pixels belonging to the three focal species and the prediction results were then processed to create a map of focal species crown objects. Crown-level cross-validation of the training data indicated that the multi-species classification model had pixel-level producer’s accuracies of 94–97% for the three focal species, and field validation of the predicted crown objects indicated that these had user’s accuracies of 94–100%. Our results demonstrate the ability of high spatial and spectral resolution remote sensing to accurately detect non-flowering crowns of focal species within a diverse tropical forest. We attribute the success of our model to recent classification and mapping techniques adapted to species detection in diverse closed-canopy forests, which can pave the way for remote species mapping in a wider variety of ecosystems. PMID:26153693

Surface temperature dataset for North America obtained by application of optimal interpolation algorithm merging tree-ring chronologies and climate model output

NASA Astrophysics Data System (ADS)

Chen, Xin; Xing, Pei; Luo, Yong; Nie, Suping; Zhao, Zongci; Huang, Jianbin; Wang, Shaowu; Tian, Qinhua

2017-02-01

A new dataset of surface temperature over North America has been constructed by merging climate model results and empirical tree-ring data through the application of an optimal interpolation algorithm. Errors of both the Community Climate System Model version 4 (CCSM4) simulation and the tree-ring reconstruction were considered to optimize the combination of the two elements. Variance matching was used to reconstruct the surface temperature series. The model simulation provided the background field, and the error covariance matrix was estimated statistically using samples from the simulation results with a running 31-year window for each grid. Thus, the merging process could continue with a time-varying gain matrix. This merging method (MM) was tested using two types of experiment, and the results indicated that the standard deviation of errors was about 0.4 °C lower than the tree-ring reconstructions and about 0.5 °C lower than the model simulation. Because of internal variabilities and uncertainties in the external forcing data, the simulated decadal warm-cool periods were readjusted by the MM such that the decadal variability was more reliable (e.g., the 1940-1960s cooling). During the two centuries (1601-1800 AD) of the preindustrial period, the MM results revealed a compromised spatial pattern of the linear trend of surface temperature, which is in accordance with the phase transition of the Pacific decadal oscillation and Atlantic multidecadal oscillation. Compared with pure CCSM4 simulations, it was demonstrated that the MM brought a significant improvement to the decadal variability of the gridded temperature via the merging of temperature-sensitive tree-ring records.

Processes, dynamics and modelling of radiocaesium cycling in a chronosequence of Chernobyl-contaminated Scots pine (Pinus sylvestris L.) plantations.

PubMed

Goor, François; Thiry, Yves

2004-06-05

In a large forested area affected by the Chernobyl radioactive fallout, especially in CIS, the lasting recycling of radiocaesium (137Cs) by the trees is a source of long-term contamination of woody products. The quantitative description of the 137Cs dynamics in contaminated forest is a prerequisite to predictive modelling and further management of such territories. Three even-aged mono-specific Scots pine stands (17, 37 and 57 years old) were selected in a contaminated woodland in southeastern Belarus to constitute an adequate chronosequence. We determined the potassium and radiocaesium annual fluxes involved in the biological cycling in each stand using a well-documented calculation methodology. Qualitatively, 137Cs was shown to be rapidly recycled in trees through the same pathways as K and to redistribute similarly between the tree components. Compared to K, a higher fraction of 137Cs, corresponding to about the half of the annual uptake, is immobilised in perennial organs. With tree development, trunk wood and bark become prevailing sinks for 137Cs since they represent an increasing pool of biomass. In the pine chronosequence, the current root absorption, respectively, mobilizes 0.53, 0.32 and 0.31% year(-1) of the total 137Cs pool in soil. Variations in the 137Cs uptake do not reflect differences in the 137Cs balance between stands. In the two older stands, 51 and 71% of the current tree contamination are related to earlier accumulation subsequent to the initial fallout interception and recycling. The soil is the dominant source of long-term tree contamination. A simple modelling based on the measured 137Cs fluxes indicates that, for young stands, radioactive decay-corrected contamination would stabilize after reaching a maximum of 25 years after the 137Cs deposition. Stemwood presents a maximum of 15 years after the deposition and decrease afterwards mainly through radioactive decay. In the older stands, the decontamination is constant without local maximum of 137Cs level in the wood. The 137Cs contamination of tree components is the result of different influential processes like root uptake, internal translocation and immobilisation. For more accurate predictions, the calibration of existing models would be benefited by comparing with the 137Cs annual fluxes instead of the simple transfer factor coefficients. In the perspective of other applications, there is a need of such data for other radionuclides as well as for heavy metals. Copryright 2003 Elsevier B.V.

Coalescent methods for estimating phylogenetic trees.

PubMed

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

2009-10-01

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

High organic inputs explain shallow and deep SOC storage in a long-term agroforestry system - combining experimental and modeling approaches

NASA Astrophysics Data System (ADS)

Cardinael, Rémi; Guenet, Bertrand; Chevallier, Tiphaine; Dupraz, Christian; Cozzi, Thomas; Chenu, Claire

2018-01-01

Agroforestry is an increasingly popular farming system enabling agricultural diversification and providing several ecosystem services. In agroforestry systems, soil organic carbon (SOC) stocks are generally increased, but it is difficult to disentangle the different factors responsible for this storage. Organic carbon (OC) inputs to the soil may be larger, but SOC decomposition rates may be modified owing to microclimate, physical protection, or priming effect from roots, especially at depth. We used an 18-year-old silvoarable system associating hybrid walnut trees (Juglans regia × nigra) and durum wheat (Triticum turgidum L. subsp. durum) and an adjacent agricultural control plot to quantify all OC inputs to the soil - leaf litter, tree fine root senescence, crop residues, and tree row herbaceous vegetation - and measured SOC stocks down to 2 m of depth at varying distances from the trees. We then proposed a model that simulates SOC dynamics in agroforestry accounting for both the whole soil profile and the lateral spatial heterogeneity. The model was calibrated to the control plot only. Measured OC inputs to soil were increased by about 40 % (+ 1.11 t C ha-1 yr-1) down to 2 m of depth in the agroforestry plot compared to the control, resulting in an additional SOC stock of 6.3 t C ha-1 down to 1 m of depth. However, most of the SOC storage occurred in the first 30 cm of soil and in the tree rows. The model was strongly validated, properly describing the measured SOC stocks and distribution with depth in agroforestry tree rows and alleys. It showed that the increased inputs of fresh biomass to soil explained the observed additional SOC storage in the agroforestry plot. Moreover, only a priming effect variant of the model was able to capture the depth distribution of SOC stocks, suggesting the priming effect as a possible mechanism driving deep SOC dynamics. This result questions the potential of soils to store large amounts of carbon, especially at depth. Deep-rooted trees modify OC inputs to soil, a process that deserves further study given its potential effects on SOC dynamics.

Quasi-Optimal Elimination Trees for 2D Grids with Singularities

DOE PAGES

Paszyńska, A.; Paszyński, M.; Jopek, K.; ...

2015-01-01

We consmore » truct quasi-optimal elimination trees for 2D finite element meshes with singularities. These trees minimize the complexity of the solution of the discrete system. The computational cost estimates of the elimination process model the execution of the multifrontal algorithms in serial and in parallel shared-memory executions. Since the meshes considered are a subspace of all possible mesh partitions, we call these minimizers quasi-optimal. We minimize the cost functionals using dynamic programming. Finding these minimizers is more computationally expensive than solving the original algebraic system. Nevertheless, from the insights provided by the analysis of the dynamic programming minima, we propose a heuristic construction of the elimination trees that has cost O N e log ⁡ N e , where N e is the number of elements in the mesh. We show that this heuristic ordering has similar computational cost to the quasi-optimal elimination trees found with dynamic programming and outperforms state-of-the-art alternatives in our numerical experiments.« less

Quasi-Optimal Elimination Trees for 2D Grids with Singularities

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

Paszyńska, A.; Paszyński, M.; Jopek, K.

We consmore » truct quasi-optimal elimination trees for 2D finite element meshes with singularities. These trees minimize the complexity of the solution of the discrete system. The computational cost estimates of the elimination process model the execution of the multifrontal algorithms in serial and in parallel shared-memory executions. Since the meshes considered are a subspace of all possible mesh partitions, we call these minimizers quasi-optimal. We minimize the cost functionals using dynamic programming. Finding these minimizers is more computationally expensive than solving the original algebraic system. Nevertheless, from the insights provided by the analysis of the dynamic programming minima, we propose a heuristic construction of the elimination trees that has cost O N e log ⁡ N e , where N e is the number of elements in the mesh. We show that this heuristic ordering has similar computational cost to the quasi-optimal elimination trees found with dynamic programming and outperforms state-of-the-art alternatives in our numerical experiments.« less

Spatial statistical analysis of tree deaths using airborne digital imagery

NASA Astrophysics Data System (ADS)

Chang, Ya-Mei; Baddeley, Adrian; Wallace, Jeremy; Canci, Michael

2013-04-01

High resolution digital airborne imagery offers unprecedented opportunities for observation and monitoring of vegetation, providing the potential to identify, locate and track individual vegetation objects over time. Analytical tools are required to quantify relevant information. In this paper, locations of trees over a large area of native woodland vegetation were identified using morphological image analysis techniques. Methods of spatial point process statistics were then applied to estimate the spatially-varying tree death risk, and to show that it is significantly non-uniform. [Tree deaths over the area were detected in our previous work (Wallace et al., 2008).] The study area is a major source of ground water for the city of Perth, and the work was motivated by the need to understand and quantify vegetation changes in the context of water extraction and drying climate. The influence of hydrological variables on tree death risk was investigated using spatial statistics (graphical exploratory methods, spatial point pattern modelling and diagnostics).

Research on complex 3D tree modeling based on L-system

NASA Astrophysics Data System (ADS)

Gang, Chen; Bin, Chen; Yuming, Liu; Hui, Li

2018-03-01

L-system as a fractal iterative system could simulate complex geometric patterns. Based on the field observation data of trees and knowledge of forestry experts, this paper extracted modeling constraint rules and obtained an L-system rules set. Using the self-developed L-system modeling software the L-system rule set was parsed to generate complex tree 3d models.The results showed that the geometrical modeling method based on l-system could be used to describe the morphological structure of complex trees and generate 3D tree models.

76 FR 38036 - Propylene Oxide; Pesticide Tolerances

Federal Register 2010, 2011, 2012, 2013, 2014

2011-06-29

... regulation amends the propylene oxide tolerance on ``nut, tree, group 14'' to ``nutmeat, processed, except... propylene oxide tolerance (40 CFR 180.491) on ``nut, tree, group 14'' to read ``nutmeat, processed, except...) on ``nut, tree, group 14'' to read ``nutmeat, processed, except peanuts.'' IV. Statutory and...

Adult tree swallow survival on the polychlorinated biphenyl-contaminated Hudson River, New York, USA, between 2006 and 2010

USGS Publications Warehouse

Custer, Christine M.; Custer, Thomas W.; Hines, James E.

2012-01-01

The upper Hudson River basin in east central New York, USA, is highly contaminated, primarily with polychlorinated biphenyls (PCBs). Reduced adult survival has been documented in tree swallows (Tachycineta bicolor) at a similarly PCB-contaminated river system in western Massachusetts. The purpose of the present study was to assess whether adult survival of tree swallows was likewise affected in the Hudson River basin. Between 2006 and 2010, a total of 521 female tree swallows were banded, of which 148 were retrapped at least once. The authors used Program MARK and an information theoretic approach to test the hypothesis that PCB contamination reduced annual survival of female tree swallows. The model that best described the processes that generated the capture history data included covariate effects of year and female plumage coloration on survival but not PCB/river. Annual survival rates of brown-plumaged females (mostly one year old) were generally lower (mean phi = 0.39) than those of blue-plumaged females (mean phi = 0.50, one year or older). Poor early spring weather in 2007 was associated with reduced survival in both plumage-color groups compared to later years. Models with the effects of PCB exposure on survival (all ΔAICc values >5.0) received little support.

Models for Predicting the Biomass of Cunninghamialanceolata Trees and Stands in Southeastern China

PubMed Central

Saeed, Sajjad

2017-01-01

Using existing equations to estimate the biomass of a single tree or a forest stand still involves large uncertainties. In this study, we developed individual-tree biomass models for Chinese Fir (Cunninghamia lanceolata.) stands in Fujian Province, southeast China, by using 74 previously established models that have been most commonly used to estimate tree biomass. We selected the best fit models and modified them. The results showed that the published model ln(B(Biomass)) = a + b * ln(D) + c * (ln(H))2 + d * (ln(H))3 + e * ln(WD) had the best fit for estimating the tree biomass of Chinese Fir stands. Furthermore, we observed that variables D(diameter at breast height), H (height), and WD(wood density)were significantly correlated with the total tree biomass estimation model. As a result, a natural logarithm structure gave the best estimates for the tree biomass structure. Finally, when a multi-step improvement on tree biomass model was performed, the tree biomass model with Tree volume(TV), WD and biomass wood density conversion factor (BECF),achieved the highest simulation accuracy, expressed as ln(TB) = −0.0703 + 0.9780 * ln(TV) + 0.0213 * ln(WD) + 1.0166 * ln(BECF). Therefore, when TV, WD and BECF were combined with tree biomass volume coefficient bi for Chinese Fir, the stand biomass (SB)model included both volume(SV) and coefficient bi variables of the stand as follows: bi = Exp(−0.0703+0.9780*ln(TV)+0.0213 * ln(WD)+1.0166*ln(BECF)). The stand biomass model is SB = SV/TV * bi. PMID:28095512

Models for Predicting the Biomass of Cunninghamialanceolata Trees and Stands in Southeastern China.

PubMed

Guangyi, Mei; Yujun, Sun; Saeed, Sajjad

2017-01-01

Using existing equations to estimate the biomass of a single tree or a forest stand still involves large uncertainties. In this study, we developed individual-tree biomass models for Chinese Fir (Cunninghamia lanceolata.) stands in Fujian Province, southeast China, by using 74 previously established models that have been most commonly used to estimate tree biomass. We selected the best fit models and modified them. The results showed that the published model ln(B(Biomass)) = a + b * ln(D) + c * (ln(H))2 + d * (ln(H))3 + e * ln(WD) had the best fit for estimating the tree biomass of Chinese Fir stands. Furthermore, we observed that variables D(diameter at breast height), H (height), and WD(wood density)were significantly correlated with the total tree biomass estimation model. As a result, a natural logarithm structure gave the best estimates for the tree biomass structure. Finally, when a multi-step improvement on tree biomass model was performed, the tree biomass model with Tree volume(TV), WD and biomass wood density conversion factor (BECF),achieved the highest simulation accuracy, expressed as ln(TB) = -0.0703 + 0.9780 * ln(TV) + 0.0213 * ln(WD) + 1.0166 * ln(BECF). Therefore, when TV, WD and BECF were combined with tree biomass volume coefficient bi for Chinese Fir, the stand biomass (SB)model included both volume(SV) and coefficient bi variables of the stand as follows: bi = Exp(-0.0703+0.9780*ln(TV)+0.0213 * ln(WD)+1.0166*ln(BECF)). The stand biomass model is SB = SV/TV * bi.

A fuzzy decision tree for fault classification.

PubMed

Zio, Enrico; Baraldi, Piero; Popescu, Irina C

2008-02-01

In plant accident management, the control room operators are required to identify the causes of the accident, based on the different patterns of evolution of the monitored process variables thereby developing. This task is often quite challenging, given the large number of process parameters monitored and the intense emotional states under which it is performed. To aid the operators, various techniques of fault classification have been engineered. An important requirement for their practical application is the physical interpretability of the relationships among the process variables underpinning the fault classification. In this view, the present work propounds a fuzzy approach to fault classification, which relies on fuzzy if-then rules inferred from the clustering of available preclassified signal data, which are then organized in a logical and transparent decision tree structure. The advantages offered by the proposed approach are precisely that a transparent fault classification model is mined out of the signal data and that the underlying physical relationships among the process variables are easily interpretable as linguistic if-then rules that can be explicitly visualized in the decision tree structure. The approach is applied to a case study regarding the classification of simulated faults in the feedwater system of a boiling water reactor.

