Phylogeny and evolutionary histories of Pyrus L. revealed by phylogenetic trees and networks based on data from multiple DNA sequences

USDA-ARS?s Scientific Manuscript database

Reconstructing the phylogeny of Pyrus has been difficult due to the wide distribution of the genus and lack of informative data. In this study, we collected 110 accessions representing 25 Pyrus species and constructed both phylogenetic trees and phylogenetic networks based on multiple DNA sequence d...

Relationships among environmental variables and distribution of tree species at high elevation in the Olympic Mountains

USGS Publications Warehouse

Woodward, Andrea

1998-01-01

Relationships among environmental variables and occurrence of tree species were investigated at Hurricane Ridge in Olympic National Park, Washington, USA. A transect consisting of three plots was established down one north-and one south-facing slope in stands representing the typical elevational sequence of tree species. Tree species included subalpine fir (Abies lasiocarpa), Douglas-fir (Pseudotsuga menziesii), mountain hemlock (Tsuga mertensiana), and Pacific silver fir (Abies amabilis). Air and soil temperature, precipitation, and soil moisture were measured during three growing seasons. Snowmelt patterns, soil carbon and moisture release curves were also determined. The plots represented a wide range in soil water potential, a major determinant of tree species distribution (range of minimum values = -1.1 to -8.0 MPa for Pacific silver fir and Douglas-fir plots, respectively). Precipitation intercepted at plots depended on topographic location, storm direction and storm type. Differences in soil moisture among plots was related to soil properties, while annual differences at each plot were most often related to early season precipitation. Changes in climate due to a doubling of atmospheric CO2 will likely shift tree species distributions within, but not among aspects. Change will be buffered by innate tolerance of adult trees and the inertia of soil properties.

Distribution and dispersal of Xylaria endophytes in two tree species in Puerto Rico

Treesearch

P. Bayman; D. J. Lodge; P. Angulo-Sandoval; Z. Baez-Ortiz

1998-01-01

Xylaria species are common endophytes in tropical plants. It is not known, however, whether transmission of Xylaria occurs horizontally or vertically, whether individual Xylaria strains have wide host ranges or are host-specific, or how they are dispersed. We compared frequency of Xylaria endophytes in leaves and seeds of two tree species in Puerto Rico, Casuarina...

An entomopathogenic fungus and nematode prove ineffective for biocontrol of an invasive leaf miner Profenusa thomsoni in Alaska

Treesearch

Robert Progar; J.J. Kruse; John Lundquist; K.P. Zogas; M.J. Rinella

2015-01-01

A non-native invasive sawfly, the amber-marked birch leaf miner Profenusa thomsoni (Konow), was first detected in south-central Alaska in 1996 and is now widely distributed throughout urban and wild birch trees in Alaska. Impacts have been considered primarily aesthetic because leaf miners cause leaves of birch trees (Betula...

Enhanced photosynthetic efficiency in trees world-wide by rising atmospheric CO2 levels

NASA Astrophysics Data System (ADS)

Ehlers, Ina; Wieloch, Thomas; Groenendijk, Peter; Vlam, Mart; van der Sleen, Peter; Zuidema, Pieter A.; Robertson, Iain; Schleucher, Jürgen