Use of Bayesian event trees in semi-quantitative volcano eruption forecasting and hazard analysis

NASA Astrophysics Data System (ADS)

Wright, Heather; Pallister, John; Newhall, Chris

2015-04-01

Use of Bayesian event trees to forecast eruptive activity during volcano crises is an increasingly common practice for the USGS-USAID Volcano Disaster Assistance Program (VDAP) in collaboration with foreign counterparts. This semi-quantitative approach combines conceptual models of volcanic processes with current monitoring data and patterns of occurrence to reach consensus probabilities. This approach allows a response team to draw upon global datasets, local observations, and expert judgment, where the relative influence of these data depends upon the availability and quality of monitoring data and the degree to which the volcanic history is known. The construction of such event trees additionally relies upon existence and use of relevant global databases and documented past periods of unrest. Because relevant global databases may be underpopulated or nonexistent, uncertainty in probability estimations may be large. Our 'hybrid' approach of combining local and global monitoring data and expert judgment facilitates discussion and constructive debate between disciplines: including seismology, gas geochemistry, geodesy, petrology, physical volcanology and technology/engineering, where difference in opinion between response team members contributes to definition of the uncertainty in the probability estimations. In collaboration with foreign colleagues, we have created event trees for numerous areas experiencing volcanic unrest. Event trees are created for a specified time frame and are updated, revised, or replaced as the crisis proceeds. Creation of an initial tree is often prompted by a change in monitoring data, such that rapid assessment of probability is needed. These trees are intended as a vehicle for discussion and a way to document relevant data and models, where the target audience is the scientists themselves. However, the probabilities derived through the event-tree analysis can also be used to help inform communications with emergency managers and the public. VDAP trees evaluate probabilities of: magmatic intrusion, likelihood of eruption, magnitude of eruption, and types of associated hazardous events and their extents. In a few cases, trees have been extended to also assess and communicate vulnerability and relative risk.

Individual tree diameter increment model for managed even-aged stands of ponderosa pine throughout the western United States using a multilevel linear mixed effects model

Treesearch

Fabian C.C. Uzoh; William W. Oliver

2008-01-01

A diameter increment model is developed and evaluated for individual trees of ponderosa pine throughout the species range in the United States using a multilevel linear mixed model. Stochastic variability is broken down among period, locale, plot, tree and within-tree components. Covariates acting at tree and stand level, as breast height diameter, density, site index...

Seasonal Climate Signals in Multiple Tree-Ring Parameters: A Pilot Study of Pinus ponderosa in the Columbia River Basin

NASA Astrophysics Data System (ADS)

Dannenberg, M.; Wise, E. K.; Keung, J. H.

2014-12-01

Proxy-based reconstructions of past climate have played an integral role in assessments of historical climate change, and tree-ring widths (TRW) have a long history of use in this paleoclimate research due to their annual resolution, widespread availability, and sensitivity of growth processes to variation in temperature and water availability. Increasingly, studies have shown that additional tree-ring metrics—including earlywood and latewood widths (EW and LW, respectively), maximum latewood density, and the intensity of reflected blue light from latewood (BI)—can provide additional information on seasonal climatic variability that is not present in TRW alone due to different processes that affect growth in different parts of the growing season. Studies of these additional tree-ring metrics highlight their utility in climate reconstructions, but to date they have mostly been limited to a few tree species and regions. Here, we extend the range of previous studies on alternative tree-ring metrics by evaluating the seasonal climate signals in TRW, EW, LW, and BI of Pinus ponderosa at six semiarid sites surrounding the Columbia River basin in the U.S. Pacific Northwest (PNW). Cores from each site were cross-dated and EW, LW, and TRW were measured using standard dendrochronological procedures. BI was obtained using a high-resolution flatbed scanner and CooRecorder software. To evaluate the unique climate processes and seasonalities contributing to different dendrochronological metrics, monthly temperature and precipitation from each site were obtained from the PRISM climate model and were correlated with each of the tree-ring metrics using the MATLAB program SEASCORR. We also evaluate the potential of using multiple tree-ring metrics (rather than a single proxy) in reconstructions of precipitation in the PNW. Initial results suggest that 1) tree growth at each site is water-limited but with substantial differences among the sites in the strength and seasonality of correlations between precipitation and tree-ring metrics, and 2) EW tends to be more dependent on conditions in the prior growing season while LW tends to be related to water availability early in the current growing season. Results from this study illustrate the potential utility of multiproxy dendroclimatology for paleoclimate research.

The long oasis: understanding and managing saline floodplains in southeastern Australia

NASA Astrophysics Data System (ADS)

Woods, J.; Green, G.; Laattoe, T.; Purczel, C.; Riches, V.; Li, C.; Denny, M.

2017-12-01

In a semi-arid region of southeastern Australia, the River Murray is the predominant source of freshwater for town water supply, irrigation, and floodplain ecosystems. The river interacts with aquifers where the salinity routinely exceeds 18,000 mg/l. River regulation, extraction, land clearance, and irrigation have reduced the size and frequency of floods while moving more salt into the floodplain. Floodplain ecosystem health has declined. Management options to improve floodplain health under these modified conditions include environmental watering, weirpool manipulation, and groundwater pumping. To benefit long-lived tree species, floodplain management needs to increase soil moisture availability. A conceptual model was developed of floodplain processes impacting soil moisture availability. The implications and limitations of the conceptualization were investigated using a series of numerical models, each of which simulated a subset of the processes under current and managed conditions. The aim was to determine what range of behaviors the models predicted, and to identify which parameters were key to accurately predicting the success of management options. Soil moisture availability was found to depend strongly on the properties of the floodplain clay, which controls vertical recharge during inundation. Groundwater freshening near surface water features depended on the riverbed conductivity and the penetration of the river into the floodplain sediments. Evapotranspiration is another critical process, and simulations revealed the limitations of standard numerical codes in environments where both evaporation and transpiration depend on salinity. Finally, maintenance of viable populations of floodplain trees is conceptually understood to rely on the persistence of adequate soil moisture availability over time, but thresholds for duration of exposure to low moisture availability that lead to decline and irreversible decline in tree condition are a major knowledge gap. The work identified critical data gaps which will be addressed in monitoring guidelines to improve management. This includes: hydrogeochemical sampling; in situ soil monitoring combined with tree health observations; monitoring of actual evapotranspiration; and monitoring of bores close to surface water sources.

Classification tree models for predicting distributions of michigan stream fish from landscape variables

USGS Publications Warehouse

Steen, P.J.; Zorn, T.G.; Seelbach, P.W.; Schaeffer, J.S.

2008-01-01

Traditionally, fish habitat requirements have been described from local-scale environmental variables. However, recent studies have shown that studying landscape-scale processes improves our understanding of what drives species assemblages and distribution patterns across the landscape. Our goal was to learn more about constraints on the distribution of Michigan stream fish by examining landscape-scale habitat variables. We used classification trees and landscape-scale habitat variables to create and validate presence-absence models and relative abundance models for Michigan stream fishes. We developed 93 presence-absence models that on average were 72% correct in making predictions for an independent data set, and we developed 46 relative abundance models that were 76% correct in making predictions for independent data. The models were used to create statewide predictive distribution and abundance maps that have the potential to be used for a variety of conservation and scientific purposes. ?? Copyright by the American Fisheries Society 2008.

Dynamic and Contextual Information in HMM Modeling for Handwritten Word Recognition.

PubMed

Bianne-Bernard, Anne-Laure; Menasri, Farès; Al-Hajj Mohamad, Rami; Mokbel, Chafic; Kermorvant, Christopher; Likforman-Sulem, Laurence

2011-10-01

This study aims at building an efficient word recognition system resulting from the combination of three handwriting recognizers. The main component of this combined system is an HMM-based recognizer which considers dynamic and contextual information for a better modeling of writing units. For modeling the contextual units, a state-tying process based on decision tree clustering is introduced. Decision trees are built according to a set of expert-based questions on how characters are written. Questions are divided into global questions, yielding larger clusters, and precise questions, yielding smaller ones. Such clustering enables us to reduce the total number of models and Gaussians densities by 10. We then apply this modeling to the recognition of handwritten words. Experiments are conducted on three publicly available databases based on Latin or Arabic languages: Rimes, IAM, and OpenHart. The results obtained show that contextual information embedded with dynamic modeling significantly improves recognition.

Pattern or process? Evaluating the peninsula effect as a determinant of species richness in coastal dune forests

PubMed Central

Olivier, Pieter I.; van Aarde, Rudi J.

2017-01-01

The peninsula effect predicts that the number of species should decline from the base of a peninsula to the tip. However, evidence for the peninsula effect is ambiguous, as different analytical methods, study taxa, and variations in local habitat or regional climatic conditions influence conclusions on its presence. We address this uncertainty by using two analytical methods to investigate the peninsula effect in three taxa that occupy different trophic levels: trees, millipedes, and birds. We surveyed 81 tree quadrants, 102 millipede transects, and 152 bird points within 150 km of coastal dune forest that resemble a habitat peninsula along the northeast coast of South Africa. We then used spatial (trend surface analyses) and non-spatial regressions (generalized linear mixed models) to test for the presence of the peninsula effect in each of the three taxa. We also used linear mixed models to test if climate (temperature and precipitation) and/or local habitat conditions (water availability associated with topography and landscape structural variables) could explain gradients in species richness. Non-spatial models suggest that the peninsula effect was present in all three taxa. However, spatial models indicated that only bird species richness declined from the peninsula base to the peninsula tip. Millipede species richness increased near the centre of the peninsula, while tree species richness increased near the tip. Local habitat conditions explained species richness patterns of birds and trees, but not of millipedes, regardless of model type. Our study highlights the idiosyncrasies associated with the peninsula effect—conclusions on the presence of the peninsula effect depend on the analytical methods used and the taxon studied. The peninsula effect might therefore be better suited to describe a species richness pattern where the number of species decline from a broader habitat base to a narrow tip, rather than a process that drives species richness. PMID:28376096

Using Mechanistic Studies to Model Riparian Tree Establishment Under Environmental Flow Scenarios on Regulated Rivers

NASA Astrophysics Data System (ADS)

Stella, J. C.; Battles, J. J.; McBride, J. R.; Orr, B. K.

2007-12-01

In the Central Valley of California, pioneer cottonwood and willow species dominate the near-river forests. Historically, seedling recruitment for these disturbance-adapted species coincided with spring floods. Changes in flow timing and magnitude due to river regulation have decreased the success of seedling cohorts and contributed to the decline of these riparian tree populations. In order to address gaps in our understanding of these species and potential restoration strategies, we field-calibrated a conceptual model of seedling recruitment for the dominant pioneer woody species, Populus fremontii, Salix gooddingii, and S. exigua. We conducted experiments to identify seedling desiccation thresholds and seed longevity, used field studies to measure seedling competition and seasonal seed release patterns, and modeled interannual differences in dispersal timing using a degree-day model. These studies were integrated into a recruitment model that generates annual estimates of seedling density and bank elevation based on inputs of seasonal river discharge, seed dispersal timing, and seedling mortality from desiccation. The model predictions successfully captured interannual and species-level patterns in recruitment observed independently throughout a 20-km reach of the lower Tuolumne River from 2002-04. The model correctly predicted that seedling densities were highest in 2004 and lowest in 2003, and that S. exigua recruitment would be less extensive than for the two tree species. This work shows promise as both a quantitative approach linking hydrology, climate and plant community dynamics, and as a process-based framework for guiding flow releases and other management actions to restore riparian tree population along Central Valley rivers.

Individual tree detection in intact forest and degraded forest areas in the north region of Mato Grosso State, Brazilian Amazon

NASA Astrophysics Data System (ADS)

Santos, E. G.; Jorge, A.; Shimabukuro, Y. E.; Gasparini, K.

2017-12-01

The State of Mato Grosso - MT has the second largest area with degraded forest among the states of the Brazilian Legal Amazon. Land use and land cover change processes that occur in this region cause the loss of forest biomass, releasing greenhouse gases that contribute to the increase of temperature on earth. These degraded forest areas lose biomass according to the intensity and magnitude of the degradation type. The estimate of forest biomass, commonly performed by forest inventory through sample plots, shows high variance in degraded forest areas. Due to this variance and complexity of tropical forests, the aim of this work was to estimate forest biomass using LiDAR point clouds in three distinct forest areas: one degraded by fire, another by selective logging and one area of intact forest. The approach applied in these areas was the Individual Tree Detection (ITD). To isolate the trees, we generated Canopy Height Models (CHM) images, which are obtained by subtracting the Digital Elevation Model (MDE) and the Digital Terrain Model (MDT), created by the cloud of LiDAR points. The trees in the CHM images are isolated by an algorithm provided by the Quantitative Ecology research group at the School of Forestry at Northern Arizona University (SILVA, 2015). With these points, metrics were calculated for some areas, which were used in the model of biomass estimation. The methodology used in this work was expected to reduce the error in biomass estimate in the study area. The cloud points of the most representative trees were analyzed, and thus field data was correlated with the individual trees found by the proposed algorithm. In a pilot study, the proposed methodology was applied generating the individual tree metrics: total height and area of the crown. When correlating 339 isolated trees, an unsatisfactory R² was obtained, as heights found by the algorithm were lower than those obtained in the field, with an average difference of 2.43 m. This shows that the algorithm used to isolate trees in temperate areas did not obtained satisfactory results in the tropical forest of Mato Grosso State. Due to this, in future works two algorithms, one developed by Dalponte et al. (2015) and another by Li et al. (2012) will be used.

Transfer Factors for Contaminant Uptake by Fruit and Nut Trees

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

Napier, Bruce A.; Fellows, Robert J.; Minc, Leah D.

Transfer of radionuclides from soils into plants is one of the key mechanisms for long-term contamination of the human food chain. Nearly all computer models that address soil-to-plant uptake of radionuclides use empirically-derived transfer factors to address this process. Essentially all available soil-to-plant transfer factors are based on measurements in annual crops. Because very few measurements are available for tree fruits, samples were taken of alfalfa and oats and the stems, leaves, and fruits and nuts of almond, apple, apricot, carob, fig, grape, nectarine, pecan, pistachio (natural and grafted), and pomegranate, along with local surface soil. The samples were dried,more » ground, weighed, and analyzed for trace constituents through a combination of induction-coupled plasma mass spectrometry and instrumental neutron activation analysis for a wide range of naturally-occurring elements. Analysis results are presented and converted to soil-to-plant transfer factors. These are compared to commonly used and internationally recommended values. Those determined for annual crops are very similar to commonly-used values; those determined for tree fruits show interesting differences. Most macro- and micronutrients are slightly reduced in fruits; non-essential elements are reduced further. These findings may be used in existing computer models and may allow development of tree-fruit-specific transfer models.« less

CASSIA--a dynamic model for predicting intra-annual sink demand and interannual growth variation in Scots pine.

PubMed

Schiestl-Aalto, Pauliina; Kulmala, Liisa; Mäkinen, Harri; Nikinmaa, Eero; Mäkelä, Annikki

2015-04-01

The control of tree growth vs environment by carbon sources or sinks remains unresolved although it is widely studied. This study investigates growth of tree components and carbon sink-source dynamics at different temporal scales. We constructed a dynamic growth model 'carbon allocation sink source interaction' (CASSIA) that calculates tree-level carbon balance from photosynthesis, respiration, phenology and temperature-driven potential structural growth of tree organs and dynamics of stored nonstructural carbon (NSC) and their modifying influence on growth. With the model, we tested hypotheses that sink demand explains the intra-annual growth dynamics of the meristems, and that the source supply is further needed to explain year-to-year growth variation. The predicted intra-annual dimensional growth of shoots and needles and the number of cells in xylogenesis phases corresponded with measurements, whereas NSC hardly limited the growth, supporting the first hypothesis. Delayed GPP influence on potential growth was necessary for simulating the yearly growth variation, indicating also at least an indirect source limitation. CASSIA combines seasonal growth and carbon balance dynamics with long-term source dynamics affecting growth and thus provides a first step to understanding the complex processes regulating intra- and interannual growth and sink-source dynamics. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

Cause-Effect Relations with Regard to Functional and Morphological Humus Characteristics in Mixed Forest Stands

NASA Astrophysics Data System (ADS)

Schua, K.; Feger, K.-H.; Wagner, S.; Eisenhauer, D.-R.; Raben, G.

2009-04-01

A major argument brought forward when giving reasons for the admixture of deciduous tree species into coniferous forest stands is the amelioration and stabilization of biogeochemical cycles. An ecologically oriented silviculture relies on detailed knowledge about the ecosystem effects of practical measures. Thus, it focuses on the ‘amelioration potential' of a specific tree species with respect to changes of topsoil characteristics in typical monocultural situations. Up-to-now, few data is available concerning the percentages of deciduous species (degree of admixture) or type of admixture (single-tree, small or large groups) required to achieve desired effects, e.g. faster decomposition and incorporation of organic matter in the mineral soil. Thus, the objective of this study is (1) to analyze the impact of admixtures on topsoil properties and processes, and (2) to establish spatial models of such effects. The experiments are conducted in even-aged Norway spruce (Picea abies [L.] KARST.) stands with a variable admixture of Silver birch (Betula pendula Roth) in the Ore Mountains (Saxony, SE Germany). The approach starts with explanation of single-tree-effects and approves in a next step the enlargement to forest stand ("from-point-to-area-approach"). This attempt is expected to provide models with few parameters which can be used to modify the common exclusive growth models.

Classification and regression trees

Treesearch

G. G. Moisen

2008-01-01

Frequently, ecologists are interested in exploring ecological relationships, describing patterns and processes, or making spatial or temporal predictions. These purposes often can be addressed by modeling the relationship between some outcome or response and a set of features or explanatory variables.

Experimental quantification of radiocesium recycling in a coniferous tree after aerial contamination: Field loss dynamics, translocation and final partitioning.

PubMed

Thiry, Y; Garcia-Sanchez, L; Hurtevent, P

2016-09-01

After foliar interception of radioactive atmospheric fallout by forest trees, the short-term recycling dynamics of radiocesium from the tree to the soil as well as within the tree is a primary area of uncertainty in the modeling of the overall cycle. The partitioning of radiocesium transfers in a spruce tree exposed to aerial deposits was investigated during one growth season to reveal the dynamics and significance of underlying processes. The rate of radiocesium loss resulting from foliage leaching (wash-off) was shown to have a functional dependence on the frequency of rainy episodes in a first early stage (weathering 60% of initial contamination during 70 days) and on the amount of precipitation in a second stage (weathering 10% of initial deposits during the following 80 days). A classical single exponential decay model with offset and continuous time as predictor lead to a removal half-life t1/2 of intercepted radiocesium of 25 days. During the growth season, the similar pattern of the internal (134)Cs content in new shoots and initially contaminated foliage confirmed that radiocesium was readily absorbed from needle surfaces and efficiently translocated to growing organs. In the crown, a pool of non-leachable (134)Cs (15-30%) was associated with the abiotic layer covering the twigs and needle surfaces. At the end of the growth season, 30% of the initial deposits were relocated to different tree parts, including organs like stemwood (5%) and roots (6%) not directly exposed to deposition. At the scale of the tree, 84% of the residual activity was assimilated by living tissues which corresponds to a foliar absorption rate coefficient of 0.25 year(-1) for modeling purposes. According to the significant amount of radiocesium which can be incorporated in tree through foliar uptake, our results support the hypothesis that further internal transfers could supply the tree internal cycle of radiocesium extensively, and possibly mask the contribution of root uptake for a long time. Copyright © 2016 Elsevier Ltd. All rights reserved.

Estimating the probability of survival of individual shortleaf pine (Pinus echinata mill.) trees

Treesearch

Sudip Shrestha; Thomas B. Lynch; Difei Zhang; James M. Guldin

2012-01-01

A survival model is needed in a forest growth system which predicts the survival of trees on individual basis or on a stand basis (Gertner, 1989). An individual-tree modeling approach is one of the better methods available for predicting growth and yield as it provides essential information about particular tree species; tree size, tree quality and tree present status...

Toward the Decision Tree for Inferring Requirements Maturation Types

NASA Astrophysics Data System (ADS)

Nakatani, Takako; Kondo, Narihito; Shirogane, Junko; Kaiya, Haruhiko; Hori, Shozo; Katamine, Keiichi

Requirements are elicited step by step during the requirements engineering (RE) process. However, some types of requirements are elicited completely after the scheduled requirements elicitation process is finished. Such a situation is regarded as problematic situation. In our study, the difficulties of eliciting various kinds of requirements is observed by components. We refer to the components as observation targets (OTs) and introduce the word “Requirements maturation.” It means when and how requirements are elicited completely in the project. The requirements maturation is discussed on physical and logical OTs. OTs Viewed from a logical viewpoint are called logical OTs, e.g. quality requirements. The requirements of physical OTs, e.g., modules, components, subsystems, etc., includes functional and non-functional requirements. They are influenced by their requesters' environmental changes, as well as developers' technical changes. In order to infer the requirements maturation period of each OT, we need to know how much these factors influence the OTs' requirements maturation. According to the observation of actual past projects, we defined the PRINCE (Pre Requirements Intelligence Net Consideration and Evaluation) model. It aims to guide developers in their observation of the requirements maturation of OTs. We quantitatively analyzed the actual cases with their requirements elicitation process and extracted essential factors that influence the requirements maturation. The results of interviews of project managers are analyzed by WEKA, a data mining system, from which the decision tree was derived. This paper introduces the PRINCE model and the category of logical OTs to be observed. The decision tree that helps developers infer the maturation type of an OT is also described. We evaluate the tree through real projects and discuss its ability to infer the requirements maturation types.

Evaluation of DGVMs in tropical areas: linking patterns of vegetation cover, climate and fire to ecological processes

NASA Astrophysics Data System (ADS)

D'Onofrio, Donatella; von Hardenberg, Jost; Baudena, Mara

2017-04-01

Many current Dynamic Global Vegetation Models (DGVMs), including those incorporated into Earth System Models (ESMs), are able to realistically reproduce the distribution of the most worldwide biomes. However, they display high uncertainty in predicting the forest, savanna and grassland distributions and the transitions between them in tropical areas. These biomes are the most productive terrestrial ecosystems, and owing to their different biogeophysical and biogeochemical characteristics, future changes in their distributions could have also impacts on climate states. In particular, expected increasing temperature and CO2, modified precipitation regimes, as well as increasing land-use intensity could have large impacts on global biogeochemical cycles and precipitation, affecting the land-climate interactions. The difficulty of the DGVMs in simulating tropical vegetation, especially savanna structure and occurrence, has been associated with the way they represent the ecological processes and feedbacks between biotic and abiotic conditions. The inclusion of appropriate ecological mechanisms under present climatic conditions is essential for obtaining reliable future projections of vegetation and climate states. In this work we analyse observed relationships of tree and grass cover with climate and fire, and the current ecological understanding of the mechanisms driving the forest-savanna-grassland transition in Africa to evaluate the outcomes of a current state-of-the-art DGVM and to assess which ecological processes need to be included or improved within the model. Specifically, we analyse patterns of woody and herbaceous cover and fire return times from MODIS satellite observations, rainfall annual average and seasonality from TRMM satellite measurements and tree phenology information from the ESA global land cover map, comparing them with the outcomes of the LPJ-GUESS DGVM, also used by the EC-Earth global climate model. The comparison analysis with the LPJ-GUESS simulations suggests possible improvements in the model representations of tree-grass competition for water and in the vegetation-fire interaction. The proposed method could be useful for evaluating DGVMs in tropical areas, especially in the phase of model setting-up, before the coupling with Earth System Models. This could help in improving the simulations of ecological processes and consequently of land-climate interactions.

The dendroclimatic proxies from the northern Quebec taiga in the PAGES 2K network: recent advances and future developments.

NASA Astrophysics Data System (ADS)

Gennaretti, Fabio; Naulier, Maud; Arseneault, Dominique; Savard, Martine; Bégin, Christian; Boucher, Etienne; Bégin, Yves; Guiot, Joël

2016-04-01

Northeastern North America was historically underrepresented in the network of climate proxies used for climate reconstructions over the last two millennia. Indeed, in North America most high-resolution climate proxies are long tree-ring chronologies but, in Northeastern North America, these chronologies are highly challenging due to short tree longevity, high frequency and severity of wildfires and remoteness of many areas. Here, we will present the efforts accomplished during the last decade by our team in developing millennial-long tree-ring chronologies in the northern Quebec taiga. We sampled black spruce [Picea mariana (Mill.) B.S.P] subfossil tree remains naturally fallen in the littoral zone of six lakes to build six site-specific ring-width chronologies as well as two chronologies of stable isotope ratios (δ18O and δ13C in tree-ring cellulose). These chronologies, which are now included in the PAGES 2K network, were independently used to reconstruct summer temperature variations showing a well-expressed Medieval Climate Anomaly and the impact of volcanic and solar forcings at regional scale. We will also discuss non-climatic influences on these chronologies (i.e. wildfires and sampling height inconsistency), as well as the ongoing effort to extend the reconstructions in time to cover the last 2500 years. Finally, a new European funded project called MAIDEN-SPRUCE will be introduced. Within MAIDEN-SPRUCE, we will use a data-model approach to improve our understanding of the links between forests and climate over the last millennium. More specifically, we will adapt the process-based ecophysiological model MAIDENiso to investigate factors influencing the growth and underlying biogeochemical processes of black spruce. One of our objectives is to provide the first multi-proxy (ring widths and δ18O and δ13C in tree-ring cellulose) regional climate reconstruction in Eastern North America over the last millennium taking into account mechanistic rules, including nonlinear or threshold relationships.

Categorizing Ideas about Trees: A Tree of Trees

PubMed Central

Fisler, Marie; Lecointre, Guillaume

2013-01-01

The aim of this study is to explore whether matrices and MP trees used to produce systematic categories of organisms could be useful to produce categories of ideas in history of science. We study the history of the use of trees in systematics to represent the diversity of life from 1766 to 1991. We apply to those ideas a method inspired from coding homologous parts of organisms. We discretize conceptual parts of ideas, writings and drawings about trees contained in 41 main writings; we detect shared parts among authors and code them into a 91-characters matrix and use a tree representation to show who shares what with whom. In other words, we propose a hierarchical representation of the shared ideas about trees among authors: this produces a “tree of trees.” Then, we categorize schools of tree-representations. Classical schools like “cladists” and “pheneticists” are recovered but others are not: “gradists” are separated into two blocks, one of them being called here “grade theoreticians.” We propose new interesting categories like the “buffonian school,” the “metaphoricians,” and those using “strictly genealogical classifications.” We consider that networks are not useful to represent shared ideas at the present step of the study. A cladogram is made for showing who is sharing what with whom, but also heterobathmy and homoplasy of characters. The present cladogram is not modelling processes of transmission of ideas about trees, and here it is mostly used to test for proximity of ideas of the same age and for categorization. PMID:23950877

Tree Height and DBH Growth Model Establishment of Main Tree Species in Wuling Mountain Small Watershed

NASA Astrophysics Data System (ADS)

Luo, Jia; Zhang, Min; Zhou, Xiaoling; Chen, Jianhua; Tian, Yuxin

2018-01-01

Taken 4 main tree species in the Wuling mountain small watershed as research objects, 57 typical sample plots were set up according to the stand type, site conditions and community structure. 311 goal diameter-class sample trees were selected according to diameter-class groups of different tree-height grades, and the optimal fitting models of tree height and DBH growth of main tree species were obtained by stem analysis using Richard, Logistic, Korf, Mitscherlich, Schumacher, Weibull theoretical growth equations, and the correlation coefficient of all optimal fitting models reached above 0.9. Through the evaluation and test, the optimal fitting models possessed rather good fitting precision and forecast dependability.

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

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

Kumagai, Tomo'omi; Mudd, Ryan; Miyazawa, Yoshiyuki

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

Development of forest regeneration imputation models using permanent plots in Oregon and Washington

Treesearch

Karin Kralicek; Andrew Sánchez Meador; Leah Rathbun

2015-01-01

Imputation models were developed and tested to estimate tree regeneration on Forest Service land in Oregon and Washington. The models were based on Forest Inventory and Analysis and Pacific Northwest Regional NFS Monitoring data. The data was processed into sets of tables containing estimates of regeneration by broad plant associations and spanning a large variety in...

Distinguishing the Forest from the Trees: Synthesizing IHRMP Research

Treesearch

Gregory B. Greenwood

1991-01-01

A conceptual model of hardwood rangelands as multi-output resource system is developed and used to achieve a synthesis of Integrated Hardwood Range Management Program (IHRMP) research. The model requires the definition of state variables which characterize the system at any time, processes that move the system to different states, outputs...

The microcomputer scientific software series 6: ECOPHYS user's manual.

Treesearch

George E. Host; H. Michael Rauscher; J. G. Isebrands; Donald I. Dickmann; Richard E. Dickson; Thomas R. Crow; D.A. Michael

1990-01-01

ECOPHYS is an ecophysiological whole-tree growth process model designed to simulate the growth of poplar in the establishment year. This microcomputer-based model may be used to test the influence of genetically determined physiological or morphological attributes on plant growth. This manual describes the installation, file structures, and operational procedures for...

Modelling effects of tree population dynamics, tree throw and pit-mound formation/diffusion on microtopography over time in different forest settings

NASA Astrophysics Data System (ADS)

Martin, Y. E.; Johnson, E. A.; Gallaway, J.; Chaikina, O.

2011-12-01

Herein we conduct a followup investigation to an earlier research project in which we developed a numerical model of tree population dynamics, tree throw, and sediment transport associated with the formation of pit-mound features for Hawk Creek watershed, Canadian Rockies (Gallaway et al., 2009). We extend this earlier work by exploring the most appropriate transport relations to simulate the diffusion over time of newly-formed pit-pound features due to tree throw. We combine our earlier model with a landscape development model that can incorporate these diffusive transport relations. Using these combined models, changes in hillslope microtopography over time associated with the formation of pit-mound features and their decay will be investigated. The following ideas have motivated this particular study: (i) Rates of pit-mound degradation remain a source of almost complete speculation, as there is almost no long-term information on process rates. Therefore, we will attempt to tackle the issue of pit-mound degradation in a methodical way that can guide future field studies; (ii) The degree of visible pit-mound topography at any point in time on the landscape is a joint function of the rate of formation of new pit-mound features due to tree death/topple and their magnitude vs. the rate of decay of pit-mound features. An example of one interesting observation that arises is the following: it appears that pit-mound topography is often more pronounced in some eastern North American forests vs. field sites along the eastern slopes of the Canadian Rockies. Why is this the case? Our investigation begins by considering whether pit-mound decay might occur by linear or nonlinear diffusion. What differences might arise depending on which diffusive approach is adopted? What is the magnitude of transport rates associated with these possible forms of transport relations? We explore linear and nonlinear diffusion at varying rates and for different sizes of pit-mound pairs using a numerical modelling approach. Model results suggest that longevity of pit-mound features is dependent on: (i) magnitude/dimensions of initial pit-mound features for forests in different regions; (ii) defining appropriate pit-mound diffusion rates for these different forests (unfortunately, almost no appropriate field observations exist for calibration of these transport relations). In the next stage of this research, we will combine our earlier model of forest disturbance/tree population dynamics, tree throw and pit-mound formation with the numerical model LandMod (Martin, 1998, 2000, 2007); the latter will be used to simulate pit-mound diffusion over time. In this way, we can observe changes in hillslope microtopographic signatures over time that are found in different forest settings.

Differential Diagnosis of Erythmato-Squamous Diseases Using Classification and Regression Tree.

PubMed

Maghooli, Keivan; Langarizadeh, Mostafa; Shahmoradi, Leila; Habibi-Koolaee, Mahdi; Jebraeily, Mohamad; Bouraghi, Hamid

2016-10-01

Differential diagnosis of Erythmato-Squamous Diseases (ESD) is a major challenge in the field of dermatology. The ESD diseases are placed into six different classes. Data mining is the process for detection of hidden patterns. In the case of ESD, data mining help us to predict the diseases. Different algorithms were developed for this purpose. we aimed to use the Classification and Regression Tree (CART) to predict differential diagnosis of ESD. we used the Cross Industry Standard Process for Data Mining (CRISP-DM) methodology. For this purpose, the dermatology data set from machine learning repository, UCI was obtained. The Clementine 12.0 software from IBM Company was used for modelling. In order to evaluation of the model we calculate the accuracy, sensitivity and specificity of the model. The proposed model had an accuracy of 94.84% (. 24.42) in order to correct prediction of the ESD disease. Results indicated that using of this classifier could be useful. But, it would be strongly recommended that the combination of machine learning methods could be more useful in terms of prediction of ESD.

Comparison of Ordinal and Nominal Classification Trees to Predict Ordinal Expert-Based Occupational Exposure Estimates in a Case–Control Study

PubMed Central

Wheeler, David C.; Archer, Kellie J.; Burstyn, Igor; Yu, Kai; Stewart, Patricia A.; Colt, Joanne S.; Baris, Dalsu; Karagas, Margaret R.; Schwenn, Molly; Johnson, Alison; Armenti, Karla; Silverman, Debra T.; Friesen, Melissa C.

2015-01-01

Objectives: To evaluate occupational exposures in case–control studies, exposure assessors typically review each job individually to assign exposure estimates. This process lacks transparency and does not provide a mechanism for recreating the decision rules in other studies. In our previous work, nominal (unordered categorical) classification trees (CTs) generally successfully predicted expert-assessed ordinal exposure estimates (i.e. none, low, medium, high) derived from occupational questionnaire responses, but room for improvement remained. Our objective was to determine if using recently developed ordinal CTs would improve the performance of nominal trees in predicting ordinal occupational diesel exhaust exposure estimates in a case–control study. Methods: We used one nominal and four ordinal CT methods to predict expert-assessed probability, intensity, and frequency estimates of occupational diesel exhaust exposure (each categorized as none, low, medium, or high) derived from questionnaire responses for the 14983 jobs in the New England Bladder Cancer Study. To replicate the common use of a single tree, we applied each method to a single sample of 70% of the jobs, using 15% to test and 15% to validate each method. To characterize variability in performance, we conducted a resampling analysis that repeated the sample draws 100 times. We evaluated agreement between the tree predictions and expert estimates using Somers’ d, which measures differences in terms of ordinal association between predicted and observed scores and can be interpreted similarly to a correlation coefficient. Results: From the resampling analysis, compared with the nominal tree, an ordinal CT method that used a quadratic misclassification function and controlled tree size based on total misclassification cost had a slightly better predictive performance that was statistically significant for the frequency metric (Somers’ d: nominal tree = 0.61; ordinal tree = 0.63) and similar performance for the probability (nominal = 0.65; ordinal = 0.66) and intensity (nominal = 0.65; ordinal = 0.65) metrics. The best ordinal CT predicted fewer cases of large disagreement with the expert assessments (i.e. no exposure predicted for a job with high exposure and vice versa) compared with the nominal tree across all of the exposure metrics. For example, the percent of jobs with expert-assigned high intensity of exposure that the model predicted as no exposure was 29% for the nominal tree and 22% for the best ordinal tree. Conclusions: The overall agreements were similar across CT models; however, the use of ordinal models reduced the magnitude of the discrepancy when disagreements occurred. As the best performing model can vary by situation, researchers should consider evaluating multiple CT methods to maximize the predictive performance within their data. PMID:25433003

Modeling Missing Remeasurement Tree Heights in Forest Inventory Data

Treesearch

Raymond M. Sheffield; Callie J. Schweitzer

2005-01-01

Missing tree heights are often problematic in compiling forest inventory remeasurement data. Heights for cut and mortality trees are usually not available; calculations of removal or mortality volumes must utilize either a modeled height at the time of tree death or the height assigned to the tree at a previous remeasurement. Less often, tree heights are not available...

Modeling missing remeasurement tree heights in forest inventory data

Treesearch

Raymond M. Sheffield; Callie J. Schweitzer

2002-01-01

Missing tree heights are often problematic in compiling forest inventory renleasureinent data. Heights for cut and niortality trees are usually not available; calculations of removal or mortality volumes must utilize either a modeled height at the time of tree death or the height assigned to the tree at a previous remeasurement. Less often, tree heights are not...

Mistletoe infection alters the transpiration flow path and suppresses water regulation of host trees during extreme events

NASA Astrophysics Data System (ADS)

Griebel, A.; Maier, C.; Barton, C. V.; Metzen, D.; Renchon, A.; Boer, M. M.; Pendall, E.

2017-12-01

Mistletoe is a globally distributed group of parasitic plants that infiltrates the vascular tissue of its host trees to acquire water, carbon and nutrients, making it a leading agent of biotic disturbance. Many mistletoes occur in water-limited ecosystems, thus mistletoe infection in combination with increased climatic stress may exacerbate water stress and potentially accelerate mortality rates of infected trees during extreme events. This is an emerging problem in Australia, as mistletoe distribution is increasing and clear links between mistletoe infection and mortality have been established. However, direct observations about how mistletoes alter host physiological processes during extreme events are rare, which impedes our understanding of mechanisms underlying increased tree mortality rates. We addressed this gap by continuously monitoring stem and branch sap flow and a range of leaf traits of infected and uninfected trees of two co-occurring eucalypt species during a severe heatwave in south-eastern Australia. We demonstrate that mistletoes' leaf water potentials were maintained 30% lower than hosts' to redirect the trees' transpiration flow path towards mistletoe leaves. Eucalypt leaves reduced water loss through stomatal regulation when atmospheric dryness exceeded 2 kPa, but the magnitude of stomatal regulation in non-infected eucalypts differed by species (between 40-80%). Remarkably, when infected, sap flow rates of stems and branches of both eucalypt species remained unregulated even under extreme atmospheric dryness (>8 kPa). Our observations indicate that excessive water use of mistletoes likely increases xylem cavitation rates in hosts during prolonged droughts and supports that hydraulic failure contributes to increased mortality of infected trees. Hence, in order to accurately model the contribution of biotic disturbances to tree mortality under a changing climate, it will be crucial to increase our process-based understanding of the interaction between biotic and abiotic dynamics, especially to establish thresholds of critical cavitation rates of infected trees.

Street trees reduce the negative effects of urbanization on birds

PubMed Central

2017-01-01

The effects of streets on biodiversity is an important aspect of urban ecology, but it has been neglected worldwide. Several vegetation attributes (e.g. street tree density and diversity) have important effects on biodiversity and ecological processes. In this study, we evaluated the influences of urban vegetation—represented by characteristics of street trees (canopy size, proportion of native tree species and tree species richness)—and characteristics of the landscape (distance to parks and vegetation quantity), and human impacts (human population size and exposure to noise) on taxonomic data and functional diversity indices of the bird community inhabiting streets. The study area was the southern region of Belo Horizonte (Minas Gerais, Brazil), a largely urbanized city in the understudied Neotropical region. Bird data were collected on 60 point count locations distributed across the streets of the landscape. We used a series of competing GLM models (using Akaike's information criterion for small sample sizes) to assess the relative contribution of the different sets of variables to explain the observed patterns. Seventy-three bird species were observed exploiting the streets: native species were the most abundant and frequent throughout this landscape. The bird community's functional richness and Rao's Quadratic Entropy presented values lower than 0.5. Therefore, this landscape was favoring few functional traits. Exposure to noise was the most limiting factor for this bird community. However, the average size of arboreal patches and, especially the characteristics of street trees, were able to reduce the negative effects of noise on the bird community. These results show the importance of adequately planning the urban afforestation process: increasing tree species richness, preserving large trees and planting more native trees species in the streets are management practices that will increase bird species richness, abundance and community functional aspects and consequently improve human wellbeing and quality of life. PMID:28333989

A Simple Model for Estimating Total and Merchantable Tree Heights

Treesearch

Alan R. Ek; Earl T. Birdsall; Rebecca J. Spears

1984-01-01

A model is described for estimating total and merchantable tree heights for Lake States tree species. It is intended to be used for compiling forest survey data and in conjunction with growth models for developing projections of tree product yield. Model coefficients are given for 25 species along with fit statistics. Supporting data sets are also described.

A discrete element modelling approach for block impacts on trees

NASA Astrophysics Data System (ADS)

Toe, David; Bourrier, Franck; Olmedo, Ignatio; Berger, Frederic

2015-04-01

These past few year rockfall models explicitly accounting for block shape, especially those using the Discrete Element Method (DEM), have shown a good ability to predict rockfall trajectories. Integrating forest effects into those models still remain challenging. This study aims at using a DEM approach to model impacts of blocks on trees and identify the key parameters controlling the block kinematics after the impact on a tree. A DEM impact model of a block on a tree was developed and validated using laboratory experiments. Then, key parameters were assessed using a global sensitivity analyse. Modelling the impact of a block on a tree using DEM allows taking into account large displacements, material non-linearities and contacts between the block and the tree. Tree stems are represented by flexible cylinders model as plastic beams sustaining normal, shearing, bending, and twisting loading. Root soil interactions are modelled using a rotation stiffness acting on the bending moment at the bottom of the tree and a limit bending moment to account for tree overturning. The crown is taken into account using an additional mass distribute uniformly on the upper part of the tree. The block is represented by a sphere. The contact model between the block and the stem consists of an elastic frictional model. The DEM model was validated using laboratory impact tests carried out on 41 fresh beech (Fagus Sylvatica) stems. Each stem was 1,3 m long with a diameter between 3 to 7 cm. Wood stems were clamped on a rigid structure and impacted by a 149 kg charpy pendulum. Finally an intensive simulation campaign of blocks impacting trees was done to identify the input parameters controlling the block kinematics after the impact on a tree. 20 input parameters were considered in the DEM simulation model : 12 parameters were related to the tree and 8 parameters to the block. The results highlight that the impact velocity, the stem diameter, and the block volume are the three input parameters that control the block kinematics after impact.

HyDe: a Python Package for Genome-Scale Hybridization Detection.

PubMed

Blischak, Paul D; Chifman, Julia; Wolfe, Andrea D; Kubatko, Laura S

2018-03-19

The analysis of hybridization and gene flow among closely related taxa is a common goal for researchers studying speciation and phylogeography. Many methods for hybridization detection use simple site pattern frequencies from observed genomic data and compare them to null models that predict an absence of gene flow. The theory underlying the detection of hybridization using these site pattern probabilities exploits the relationship between the coalescent process for gene trees within population trees and the process of mutation along the branches of the gene trees. For certain models, site patterns are predicted to occur in equal frequency (i.e., their difference is 0), producing a set of functions called phylogenetic invariants. In this paper we introduce HyDe, a software package for detecting hybridization using phylogenetic invariants arising under the coalescent model with hybridization. HyDe is written in Python, and can be used interactively or through the command line using pre-packaged scripts. We demonstrate the use of HyDe on simulated data, as well as on two empirical data sets from the literature. We focus in particular on identifying individual hybrids within population samples and on distinguishing between hybrid speciation and gene flow. HyDe is freely available as an open source Python package under the GNU GPL v3 on both GitHub (https://github.com/pblischak/HyDe) and the Python Package Index (PyPI: https://pypi.python.org/pypi/phyde).

Determination of Tree and Understory Water Sources and Residence Times Using Stable Isotopes in a Southern Appalachian Forest

NASA Astrophysics Data System (ADS)

Stewart, A. N.; Knoepp, J.; Miniat, C.; Oishi, A. C.; Emanuel, R. E.

2017-12-01

The development of accurate hydrologic models is key to describing changes in hydrologic processes due to land use and climate change. Hydrologic models typically simplify biological processes associated with plant water uptake and transpiration, assuming that roots take up water from the same moisture pool that feeds the stream; however, this assumption is not valid for all systems. Novel combinations of climate and forest composition and structure, caused by ecosystem succession, management decisions, and climate variability, will require a better understanding of sources of water for transpiration in order to accurately estimate impact on forest water yield. Here we examine red maple (Acer rubrum), rhododendron (Rhododendron maximum), tulip poplar (Liriodendron tulipifera), and white oak (Quercus alba) trees at Coweeta Hydrologic Laboratory, a long-term hydrological and ecological research site in western NC, USA, and explore whether source water use differs by species and landscape position. We analyzed stable isotopes of water (18O and 2H) in tree cores, stream water, soil water, and precipitation using laser spectrometry and compare the isotopic composition of the various pools. We place these results in broader context using meteorological and ecophysiological data collected nearby. These findings have implications for plant water stress and drought vulnerability. They also contribute to process-based knowledge of plant water use that better captures the sensitivity of transpiration to physical and biological controls at the sub-catchment scale. This work aims to help establish novel ways to model transpiration and improve understanding of water balance, biogeochemical cycling, and transport of nutrients to streams.

Drivers of leaf carbon exchange capacity across biomes at the continental scale.

PubMed

Smith, Nicholas G; Dukes, Jeffrey S

2018-04-29

Realistic representations of plant carbon exchange processes are necessary to reliably simulate biosphere-atmosphere feedbacks. These processes are known to vary over time and space, though the drivers of the underlying rates are still widely debated in the literature. Here, we measured leaf carbon exchange in >500 individuals of 98 species from the Neotropics to high boreal biomes to determine the drivers of photosynthetic and dark respiration capacity. Covariate abiotic (long- and short-term climate) and biotic (plant type, plant size, ontogeny, water status) data were used to explore significant drivers of temperature-standardized leaf carbon exchange rates. Using model selection, we found the previous week's temperature and soil moisture at the time of measurement to be a better predictor of photosynthetic capacity than long-term climate, with the combination of high recent temperatures and low soil moisture tending to decrease photosynthetic capacity. Non-trees (annual and perennials) tended to have greater photosynthetic capacity than trees, and, within trees, adults tended to have greater photosynthetic capacity than juveniles, possibly as a result of differences in light availability. Dark respiration capacity was less responsive to the assessed drivers than photosynthetic capacity, with rates best predicted by multi-year average site temperature alone. Our results suggest that, across large spatial scales, photosynthetic capacity quickly adjusts to changing environmental conditions, namely light, temperature, and soil moisture. Respiratory capacity is more conservative and most responsive to longer-term conditions. Our results provide a framework for incorporating these processes into large-scale models and a data set to benchmark such models. © 2018 by the Ecological Society of America.

A dynamic fault tree model of a propulsion system

NASA Technical Reports Server (NTRS)

Xu, Hong; Dugan, Joanne Bechta; Meshkat, Leila

2006-01-01

We present a dynamic fault tree model of the benchmark propulsion system, and solve it using Galileo. Dynamic fault trees (DFT) extend traditional static fault trees with special gates to model spares and other sequence dependencies. Galileo solves DFT models using a judicious combination of automatically generated Markov and Binary Decision Diagram models. Galileo easily handles the complexities exhibited by the benchmark problem. In particular, Galileo is designed to model phased mission systems.

The influence of prefire tree growth and crown condition on postfire mortality of sugar pine following prescribed fire in Sequoia National Park

USGS Publications Warehouse

Nesmith, Jonathan C. B.; Das, Adrian J.; O'Hara, Kevin L.; van Mantgem, Phillip J.

2015-01-01

Tree mortality is a vital component of forest management in the context of prescribed fires; however, few studies have examined the effect of prefire tree health on postfire mortality. This is especially relevant for sugar pine (Pinus lambertiana Douglas), a species experiencing population declines due to a suite of anthropogenic factors. Using data from an old-growth mixed-conifer forest in Sequoia National Park, we evaluated the effects of fire, tree size, prefire radial growth, and crown condition on postfire mortality. Models based only on tree size and measures of fire damage were compared with models that included tree size, fire damage, and prefire tree health (e.g., measures of prefire tree radial growth or crown condition). Immediately following the fire, the inclusion of different metrics of prefire tree health produced variable improvements over the models that included only tree size and measures of fire damage, as models that included measures of crown condition performed better than fire-only models, but models that included measures of prefire radial growth did not perform better. However, 5 years following the fire, sugar pine mortality was best predicted by models that included measures of both fire damage and prefire tree health, specifically, diameter at breast height (DBH, 1.37 m), crown scorch, 30-year mean growth, and the number of sharp declines in growth over a 30-year period. This suggests that factors that influence prefire tree health (e.g., drought, competition, pathogens, etc.) may partially determine postfire mortality, especially when accounting for delayed mortality following fire.

Tree-mediated methane emissions from tropical and temperate peatlands.

NASA Astrophysics Data System (ADS)

Pangala, S. R.; Gauci, V.; Hornibrook, E. R. C.; Gowing, D. J.

2012-04-01

Methane production and transport processes in peatlands are fairly well understood, but growing evidence for emission of methane through trees has highlighted the need to revisit methane transport processes. In wetland trees, morphological adaptations such as development of hypertrophied lenticels, aerenchyma and adventitious roots in response to soil anoxia mediates gas transport, transporting both oxygen from the atmosphere to oxygen-deprived roots and soil-produced methane from the root-zone to the atmosphere. Although, tree-mediated methane emissions from temperate tree species have been confirmed, methane emissions from tropical tree species and processes that control tree-mediated methane emissions remain unclear. This study explains the role of trees in transporting soil-produced methane to the atmosphere and uncovers the principal mechanisms of tree-mediated methane emissions. Methane emissions from eight tropical tree species and two temperate tree species were studied in situ. The mechanisms and controls on tree-mediated methane emissions were investigated using three year old common alder (Alnus glutinosa; 50 trees) grown under two artificially controlled water-table positions. Methane fluxes from whole mesocosms, the soil surface and tree stems were measured using static closed chambers. Both temperate and tropical tree species released significant quantities of methane, with tropical trees dominating ecosystem level methane fluxes. In temperate peatlands, both the methane gas transport mechanism and quantity of methane emitted from stems is tree-species dependent. In Alnus glutinosa, no correlations were observed between stomatal behaviour and tree-mediated methane emissions, however, stem methane emissions were positively correlated with both stem lenticel density and dissolved soil methane concentration. In Alnus glutinosa, no emissions were observed from leaf surfaces. The results demonstrate that exclusion of tree-mediated methane emissions from flux measurement campaigns in forested peatlands will lead to an underestimation of ecosystem-wide methane emissions.

Systematic Model-in-the-Loop Test of Embedded Control Systems

NASA Astrophysics Data System (ADS)

Krupp, Alexander; Müller, Wolfgang

Current model-based development processes offer new opportunities for verification automation, e.g., in automotive development. The duty of functional verification is the detection of design flaws. Current functional verification approaches exhibit a major gap between requirement definition and formal property definition, especially when analog signals are involved. Besides lack of methodical support for natural language formalization, there does not exist a standardized and accepted means for formal property definition as a target for verification planning. This article addresses several shortcomings of embedded system verification. An Enhanced Classification Tree Method is developed based on the established Classification Tree Method for Embeded Systems CTM/ES which applies a hardware verification language to define a verification environment.

Stimulating seedling growth in early stages of secondary forest succession: a modeling approach to guide tree liberation

PubMed Central

van Kuijk, Marijke; Anten, Niels P. R.; Oomen, Roelof J.; Schieving, Feike

2014-01-01

Excessive growth of non-woody plants and shrubs on degraded lands can strongly hamper tree growth and thus secondary forest succession. A common method to accelerate succession, called liberation, involves opening up the vegetation canopy around young target trees. This can increase growth of target trees by reducing competition for light with neighboring plants. However, liberation has not always had the desired effect, likely due to differences in light requirement between tree species. Here we present a 3D-model, which calculates photosynthetic rate of individual trees in a vegetation stand. It enables us to examine how stature, crown structure, and physiological traits of target trees and characteristics of the surrounding vegetation together determine effects of light on tree growth. The model was applied to a liberation experiment conducted with three pioneer species in a young secondary forest in Vietnam. Species responded differently to the treatment depending on their height, crown structure and their shade-tolerance level. Model simulations revealed practical thresholds over which the tree growth response is heavily influenced by the height and density of surrounding vegetation and gap radius. There were strong correlations between calculated photosynthetic rates and observed growth: the model was well able to predict growth of trees in young forests and the effects of liberation there upon. Thus, our model serves as a useful tool to analyze light competition between young trees and surrounding vegetation and may help assess the potential effect of tree liberation. PMID:25101100

Populus: arabidopsis for forestry. Do we need a model tree?

PubMed

Taylor, Gail

2002-12-01

Trees are used to produce a variety of wood-based products including timber, pulp and paper. More recently, their use as a source of renewable energy has also been highlighted, as has their value for carbon mitigation within the Kyoto Protocol. Relative to food crops, the domestication of trees has only just begun; the long generation time and complex nature of juvenile and mature growth forms are contributory factors. To accelerate domestication, and to understand further some of the unique processes that occur in woody plants such as dormancy and secondary wood formation, a 'model' tree is needed. Here it is argued that Populus is rapidly becoming accepted as the 'model' woody plant and that such a 'model' tree is necessary to complement the genetic resource being developed in arabidopsis. The genus Populus (poplars, cottonwoods and aspens) contains approx. 30 species of woody plant, all found in the Northern hemisphere and exhibiting some of the fastest growth rates observed in temperate trees. Populus is fulfilling the 'model' role for a number of reasons. First, and most important, is the very recent commitment to sequence the Populus genome, a project initiated in February 2002. This will be the first woody plant to be sequenced. Other reasons include the relatively small genome size (450-550 Mbp) of Populus, the large number of molecular genetic maps and the ease of genetic transformation. Populus may also be propagated vegetatively, making mapping populations immortal and facilitating the production of large amounts of clonal material for experimentation. Hybridization occurs routinely and, in these respects, Populus has many similarities to arabidopsis. However, Populus also differs from arabidopsis in many respects, including being dioecious, which makes selfing and back-cross manipulations impossible. The long time-to-flower is also a limitation, whilst physiological and biochemical experiments are more readily conducted in Populus compared with the small-statured arabidopsis. Recent advances in the development of large expressed sequence tagged collections, microarray analysis and the free distribution of mapping pedigrees for quantitative trait loci analysis secure Populus as the ideal subject for further exploitation by a wide range of scientists including breeders, physiologists, biochemists and molecular biologists. In addition, and in contrast to other model plants, the genus Populus also has genuine commercial value as a tree for timber, plywood, pulp and paper. Copyright 2002 Annals of Botany Company

Boron deficiency in woody plants: various responses and tolerance mechanisms

PubMed Central

Wang, Nannan; Yang, Chengquan; Pan, Zhiyong; Liu, Yongzhong; Peng, Shu’ang

2015-01-01

Boron (B) is an essential microelement for higher plants, and its deficiency is widespread around the world and constrains the productivity of both agriculture and forestry. In the last two decades, numerous studies on model or herbaceous plants have contributed greatly to our understanding of the complex network of B-deficiency responses and mechanisms for tolerance. In woody plants, however, fewer studies have been conducted and they have not well been recently synthesized or related to the findings on model species on B transporters. Trees have a larger body size, longer lifespan and more B reserves than do herbaceous plants, indicating that woody species might undergo long-term or mild B deficiency more commonly and that regulation of B reserves helps trees cope with B deficiency. In addition, the highly heterozygous genetic background of tree species suggests that they may have more complex mechanisms of response and tolerance to B deficiency than do model plants. Boron-deficient trees usually exhibit two key visible symptoms: depression of growing points (root tip, bud, flower, and young leaf) and deformity of organs (root, shoot, leaf, and fruit). These symptoms may be ascribed to B functioning in the cell wall and membrane, and particularly to damage to vascular tissues and the suppression of both B and water transport. Boron deficiency also affects metabolic processes such as decreased leaf photosynthesis, and increased lignin and phenol content in trees. These negative effects will influence the quality and quantity of wood, fruit and other agricultural products. Boron efficiency probably originates from a combined effect of three processes: B uptake, B translocation and retranslocation, and B utilization. Root morphology and mycorrhiza can affect the B uptake efficiency of trees. During B translocation from the root to shoot, differences in B concentration between root cell sap and xylem exudate, as well as water use efficiency, may play key roles in tolerance to B deficiency. In addition, B retranslocation efficiency primarily depends on the extent of xylem-to-phloem transfer and the variety and amount of cis-diol moieties in the phloem. The B requirement for cell wall construction also contribute to the B use efficiency in trees. The present review will provide an update on the physiological and molecular responses and tolerance mechanisms to B deficiency in woody plants. Emphasis is placed on the roles of B reserves that are more important for tolerance to B deficiency in trees than in herbaceous plants and the possible physiological and molecular mechanisms of differential B efficiency in trees. We propose that B may be used to study the relationship between the cell wall and the membrane via the B-bridge. Transgenic B-efficient tree cultivars have considerable potential for forestry or fruit rootstock production on low B soils in the future. PMID:26579163

The Galactic Chemical Evolution of r-Process Elements by Neutron Star Mergers

NASA Astrophysics Data System (ADS)

Komiya, Yutaka; Shigeyama, Toshikazu

Neutron star mergers (NSMs) are prime candidate sources of r-process elements in the universe but it have been said that NSMs cannot reproduce r-process elements on extremely metal-poor (EMP) stars. We revisit this problem using a new chemical evolution model with merger trees of galaxies. We consider (1) propagation of NSM ejecta of kilo-parsec scale due to its very large velocity and (2) star formation efficiency depending on the galaxy mass. In our model with these ingredients, NSMs can successfully reproduce the abundance distribution of EMP stars.

Modeling and experimental characterization of electromigration in interconnect trees

NASA Astrophysics Data System (ADS)

Thompson, C. V.; Hau-Riege, S. P.; Andleigh, V. K.

1999-11-01

Most modeling and experimental characterization of interconnect reliability is focussed on simple straight lines terminating at pads or vias. However, laid-out integrated circuits often have interconnects with junctions and wide-to-narrow transitions. In carrying out circuit-level reliability assessments it is important to be able to assess the reliability of these more complex shapes, generally referred to as `trees.' An interconnect tree consists of continuously connected high-conductivity metal within one layer of metallization. Trees terminate at diffusion barriers at vias and contacts, and, in the general case, can have more than one terminating branch when they include junctions. We have extended the understanding of `immortality' demonstrated and analyzed for straight stud-to-stud lines, to trees of arbitrary complexity. This leads to a hierarchical approach for identifying immortal trees for specific circuit layouts and models for operation. To complete a circuit-level-reliability analysis, it is also necessary to estimate the lifetimes of the mortal trees. We have developed simulation tools that allow modeling of stress evolution and failure in arbitrarily complex trees. We are testing our models and simulations through comparisons with experiments on simple trees, such as lines broken into two segments with different currents in each segment. Models, simulations and early experimental results on the reliability of interconnect trees are shown to be consistent.

Demographic threats to the sustainability of Brazil nut exploitation.

PubMed

Peres, Carlos A; Baider, Claudia; Zuidema, Pieter A; Wadt, Lúcia H O; Kainer, Karen A; Gomes-Silva, Daisy A P; Salomão, Rafael P; Simões, Luciana L; Franciosi, Eduardo R N; Cornejo Valverde, Fernando; Gribel, Rogério; Shepard, Glenn H; Kanashiro, Milton; Coventry, Peter; Yu, Douglas W; Watkinson, Andrew R; Freckleton, Robert P

2003-12-19

A comparative analysis of 23 populations of the Brazil nut tree (Bertholletia excelsa) across the Brazilian, Peruvian, and Bolivian Amazon shows that the history and intensity of Brazil nut exploitation are major determinants of population size structure. Populations subjected to persistent levels of harvest lack juvenile trees less than 60 centimeters in diameter at breast height; only populations with a history of either light or recent exploitation contain large numbers of juvenile trees. A harvesting model confirms that intensive exploitation levels over the past century are such that juvenile recruitment is insufficient to maintain populations over the long term. Without management, intensively harvested populations will succumb to a process of senescence and demographic collapse, threatening this cornerstone of the Amazonian extractive economy.

Prediction and measurement of thermally induced cambial tissue necrosis in tree stems

Treesearch

Joshua L. Jones; Brent W. Webb; Bret W. Butler; Matthew B. Dickinson; Daniel Jimenez; James Reardon; Anthony S. Bova

2006-01-01

A model for fire-induced heating in tree stems is linked to a recently reported model for tissue necrosis. The combined model produces cambial tissue necrosis predictions in a tree stem as a function of heating rate, heating time, tree species, and stem diameter. Model accuracy is evaluated by comparison with experimental measurements in two hardwood and two softwood...

A stochastic simulator of birth-death master equations with application to phylodynamics.

PubMed

Vaughan, Timothy G; Drummond, Alexei J

2013-06-01

In this article, we present a versatile new software tool for the simulation and analysis of stochastic models of population phylodynamics and chemical kinetics. Models are specified via an expressive and human-readable XML format and can be used as the basis for generating either single population histories or large ensembles of such histories. Importantly, phylogenetic trees or networks can be generated alongside the histories they correspond to, enabling investigations into the interplay between genealogies and population dynamics. Summary statistics such as means and variances can be recorded in place of the full ensemble, allowing for a reduction in the amount of memory used--an important consideration for models including large numbers of individual subpopulations or demes. In the case of population size histories, the resulting simulation output is written to disk in the flexible JSON format, which is easily read into numerical analysis environments such as R for visualization or further processing. Simulated phylogenetic trees can be recorded using the standard Newick or NEXUS formats, with extensions to these formats used for non-tree-like inheritance relationships.

A Stochastic Simulator of Birth–Death Master Equations with Application to Phylodynamics

PubMed Central

Vaughan, Timothy G.; Drummond, Alexei J.

2013-01-01

In this article, we present a versatile new software tool for the simulation and analysis of stochastic models of population phylodynamics and chemical kinetics. Models are specified via an expressive and human-readable XML format and can be used as the basis for generating either single population histories or large ensembles of such histories. Importantly, phylogenetic trees or networks can be generated alongside the histories they correspond to, enabling investigations into the interplay between genealogies and population dynamics. Summary statistics such as means and variances can be recorded in place of the full ensemble, allowing for a reduction in the amount of memory used—an important consideration for models including large numbers of individual subpopulations or demes. In the case of population size histories, the resulting simulation output is written to disk in the flexible JSON format, which is easily read into numerical analysis environments such as R for visualization or further processing. Simulated phylogenetic trees can be recorded using the standard Newick or NEXUS formats, with extensions to these formats used for non-tree-like inheritance relationships. PMID:23505043

Graphical workstation capability for reliability modeling

NASA Technical Reports Server (NTRS)

Bavuso, Salvatore J.; Koppen, Sandra V.; Haley, Pamela J.

1992-01-01

In addition to computational capabilities, software tools for estimating the reliability of fault-tolerant digital computer systems must also provide a means of interfacing with the user. Described here is the new graphical interface capability of the hybrid automated reliability predictor (HARP), a software package that implements advanced reliability modeling techniques. The graphics oriented (GO) module provides the user with a graphical language for modeling system failure modes through the selection of various fault-tree gates, including sequence-dependency gates, or by a Markov chain. By using this graphical input language, a fault tree becomes a convenient notation for describing a system. In accounting for any sequence dependencies, HARP converts the fault-tree notation to a complex stochastic process that is reduced to a Markov chain, which it can then solve for system reliability. The graphics capability is available for use on an IBM-compatible PC, a Sun, and a VAX workstation. The GO module is written in the C programming language and uses the graphical kernal system (GKS) standard for graphics implementation. The PC, VAX, and Sun versions of the HARP GO module are currently in beta-testing stages.

The probability of monophyly of a sample of gene lineages on a species tree

PubMed Central

Mehta, Rohan S.; Bryant, David; Rosenberg, Noah A.

2016-01-01

Monophyletic groups—groups that consist of all of the descendants of a most recent common ancestor—arise naturally as a consequence of descent processes that result in meaningful distinctions between organisms. Aspects of monophyly are therefore central to fields that examine and use genealogical descent. In particular, studies in conservation genetics, phylogeography, population genetics, species delimitation, and systematics can all make use of mathematical predictions under evolutionary models about features of monophyly. One important calculation, the probability that a set of gene lineages is monophyletic under a two-species neutral coalescent model, has been used in many studies. Here, we extend this calculation for a species tree model that contains arbitrarily many species. We study the effects of species tree topology and branch lengths on the monophyly probability. These analyses reveal new behavior, including the maintenance of nontrivial monophyly probabilities for gene lineage samples that span multiple species and even for lineages that do not derive from a monophyletic species group. We illustrate the mathematical results using an example application to data from maize and teosinte. PMID:27432988

Rainfall interception by tree crown and leaf litter: an interactive process

Treesearch

Xiang Li; Qingfu Xiao; Jianzhi Niu; Salli Dymond; E. Gregory McPherson; Natalie van Doorn; Xinxiao Yu; Baoyuan Xie; Kebin Zhang; Jiao Li

2017-01-01

Rainfall interception research in forest ecosystems usually focuses on interception by either tree crown or leaf litter, although the 2 components interact when rainfall occurs. A process-based study was conducted to jointly measure rainfall interception by crown and litter and the interaction between the 2 interception processes for 4 tree species (...

Emergent climate and CO2 sensitivities of net primary productivity in ecosystem models do not agree with empirical data in temperate forests of eastern North America.

PubMed

Rollinson, Christine R; Liu, Yao; Raiho, Ann; Moore, David J P; McLachlan, Jason; Bishop, Daniel A; Dye, Alex; Matthes, Jaclyn H; Hessl, Amy; Hickler, Thomas; Pederson, Neil; Poulter, Benjamin; Quaife, Tristan; Schaefer, Kevin; Steinkamp, Jörg; Dietze, Michael C

2017-07-01

Ecosystem models show divergent responses of the terrestrial carbon cycle to global change over the next century. Individual model evaluation and multimodel comparisons with data have largely focused on individual processes at subannual to decadal scales. Thus far, data-based evaluations of emergent ecosystem responses to climate and CO 2 at multidecadal and centennial timescales have been rare. We compared the sensitivity of net primary productivity (NPP) to temperature, precipitation, and CO 2 in ten ecosystem models with the sensitivities found in tree-ring reconstructions of NPP and raw ring-width series at six temperate forest sites. These model-data comparisons were evaluated at three temporal extents to determine whether the rapid, directional changes in temperature and CO 2 in the recent past skew our observed responses to multiple drivers of change. All models tested here were more sensitive to low growing season precipitation than tree-ring NPP and ring widths in the past 30 years, although some model precipitation responses were more consistent with tree rings when evaluated over a full century. Similarly, all models had negative or no response to warm-growing season temperatures, while tree-ring data showed consistently positive effects of temperature. Although precipitation responses were least consistent among models, differences among models to CO 2 drive divergence and ensemble uncertainty in relative change in NPP over the past century. Changes in forest composition within models had no effect on climate or CO 2 sensitivity. Fire in model simulations reduced model sensitivity to climate and CO 2 , but only over the course of multiple centuries. Formal evaluation of emergent model behavior at multidecadal and multicentennial timescales is essential to reconciling model projections with observed ecosystem responses to past climate change. Future evaluation should focus on improved representation of disturbance and biomass change as well as the feedbacks with moisture balance and CO 2 in individual models. © 2017 John Wiley & Sons Ltd.

Inter-annual Variability of Evapotranspiration in a Semi-arid Oak-savanna Ecosystem: Measured and Modeled Buffering to Precipitation Changes

NASA Astrophysics Data System (ADS)

Raz-Yaseef, N.; Sonnentag, O.; Kobayashi, H.; Baldocchi, D. D.

2010-12-01

Precipitation (P) is the primary control on vegetation dynamics and productivity, implying that climate induced disturbances in frequency and timing of P are intimately coupled with fluxes of carbon, water and energy. Future climate change is expected to increase extreme rainfall events as well as droughts, suggesting linked vegetation changes to an unknown extent. Semi-arid climates experience large inter-annual variability (IAV) in P, creating natural conditions adequate to study how year-to-year changes in P affect atmosphere-biosphere fluxes. We used a 10-year flux database collected at a semi-arid savanna site in order to: (1) define IAV in P by means of frequency and timing; (2) investigate how changes in P affect the ecohydrology of the forest and its partitioning into the main vapor fluxes, and (3) evaluate model capability to predict IAV of carbon and water fluxes above and below the canopy. This is based on the perception that the capability of process-oriented models to construct the deviation, and not the average, is important in order to correctly predict ecosystem sensitivity to climate change. Our research site was a low density and low LAI (0.8) semi-arid (P=523±180 mm yr-1) savanna site, combined of oaks and grass, and located at Tonzi ranch, California. Measurements of carbon and water fluxes above and below the tree canopy using eddy covariance and supplementary measurements have been made since 2001. Measured fluxes were compared to modeled based on two bio-meteorological process-oriented ecosystem models: BEPS and 3D-CAONAK. Our results show that IAV in P was large, and standard deviation (STD) was 38% of the average. Accordingly, the wet soil period (measured volumetric water content > 8%) varied between 156 days in dry years to 301 days in wet years. IAV of the vapor fluxes were lower than that of P (STD was 17% for the trees and 23% for the floor components), suggesting on ecosystem buffering to changes in P. The timing of grass green up was correlated with the timing of first rains, emphasizing the higher dependence of the floor component on P, as reflected in higher IAV of the grasses compared to the trees. On average, models simulated annual fluxes well (R2>0.93), but IAV of the trees was higher than measured (24%), mostly due to model underestimation during dry years. A threshold at P~500 mm yr-1 was observed (both in measurements and modeled results), above which tree transpiration barely increased. The high IAV of the floor component was not replicated in the models (SDV=5%), although this flux accounted for 55% of total ET. Based on our study we conclude that trees in this semi-arid ecosystem have developed adaptive mechanisms that buffer themselves from the year-to-year variations in precipitation.

Effect of Liberibacter infection (huanglongbing or "greening" disease) of citrus on orange juice flavor quality by sensory evaluation.

PubMed

Plotto, Anne; Baldwin, Elizabeth; McCollum, Greg; Manthey, John; Narciso, Jan; Irey, Mike

2010-05-01

Some anecdotal reports suggest that infection of citrus trees with Candidatus Liberibacter asiaticus (Las), the suspected causal agent of huanglongbing (HLB) disease, imparts off flavor to orange juice. It is of interest to the industry to know how Las infection affects juice quality with respect to cultivar, maturity, or processing method. Hamlin, Midsweet, and Valencia oranges were harvested over 2 y from trees that tested negative (Las-) or positive (Las+) for Las from different groves and included normal looking (nonsymptomatic) and symptomatic fruit (small, green, and lopsided) from Las+ trees. In the 1st year, fruit were manually juiced, while in the 2nd year, a commercial process was used. Juice from Las+ trees was compared to juice from Las- trees in difference-from-control tests, and by descriptive analysis. Results showed large variability due to tree, harvest date, and cultivar. Juice from Hamlin Las+ trees tended to be more bitter and sour than its Las- counterpart. In contrast, hand processed Valencia juice from Las+ trees was perceived to have some off-flavor and bitterness compared to control, but the following year, commercially processed Valencia juice from Las+ trees was perceived to be only slightly more sour than juice from Las- trees for the April harvest, and to be sweeter for the June harvest. When juice from individual replicates was pooled to be more representative of a commercial situation, there was no difference between Las+ and Las- juice in Valencia. Trained panel differences were noted for juice from Hamlin Las+ fruit, especially for symptomatic fruit. Assumptions that juice made from oranges harvested from Huanglongbing (from infection with Liberibacter sp.) affected trees is off-flavored appeared to be generally more true for Hamlin juice than for Midsweet or Valencia, especially for Hamlin juice made from symptomatic fruit. For Midsweet and Valencia, flavor differences between juice made from fruit harvested from diseased or healthy trees varied greatly between trees, season, and even processing method. Under a commercial processing situation, where juice is blended from several varieties, seasons, and multiple locations, it is expected that off-flavor will not be a major problem.

An investigation on generalization ability of artificial neural networks and M5 model tree in modeling reference evapotranspiration

NASA Astrophysics Data System (ADS)

Kisi, Ozgur; Kilic, Yasin

2016-11-01

The generalization ability of artificial neural networks (ANNs) and M5 model tree (M5Tree) in modeling reference evapotranspiration ( ET 0 ) is investigated in this study. Daily climatic data, average temperature, solar radiation, wind speed, and relative humidity from six different stations operated by California Irrigation Management Information System (CIMIS) located in two different regions of the USA were used in the applications. King-City Oasis Rd., Arroyo Seco, and Salinas North stations are located in San Joaquin region, and San Luis Obispo, Santa Monica, and Santa Barbara stations are located in the Southern region. In the first part of the study, the ANN and M5Tree models were used for estimating ET 0 of six stations and results were compared with the empirical methods. The ANN and M5Tree models were found to be better than the empirical models. In the second part of the study, the ANN and M5Tree models obtained from one station were tested using the data from the other two stations for each region. ANN models performed better than the CIMIS Penman, Hargreaves, Ritchie, and Turc models in two stations while the M5Tree models generally showed better accuracy than the corresponding empirical models in all stations. In the third part of the study, the ANN and M5Tree models were calibrated using three stations located in San Joaquin region and tested using the data from the other three stations located in the Southern region. Four-input ANN and M5Tree models performed better than the CIMIS Penman in only one station while the two-input ANN models were found to be better than the Hargreaves, Ritchie, and Turc models in two stations.

Simulation of carbon allocation and organ growth variability in apple tree by connecting architectural and source–sink models

PubMed Central

Pallas, Benoît; Da Silva, David; Valsesia, Pierre; Yang, Weiwei; Guillaume, Olivier; Lauri, Pierre-Eric; Vercambre, Gilles; Génard, Michel; Costes, Evelyne

2016-01-01

Background and aims Plant growth depends on carbon availability and allocation among organs. QualiTree has been designed to simulate carbon allocation and partitioning in the peach tree (Prunus persica), whereas MappleT is dedicated to the simulation of apple tree (Malus × domestica) architecture. The objective of this study was to couple both models and adapt QualiTree to apple trees to simulate organ growth traits and their within-tree variability. Methods MappleT was used to generate architectures corresponding to the ‘Fuji’ cultivar, accounting for the variability within and among individuals. These architectures were input into QualiTree to simulate shoot and fruit growth during a growth cycle. We modified QualiTree to account for the observed shoot polymorphism in apple trees, i.e. different classes (long, medium and short) that were characterized by different growth function parameters. Model outputs were compared with observed 3D tree geometries, considering shoot and final fruit size and growth dynamics. Key Results The modelling approach connecting MappleT and QualiTree was appropriate to the simulation of growth and architectural characteristics at the tree scale (plant leaf area, shoot number and types, fruit weight at harvest). At the shoot scale, mean fruit weight and its variability within trees was accurately simulated, whereas the model tended to overestimate individual shoot leaf area and underestimate its variability for each shoot type. Varying the parameter related to the intensity of carbon exchange between shoots revealed that behaviour intermediate between shoot autonomy and a common assimilate pool was required to properly simulate within-tree fruit growth variability. Moreover, the model correctly dealt with the crop load effect on organ growth. Conclusions This study provides understanding of the integration of shoot ontogenetic properties, carbon supply and transport between entities for simulating organ growth in trees. Further improvements regarding the integration of retroaction loops between carbon allocation and the resulting plant architecture are expected to allow multi-year simulations. PMID:27279576

Evaluating effectiveness of down-sampling for stratified designs and unbalanced prevalence in Random Forest models of tree species distributions in Nevada

Treesearch

Elizabeth A. Freeman; Gretchen G. Moisen; Tracy S. Frescino

2012-01-01

Random Forests is frequently used to model species distributions over large geographic areas. Complications arise when data used to train the models have been collected in stratified designs that involve different sampling intensity per stratum. The modeling process is further complicated if some of the target species are relatively rare on the landscape leading to an...

Synchrony of forest responses to climate from the aspect of tree mortality in South Korea

NASA Astrophysics Data System (ADS)

Kim, M.; Lee, W. K.; Piao, D.; Choi, G. M.; Gang, H. U.

2016-12-01

Mortality is a key process in forest-stand dynamics. However, tree mortality is not well understood, particularly in relation to climatic factors. The objectives of this study were to: (i) determine the patterns of maximum stem number (MSN) per ha over dominant tree height from 5-year remeasurements of the permanent sample plots for temperate forests [Red pine (Pinus densiflora), Japanese larch (Larix kaempferi), Korean pine (Pinus koraiensis), Chinese cork oak (Quercus variabilis), and Mongolian oak (Quercus mongolica)] using Sterba's theory and Korean National Forest Inventory (NFI) data, (ii) develop a stand-level mortality (self-thinning) model using the MSN curve, and (iii) assess the impact of temperature on tree mortality in semi-variogram and linear regression models. The MSN curve represents the upper range of observed stem numbers per ha. The mortality model and validation statistic reveal significant differences between the observed data and the model predictions (R2 = 0.55-0.81), and no obvious dependencies or patterns that indicate systematic trends between the residuals and the independent variable. However, spatial autocorrelation was detected from residuals of coniferous species (Red pine, Japanese larch and Korean pine), but not of oak species (Chinese cork oak and Mongolian oak). Based on linear regression from residuals, we found that the mortality of coniferous forests tended to increase when the annual mean temperature increased. Conversely, oak mortality nonsignificantly decreased with increasing temperature. These findings indicate that enhanced tree mortality due to rising temperatures in response to climate change is possible, especially in coniferous forests, and are expected to contribute to policy decisions to support and forest management practices.

Avalaunch

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

Moody, A. T.

2014-12-26

Avalaunch implements a tree-based process launcher. It first bootstraps itself on to a set of compute nodes by launching children processes, which immediately connect back to the parent process to acquire info needed t launch their own children. Once the tree is established, user processes are started by broadcasting commands and application binaries through the tree. All communication flows over high-performance network protocols via spawnnet. The goal is to start MPI jobs having hundreds of thousands of processes within seconds.

Growth rate predicts mortality of Abies concolor in both burned and unburned stands

USGS Publications Warehouse

van Mantgem, Phillip J.; Stephenson, Nathan L.; Mutch, Linda S.; Johnson, Veronica G.; Esperanza, Annie M.; Parsons, David J.

2003-01-01

Tree mortality is often the result of both long-term and short-term stress. Growth rate, an indicator of long-term stress, is often used to estimate probability of death in unburned stands. In contrast, probability of death in burned stands is modeled as a function of short-term disturbance severity. We sought to narrow this conceptual gap by determining (i) whether growth rate, in addition to crown scorch, is a predictor of mortality in burned stands and (ii) whether a single, simple model could predict tree death in both burned and unburned stands. Observations of 2622 unburned and 688 burned Abies concolor (Gord. & Glend.) Lindl. (white fir) in the Sierra Nevada of California, U.S.A., indicated that growth rate was a significant predictor of mortality in the unburned stands, while both crown scorch and radial growth were significant predictors of mortality in the burned stands. Applying the burned stand model to unburned stands resulted in an overestimation of the unburned stand mortality rate. While failing to create a general model of tree death for A. concolor, our findings underscore the idea that similar processes may affect mortality in disturbed and undisturbed stands.

[Construction of information management-based virtual forest landscape and its application].

PubMed

Chen, Chongcheng; Tang, Liyu; Quan, Bing; Li, Jianwei; Shi, Song

2005-11-01

Based on the analysis of the contents and technical characteristics of different scale forest visualization modeling, this paper brought forward the principles and technical systems of constructing an information management-based virtual forest landscape. With the combination of process modeling and tree geometric structure description, a software method of interactively and parameterized tree modeling was developed, and the corresponding renderings and geometrical elements simplification algorithms were delineated to speed up rendering run-timely. As a pilot study, the geometrical model bases associated with the typical tree categories in Zhangpu County of Fujian Province, southeast China were established as template files. A Virtual Forest Management System prototype was developed with GIS component (ArcObject), OpenGL graphics environment, and Visual C++ language, based on forest inventory and remote sensing data. The prototype could be used for roaming between 2D and 3D, information query and analysis, and virtual and interactive forest growth simulation, and its reality and accuracy could meet the needs of forest resource management. Some typical interfaces of the system and the illustrative scene cross-sections of simulated masson pine growth under conditions of competition and thinning were listed.

A generalized system of models forecasting Central States tree growth.

Treesearch

Stephen R. Shifley

1987-01-01

Describes the development and testing of a system of individual tree-based growth projection models applicable to species in Indiana, Missouri, and Ohio. Annual tree basal area growth is estimated as a function of tree size, crown ratio, stand density, and site index. Models are compatible with the STEMS and TWIGS Projection System.

Plant traits, productivity, biomass and soil properties from forest sites in the Pacific Northwest, 1999–2014

PubMed Central

Berner, Logan T.; Law, Beverly E.

2016-01-01

Plant trait measurements are needed for evaluating ecological responses to environmental conditions and for ecosystem process model development, parameterization, and testing. We present a standardized dataset integrating measurements from projects conducted by the Terrestrial Ecosystem Research and Regional Analysis- Pacific Northwest (TERRA-PNW) research group between 1999 and 2014 across Oregon and Northern California, where measurements were collected for scaling and modeling regional terrestrial carbon processes with models such as Biome-BGC and the Community Land Model. The dataset contains measurements of specific leaf area, leaf longevity, leaf carbon and nitrogen for 35 tree and shrub species derived from more than 1,200 branch samples collected from over 200 forest plots, including several AmeriFlux sites. The dataset also contains plot-level measurements of forest composition, structure (e.g., tree biomass), and productivity, as well as measurements of soil structure (e.g., bulk density) and chemistry (e.g., carbon). Publically-archiving regional datasets of standardized, co-located, and geo-referenced plant trait measurements will advance the ability of earth system models to capture species-level climate sensitivity at regional to global scales. PMID:26784559

Plant traits, productivity, biomass and soil properties from forest sites in the Pacific Northwest, 1999–2014

DOE PAGES

Berner, Logan T.; Law, Beverly E.

2016-01-19

Plant trait measurements are needed for evaluating ecological responses to environmental conditions and for ecosystem process model development, parameterization, and testing. Here, we present a standardized dataset integrating measurements from projects conducted by the Terrestrial Ecosystem Research and Regional Analysis- Pacific Northwest (TERRA-PNW) research group between 1999 and 2014 across Oregon and Northern California, where measurements were collected for scaling and modeling regional terrestrial carbon processes with models such as Biome-BGC and the Community Land Model. The dataset contains measurements of specific leaf area, leaf longevity, leaf carbon and nitrogen for 35 tree and shrub species derived from more thanmore » 1,200 branch samples collected from over 200 forest plots, including several AmeriFlux sites. The dataset also contains plot-level measurements of forest composition, structure (e.g., tree biomass), and productivity, as well as measurements of soil structure (e.g., bulk density) and chemistry (e.g., carbon). Publically-archiving regional datasets of standardized, co-located, and geo-referenced plant trait measurements will advance the ability of earth system models to capture species-level climate sensitivity at regional to global scales.« less

Estimating root collar diameter growth for multi-stem western woodland tree species on remeasured forest inventory and analysis plots

Treesearch

Michael T. Thompson; Maggie. Toone

2012-01-01

Tree diameter growth models are widely used in many forestry applications, often to predict tree size at a future point in time. Also, there are instances where projections of past diameters are needed. An individual tree model has been developed to estimate diameter growth of multi-stem woodland tree species where the diameter is measured at root collar. The model was...

Technology transfer by means of fault tree synthesis

NASA Astrophysics Data System (ADS)

Batzias, Dimitris F.

2012-12-01

Since Fault Tree Analysis (FTA) attempts to model and analyze failure processes of engineering, it forms a common technique for good industrial practice. On the contrary, fault tree synthesis (FTS) refers to the methodology of constructing complex trees either from dentritic modules built ad hoc or from fault tress already used and stored in a Knowledge Base. In both cases, technology transfer takes place in a quasi-inductive mode, from partial to holistic knowledge. In this work, an algorithmic procedure, including 9 activity steps and 3 decision nodes is developed for performing effectively this transfer when the fault under investigation occurs within one of the latter stages of an industrial procedure with several stages in series. The main parts of the algorithmic procedure are: (i) the construction of a local fault tree within the corresponding production stage, where the fault has been detected, (ii) the formation of an interface made of input faults that might occur upstream, (iii) the fuzzy (to count for uncertainty) multicriteria ranking of these faults according to their significance, and (iv) the synthesis of an extended fault tree based on the construction of part (i) and on the local fault tree of the first-ranked fault in part (iii). An implementation is presented, referring to 'uneven sealing of Al anodic film', thus proving the functionality of the developed methodology.

Trees Wanted—Dead or Alive! Host Selection and Population Dynamics in Tree-Killing Bark Beetles

PubMed Central

Kausrud, Kyrre L.; Grégoire, Jean-Claude; Skarpaas, Olav; Erbilgin, Nadir; Gilbert, Marius; Økland, Bjørn; Stenseth, Nils Chr.

2011-01-01

Bark beetles (Coleoptera: Curculionidae, Scolytinae) feed and breed in dead or severely weakened host trees. When their population densities are high, some species aggregate on healthy host trees so that their defences may be exhausted and the inner bark successfully colonized, killing the tree in the process. Here we investigate under what conditions participating with unrelated conspecifics in risky mass attacks on living trees is an adaptive strategy, and what this can tell us about bark beetle outbreak dynamics. We find that the outcome of individual host selection may deviate from the ideal free distribution in a way that facilitates the emergence of tree-killing (aggressive) behavior, and that any heritability on traits governing aggressiveness seems likely to exist in a state of flux or cycles consistent with variability observed in natural populations. This may have implications for how economically and ecologically important species respond to environmental changes in climate and landscape (forest) structure. The population dynamics emerging from individual behavior are complex, capable of switching between “endemic” and “epidemic” regimes spontaneously or following changes in host availability or resistance. Model predictions are compared to empirical observations, and we identify some factors determining the occurrence and self-limitation of epidemics. PMID:21647433

Tree cover in sub-Saharan Africa: rainfall and fire constrain forest and savanna as alternative stable states.

PubMed

Staver, A Carla; Archibald, Sally; Levin, Simon

2011-05-01

Savannas are known as ecosystems with tree cover below climate-defined equilibrium values. However, a predictive framework for understanding constraints on tree cover is lacking. We present (a) a spatially extensive analysis of tree cover and fire distribution in sub-Saharan Africa, and (b) a model, based on empirical results, demonstrating that savanna and forest may be alternative stable states in parts of Africa, with implications for understanding savanna distributions. Tree cover does not increase continuously with rainfall, but rather is constrained to low (<50%, "savanna") or high tree cover (>75%, "forest"). Intermediate tree cover rarely occurs. Fire, which prevents trees from establishing, differentiates high and low tree cover, especially in areas with rainfall between 1000 mm and 2000 mm. Fire is less important at low rainfall (<1000 mm), where rainfall limits tree cover, and at high rainfall (>2000 mm), where fire is rare. This pattern suggests that complex interactions between climate and disturbance produce emergent alternative states in tree cover. The relationship between tree cover and fire was incorporated into a dynamic model including grass, savanna tree saplings, and savanna trees. Only recruitment from sapling to adult tree varied depending on the amount of grass in the system. Based on our empirical analysis and previous work, fires spread only at tree cover of 40% or less, producing a sigmoidal fire probability distribution as a function of grass cover and therefore a sigmoidal sapling to tree recruitment function. This model demonstrates that, given relatively conservative and empirically supported assumptions about the establishment of trees in savannas, alternative stable states for the same set of environmental conditions (i.e., model parameters) are possible via a fire feedback mechanism. Integrating alternative stable state dynamics into models of biome distributions could improve our ability to predict changes in biome distributions and in carbon storage under climate and global change scenarios.

Quantification of live aboveground forest biomass dynamics with Landsat time-series and field inventory data: A comparison of empirical modeling approaches

Treesearch

Scott L. Powell; Warren B. Cohen; Sean P. Healey; Robert E. Kennedy; Gretchen G. Moisen; Kenneth B. Pierce; Janet L. Ohmann

2010-01-01

Spatially and temporally explicit knowledge of biomass dynamics at broad scales is critical to understanding how forest disturbance and regrowth processes influence carbon dynamics. We modeled live, aboveground tree biomass using Forest Inventory and Analysis (FIA) field data and applied the models to 20+ year time-series of Landsat satellite imagery to...

TreeVector: scalable, interactive, phylogenetic trees for the web.

PubMed

Pethica, Ralph; Barker, Gary; Kovacs, Tim; Gough, Julian

2010-01-28

Phylogenetic trees are complex data forms that need to be graphically displayed to be human-readable. Traditional techniques of plotting phylogenetic trees focus on rendering a single static image, but increases in the production of biological data and large-scale analyses demand scalable, browsable, and interactive trees. We introduce TreeVector, a Scalable Vector Graphics-and Java-based method that allows trees to be integrated and viewed seamlessly in standard web browsers with no extra software required, and can be modified and linked using standard web technologies. There are now many bioinformatics servers and databases with a range of dynamic processes and updates to cope with the increasing volume of data. TreeVector is designed as a framework to integrate with these processes and produce user-customized phylogenies automatically. We also address the strengths of phylogenetic trees as part of a linked-in browsing process rather than an end graphic for print. TreeVector is fast and easy to use and is available to download precompiled, but is also open source. It can also be run from the web server listed below or the user's own web server. It has already been deployed on two recognized and widely used database Web sites.

Modelling the effect of low soil temperatures on transpiration by Scots pine

NASA Astrophysics Data System (ADS)

Mellander, Per-Erik; Stähli, Manfred; Gustafsson, David; Bishop, Kevin

2006-06-01

For ecosystem modelling of the Boreal forest it is important to include processes associated with low soil temperature during spring-early summer, as these affect the tree water uptake. The COUP model, a physically based SVAT model, was tested with 2 years of soil and snow physical measurements and sap flow measurements in a 70-year-old Scots pine stand in the boreal zone of northern Sweden. During the first year the extent and duration of soil frost was manipulated in the field. The model was successful in reproducing the timing of the soil warming after the snowmelt and frost thaw. A delayed soil warming, into the growing season, severely reduced the transpiration. We demonstrated the potential for considerable overestimation of transpiration by the model if the reduction of the trees' capacity to transpire due to low soil temperatures is not taken into account. We also demonstrated that the accumulated effect of aboveground conditions could be included when simulating the relationship between soil temperature and tree water uptake. This improved the estimated transpiration for the control plot and when soil warming was delayed into the growing season. The study illustrates the need of including antecedent conditions on root growth in the model in order to catch these effects on transpiration. The COUP model is a promising tool for predicting transpiration in high-latitude stands.

Evaluating the ecosystem water use efficiency and gross primary productivity in boreal forest based on tree ring data

NASA Astrophysics Data System (ADS)

Liu, S.; Zhuang, Q.

2016-12-01

Climatic change affects the plant physiological and biogeochemistry processes, and therefore on the ecosystem water use efficiency (WUE). Therefore, a comprehensive understanding of WUE would help us understand the adaptability of ecosystem to variable climate conditions. Tree ring data have great potential in addressing the forest response to climatic changes compared with mechanistic model simulations, eddy flux measurement and manipulative experiments. Here, we collected the tree ring isotopic carbon data in 12 boreal forest sites to develop a multiple linear regression model, and the model was extrapolated to the whole boreal region to obtain the WUE spatial and temporal variation from 1948 to 2010. Two algorithms were also used to estimate the inter-annual gross primary productivity (GPP) based on our derived WUE. Our results demonstrated that most of boreal regions showed significant increasing WUE trend during the period except parts of Alaska. The spatial averaged annual mean WUE was predicted to increase by 13%, from 2.3±0.4 g C kg-1 H2O at 1948 to 2.6±0.7 g C kg-1 H2O at 2012, which was much higher than other land surface models. Our predicted GPP by the WUE definition algorithm was comparable with site observation, while for the revised light use efficiency algorithm, GPP estimation was higher than site observation as well as than land surface models. In addition, the increasing GPP trends by two algorithms were similar with land surface model simulations. This is the first study to evaluate regional WUE and GPP in forest ecosystem based on tree ring data and future work should consider other variables (elevation, nitrogen deposition) that influence tree ring isotopic signals and the dual-isotope approach may help improve predicting the inter-annual WUE variation.

Predicting Error Bars for QSAR Models

NASA Astrophysics Data System (ADS)

Schroeter, Timon; Schwaighofer, Anton; Mika, Sebastian; Ter Laak, Antonius; Suelzle, Detlev; Ganzer, Ursula; Heinrich, Nikolaus; Müller, Klaus-Robert

2007-09-01

Unfavorable physicochemical properties often cause drug failures. It is therefore important to take lipophilicity and water solubility into account early on in lead discovery. This study presents log D7 models built using Gaussian Process regression, Support Vector Machines, decision trees and ridge regression algorithms based on 14556 drug discovery compounds of Bayer Schering Pharma. A blind test was conducted using 7013 new measurements from the last months. We also present independent evaluations using public data. Apart from accuracy, we discuss the quality of error bars that can be computed by Gaussian Process models, and ensemble and distance based techniques for the other modelling approaches.

Object-oriented fault tree models applied to system diagnosis

NASA Technical Reports Server (NTRS)

Iverson, David L.; Patterson-Hine, F. A.

1990-01-01

When a diagnosis system is used in a dynamic environment, such as the distributed computer system planned for use on Space Station Freedom, it must execute quickly and its knowledge base must be easily updated. Representing system knowledge as object-oriented augmented fault trees provides both features. The diagnosis system described here is based on the failure cause identification process of the diagnostic system described by Narayanan and Viswanadham. Their system has been enhanced in this implementation by replacing the knowledge base of if-then rules with an object-oriented fault tree representation. This allows the system to perform its task much faster and facilitates dynamic updating of the knowledge base in a changing diagnosis environment. Accessing the information contained in the objects is more efficient than performing a lookup operation on an indexed rule base. Additionally, the object-oriented fault trees can be easily updated to represent current system status. This paper describes the fault tree representation, the diagnosis algorithm extensions, and an example application of this system. Comparisons are made between the object-oriented fault tree knowledge structure solution and one implementation of a rule-based solution. Plans for future work on this system are also discussed.

Estimation of carbon storage based on individual tree detection in Pinus densiflora stands using a fusion of aerial photography and LiDAR data.

PubMed

Kim, So-Ra; Kwak, Doo-Ahn; Lee, Woo-Kyun; oLee, Woo-Kyun; Son, Yowhan; Bae, Sang-Won; Kim, Choonsig; Yoo, Seongjin

2010-07-01

The objective of this study was to estimate the carbon storage capacity of Pinus densiflora stands using remotely sensed data by combining digital aerial photography with light detection and ranging (LiDAR) data. A digital canopy model (DCM), generated from the LiDAR data, was combined with aerial photography for segmenting crowns of individual trees. To eliminate errors in over and under-segmentation, the combined image was smoothed using a Gaussian filtering method. The processed image was then segmented into individual trees using a marker-controlled watershed segmentation method. After measuring the crown area from the segmented individual trees, the individual tree diameter at breast height (DBH) was estimated using a regression function developed from the relationship observed between the field-measured DBH and crown area. The above ground biomass of individual trees could be calculated by an image-derived DBH using a regression function developed by the Korea Forest Research Institute. The carbon storage, based on individual trees, was estimated by simple multiplication using the carbon conversion index (0.5), as suggested in guidelines from the Intergovernmental Panel on Climate Change. The mean carbon storage per individual tree was estimated and then compared with the field-measured value. This study suggested that the biomass and carbon storage in a large forest area can be effectively estimated using aerial photographs and LiDAR data.

Analysis of the effect of evergreen and deciduous trees on urban nitrogen dioxide levels in the U.S. using land-use regression

NASA Astrophysics Data System (ADS)

Rao, M.; George, L. A.

2012-12-01

Nitrogen dioxide (NO2), an atmospheric pollutant generated primarily by anthropogenic combustion processes, is typically found at higher concentrations in urban areas compared to non-urbanized environments. Elevated NO2 levels have multiple ecosystem effects at different spatial scales. At the local scale, elevated levels affect human health directly and through the formation of secondary pollutants such as ozone and aerosols; at the regional scale secondary pollutants such as nitric acid and organic nitrates have deleterious effects on non-urbanized areas; and, at the global scale, nitrogen oxide emissions significantly alter the natural biogeochemical nitrogen cycle. As cities globally become larger and larger sources of nitrogen oxide emissions, it is important to assess possible mitigation strategies to reduce the impact of emissions locally, regionally and globally. In this study, we build a national land-use regression (LUR) model to compare the impacts of deciduous and evergreen trees on urban NO2 levels in the United States. We use the EPA monitoring network values of NO2 levels for 2006, the 2006 NLCD tree canopy data for deciduous and evergreen canopies, and the US Census Bureau's TIGER shapefiles for roads, railroads, impervious area & population density as proxies for NO2 sources on-road traffic, railroad traffic, off-road and area sources respectively. Our preliminary LUR model corroborates previous LUR studies showing that the presence of trees is associated with reduced urban NO2 levels. Additionally, our model indicates that deciduous and evergreen trees reduce NO2 to different extents, and that the amount of NO2 reduced varies seasonally. The model indicates that every square kilometer of deciduous canopy within a 2km buffer is associated with a reduction in ambient NO2 levels of 0.64 ppb in summer and 0.46ppb in winter. Similarly, every square kilometer of evergreen tree canopy within a 2 km buffer is associated with a reduction in ambient NO2 by 0.53 ppb in summer and 0.84 ppb in winter. Thus, the model indicates that deciduous trees are associated with a 30% smaller reduction in NO2 in winter as compared to summer, while evergreens are associated with a 60% increase in the reduction of NO2 in winter, for every square kilometer of deciduous or evergreen canopy within a 2 km buffer. Leaf- and local canopy-level studies have shown that trees are a sink for urban NO2 through deposition as well as stomatal and cuticular uptake. The winter time versus summer time effects suggest that leaf-level deposition may not be the only uptake mechanism and points to the need for a more holistic analysis of tree and canopy-level deposition for urban air pollution models. Since deposition velocities for NO2 vary by tree species, the reduction may also vary by species. These findings have implications for designing cities to reduce the impact of air pollution.

Modeling impacts of management on carbon sequestration and trace gas emissions in forested wetland ecosystems

Treesearch

Changsheng Li; Jianbo Cui

2004-01-01

A process- based model, Wetland-DNDC, was modified to enhance its capacity to predict the impacts of management practices on carbon sequestration in and trace gas emissions from forested wetland ecosystems. The modifications included parameterization of management practices fe.g., forest harvest, chopping, burning, water management, fertilization, and tree planting),...

Modeling Skipped and Not-Reached Items Using IRTrees

ERIC Educational Resources Information Center

Debeer, Dries; Janssen, Rianne; De Boeck, Paul

2017-01-01

When dealing with missing responses, two types of omissions can be discerned: items can be skipped or not reached by the test taker. When the occurrence of these omissions is related to the proficiency process the missingness is nonignorable. The purpose of this article is to present a tree-based IRT framework for modeling responses and omissions…

The Source of Adult Age Differences in Event-Based Prospective Memory: A Multinomial Modeling Approach

ERIC Educational Resources Information Center

Smith, Rebekah E.; Bayen, Ute J.

2006-01-01

Event-based prospective memory involves remembering to perform an action in response to a particular future event. Normal younger and older adults performed event-based prospective memory tasks in 2 experiments. The authors applied a formal multinomial processing tree model of prospective memory (Smith & Bayen, 2004) to disentangle age differences…

A constrained rasch model of trace redintegration in serial recall.

PubMed

Roodenrys, Steven; Miller, Leonie M

2008-04-01

The notion that verbal short-term memory tasks, such as serial recall, make use of information in long-term as well as in short-term memory is instantiated in many models of these tasks. Such models incorporate a process in which degraded traces retrieved from a short-term store are reconstructed, or redintegrated (Schweickert, 1993), through the use of information in long-term memory. This article presents a conceptual and mathematical model of this process based on a class of item-response theory models. It is demonstrated that this model provides a better fit to three sets of data than does the multinomial processing tree model of redintegration (Schweickert, 1993) and that a number of conceptual accounts of serial recall can be related to the parameters of the model.

Spatial elements of mortality risk in old-growth forests

USGS Publications Warehouse

Das, Adrian; Battles, John; van Mantgem, Phillip J.; Stephenson, Nathan L.

2008-01-01

For many species of long-lived organisms, such as trees, survival appears to be the most critical vital rate affecting population persistence. However, methods commonly used to quantify tree death, such as relating tree mortality risk solely to diameter growth, almost certainly do not account for important spatial processes. Our goal in this study was to detect and, if present, to quantify the relevance of such processes. For this purpose, we examined purely spatial aspects of mortality for four species, Abies concolor, Abies magnifica, Calocedrus decurrens, and Pinus lambertiana, in an old-growth conifer forest in the Sierra Nevada of California, USA. The analysis was performed using data from nine fully mapped long-term monitoring plots.In three cases, the results unequivocally supported the inclusion of spatial information in models used to predict mortality. For Abies concolor, our results suggested that growth rate may not always adequately capture increased mortality risk due to competition. We also found evidence of a facilitative effect for this species, with mortality risk decreasing with proximity to conspecific neighbors. For Pinus lambertiana, mortality risk increased with density of conspecific neighbors, in keeping with a mechanism of increased pathogen or insect pressure (i.e., a Janzen-Connell type effect). Finally, we found that models estimating risk of being crushed were strongly improved by the inclusion of a simple index of spatial proximity.Not only did spatial indices improve models, those improvements were relevant for mortality prediction. For P. lambertiana, spatial factors were important for estimation of mortality risk regardless of growth rate. For A. concolor, although most of the population fell within spatial conditions in which mortality risk was well described by growth, trees that died occurred outside those conditions in a disproportionate fashion. Furthermore, as stands of A. concolor become increasingly dense, such spatial factors are likely to become increasingly important. In general, models that fail to account for spatial pattern are at risk of failure as conditions change.

A Functional and Structural Mongolian Scots Pine (Pinus sylvestris var. mongolica) Model Integrating Architecture, Biomass and Effects of Precipitation

PubMed Central

Wang, Feng; Letort, Véronique; Lu, Qi; Bai, Xuefeng; Guo, Yan; de Reffye, Philippe; Li, Baoguo

2012-01-01

Mongolian Scots pine (Pinus sylvestris var. mongolica) is one of the principal tree species in the network of Three-North Shelterbelt for windbreak and sand stabilisation in China. The functions of shelterbelts are highly correlated with the architecture and eco-physiological processes of individual tree. Thus, model-assisted analysis of canopy architecture and function dynamic in Mongolian Scots pine is of value for better understanding its role and behaviour within shelterbelt ecosystems in these arid and semiarid regions. We present here a single-tree functional and structural model, derived from the GreenLab model, which is adapted for young Mongolian Scots pines by incorporation of plant biomass production, allocation, allometric rules and soil water dynamics. The model is calibrated and validated based on experimental measurements taken on Mongolian Scots pines in 2007 and 2006 under local meteorological conditions. Measurements include plant biomass, topology and geometry, as well as soil attributes and standard meteorological data. After calibration, the model allows reconstruction of three-dimensional (3D) canopy architecture and biomass dynamics for trees from one- to six-year-old at the same site using meteorological data for the six years from 2001 to 2006. Sensitivity analysis indicates that rainfall variation has more influence on biomass increment than on architecture, and the internode and needle compartments and the aboveground biomass respond linearly to increases in precipitation. Sensitivity analysis also shows that the balance between internode and needle growth varies only slightly within the range of precipitations considered here. The model is expected to be used to investigate the growth of Mongolian Scots pines in other regions with different soils and climates. PMID:22927982

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.

Effects of phylogenetic reconstruction method on the robustness of species delimitation using single-locus data

PubMed Central

Tang, Cuong Q; Humphreys, Aelys M; Fontaneto, Diego; Barraclough, Timothy G; Paradis, Emmanuel

2014-01-01

Coalescent-based species delimitation methods combine population genetic and phylogenetic theory to provide an objective means for delineating evolutionarily significant units of diversity. The generalised mixed Yule coalescent (GMYC) and the Poisson tree process (PTP) are methods that use ultrametric (GMYC or PTP) or non-ultrametric (PTP) gene trees as input, intended for use mostly with single-locus data such as DNA barcodes. Here, we assess how robust the GMYC and PTP are to different phylogenetic reconstruction and branch smoothing methods. We reconstruct over 400 ultrametric trees using up to 30 different combinations of phylogenetic and smoothing methods and perform over 2000 separate species delimitation analyses across 16 empirical data sets. We then assess how variable diversity estimates are, in terms of richness and identity, with respect to species delimitation, phylogenetic and smoothing methods. The PTP method generally generates diversity estimates that are more robust to different phylogenetic methods. The GMYC is more sensitive, but provides consistent estimates for BEAST trees. The lower consistency of GMYC estimates is likely a result of differences among gene trees introduced by the smoothing step. Unresolved nodes (real anomalies or methodological artefacts) affect both GMYC and PTP estimates, but have a greater effect on GMYC estimates. Branch smoothing is a difficult step and perhaps an underappreciated source of bias that may be widespread among studies of diversity and diversification. Nevertheless, careful choice of phylogenetic method does produce equivalent PTP and GMYC diversity estimates. We recommend simultaneous use of the PTP model with any model-based gene tree (e.g. RAxML) and GMYC approaches with BEAST trees for obtaining species hypotheses. PMID:25821577

Analysis of Wave Velocity Patterns in Black Cherry Trees and its Effect on Internal Decay Detection

Treesearch

Guanghui Li; Xiping Wang; Jan Wiedenbeck; Robert J. Ross

2013-01-01

In this study, we examined stress wave velocity patterns in the cross sections of black cherry trees, developed analytical models of stress wave velocity in sound healthy trees, and then tested the effectiveness of the models as a tool for tree decay diagnosis. Acoustic tomography data of the tree cross sections were collected from 12 black cherry trees at a production...

Analysis of wave velocity patterns in black cherry trees and its effect on internal decay detection

Treesearch

Guanghui Li; Xiping Wang; Hailin Feng; Jan Wiedenbeck; Robert J. Ross

2014-01-01

In this study, we examined stress wave velocity patterns in the cross sections of black cherry trees, developed analytical models of stress wave velocity in sound healthy trees, and then tested the effectiveness of the models as a tool for tree decay diagnosis. Acoustic tomography data of the tree cross sections were collected from 12 black cherry trees at a production...

Development and Evaluation of Models for the Relationship between Tree Height and Diameter at Breast Height for Chinese-Fir Plantations in Subtropical China.

PubMed

Li, Yan-qiong; Deng, Xiang-wen; Huang, Zhi-hong; Xiang, Wen-hua; Yan, Wen-de; Lei, Pi-feng; Zhou, Xiao-lu; Peng, Chang-hui

2015-01-01

Tree diameter at breast height (dbh) and height are the most important variables used in forest inventory and management as well as forest carbon-stock estimation. In order to identify the key stand variables that influence the tree height-dbh relationship and to develop and validate a suit of models for predicting tree height, data from 5961 tree samples aged from 6 years to 53 years and collected from 80 Chinese-fir plantation plots were used to fit 39 models, including 33 nonlinear models and 6 linear models, were developed and evaluated into two groups. The results showed that composite models performed better in height estimate than one-independent-variable models. Nonlinear composite Model 34 and linear composite Model 6 were recommended for predicting tree height in Chinese fir plantations with a dbh range between 4 cm and 40 cm when the dbh data for each tree and the quadratic mean dbh of the stand (Dq) and mean height of the stand (Hm) were available. Moreover, Hm could be estimated by using the formula Hm = 11.707 × l n(Dq)-18.032. Clearly, Dq was the primary stand variable that influenced the height-dbh relationship. The parameters of the models varied according to stand age and site. The inappropriate application of provincial or regional height-dbh models for predicting small tree height at local scale may result in larger uncertainties. The method and the recommended models developed in this study were statistically reliable for applications in growth and yield estimation for even-aged Chinese-fir plantation in Huitong and Changsha. The models could be extended to other regions and to other tree species only after verification in subtropical China.

Development and Evaluation of Models for the Relationship between Tree Height and Diameter at Breast Height for Chinese-Fir Plantations in Subtropical China

PubMed Central

Li, Yan-qiong; Deng, Xiang-wen; Huang, Zhi-hong; Xiang, Wen-hua; Yan, Wen-de; Lei, Pi-feng; Zhou, Xiao-lu; Peng, Chang-hui

2015-01-01

Tree diameter at breast height (dbh) and height are the most important variables used in forest inventory and management as well as forest carbon-stock estimation. In order to identify the key stand variables that influence the tree height-dbh relationship and to develop and validate a suit of models for predicting tree height, data from 5961 tree samples aged from 6 years to 53 years and collected from 80 Chinese-fir plantation plots were used to fit 39 models, including 33 nonlinear models and 6 linear models, were developed and evaluated into two groups. The results showed that composite models performed better in height estimate than one-independent-variable models. Nonlinear composite Model 34 and linear composite Model 6 were recommended for predicting tree height in Chinese fir plantations with a dbh range between 4 cm and 40 cm when the dbh data for each tree and the quadratic mean dbh of the stand (Dq) and mean height of the stand (Hm) were available. Moreover, Hm could be estimated by using the formula Hm=11.707×ln(Dq)-18.032. Clearly, Dq was the primary stand variable that influenced the height-dbh relationship. The parameters of the models varied according to stand age and site. The inappropriate application of provincial or regional height-dbh models for predicting small tree height at local scale may result in larger uncertainties. The method and the recommended models developed in this study were statistically reliable for applications in growth and yield estimation for even-aged Chinese-fir plantation in Huitong and Changsha. The models could be extended to other regions and to other tree species only after verification in subtropical China. PMID:25905458