2014-05-01

The atmospheric CO2 concentration is increasing rapidly due to anthropogenic emissions but the effect on the Earth's biosphere is poorly understood. The ability of the biosphere to fix CO2 through photosynthesis will determine future atmospheric CO2 concentrations as well as future productivity of crops and forests. Manipulative CO2 enrichment experiments (e.g. FACE) are limited to (i) short time spans, (ii) few locations and (iii) large step increases in [CO2]. Here, we apply new stable isotope methodology to tree-ring archives, to study the effect of increasing CO2 concentrations retrospectively during the past centuries. We cover the whole [CO2] increase since industrialization, and sample trees with global distribution. Instead of isotope ratios of whole molecules, we use intramolecular isotope distributions, a new tool for tree-ring analysis with decisive advantages. In experiments on annual plants, we have found that the intramolecular distribution of deuterium (equivalent to ratios of isotopomer abundances) in photosynthetic glucose depends on growth [CO2] and reflects the metabolic flux ratio of photosynthesis to photorespiration. By applying this isotopomer methodology to trees from Oak Ridge FACE experiment, we show that this CO2 response is present in trees on the leaf level. This CO2 dependence constitutes a physiological signal, which is transferred to the wood of the tree rings. In trees from 13 locations on all continents the isotopomer ratio of tree-ring cellulose is correlated to atmospheric [CO2] during the past 200 years. The shift of the isotopomer ratio is universal for all 12 species analyzed, including both broad-leafed trees and conifers. Because the trees originate from sites with widely differing D/H ratios of precipitation, the generality of the response demonstrates that the signal is independent of the source isotope ratio, because it is encoded in an isotopomer abundance ratio. This decoupling of climate signals and physiological signals is a fundamental advantage of isotopomer ratios (Augusti et al., Chem. Geol 2008). These results demonstrate that increasing [CO2] has reduced the ratio of photorespiration to photosynthesis on a global scale. Photorespiration is a side reaction that decreases the C gain of plants; the suppression of photorespiration in all analyzed trees indicates that increasing atmospheric [CO2] is enhancing the photosynthetic efficiency of trees world-wide. The consensus response of the trees agrees with the response of annual plants in greenhouse experiments, with three important conclusions. First, the generality of the isotopomer shift confirms that the CO2 response reflects the ratio of photosynthesis to photorespiration, and that it creates a robust signal in tree rings. Second, the agreement between greenhouse-grown plants and trees indicates that there has not been an acclimation response of the trees during the past centuries. Third, the results show that the regulation of tree gas exchange has during past centuries been governed by the same rules as observed in manipulative experiments, in contradiction to recent reports (Keenan et al., Nature 2013).

Photosynthetic capacity and leaf nitrogen decline along a controlled climate gradient in provenances of two widely distributed Eucalyptus species.

PubMed

Crous, Kristine Y; Drake, John E; Aspinwall, Michael J; Sharwood, Robert E; Tjoelker, Mark G; Ghannoum, Oula

2018-05-27

Climate is an important factor limiting tree distributions and adaptation to different thermal environments may influence how tree populations respond to climate warming. Given the current rate of warming, it has been hypothesized that tree populations in warmer, more thermally stable climates may have limited capacity to respond physiologically to warming compared to populations from cooler, more seasonal climates. We determined in a controlled environment how several provenances of widely distributed Eucalyptus tereticornis and E. grandis adjusted their photosynthetic capacity to +3.5°C warming along their native distribution range (~16-38°S) and whether climate of seed origin of the provenances influenced their response to different growth temperatures. We also tested how temperature optima (T opt ) of photosynthesis and J max responded to higher growth temperatures. Our results showed increased photosynthesis rates at a standardized temperature with warming in temperate provenances, while rates in tropical provenances were reduced by about 40% compared to their temperate counterparts. Temperature optima of photosynthesis increased as provenances were exposed to warmer growth temperatures. Both species had ~30% reduced photosynthetic capacity in tropical and subtropical provenances related to reduced leaf nitrogen and leaf Rubisco content compared to temperate provenances. Tropical provenances operated closer to their thermal optimum and came within 3% of the T opt of J max during the daily temperature maxima. Hence, further warming may negatively affect C uptake and tree growth in warmer climates, whereas eucalypts in cooler climates may benefit from moderate warming. © 2018 John Wiley & Sons Ltd.

Decay and Discoloration of Aspen

Treesearch

Gerald W. Anderson; Thomas E. Hinds; Donald M. Knutson

1977-01-01

Quaking aspen (Populus tremuloides Michx.) is the most widely distributed tree species in North America. It has a transcontinental range and grows under a wide variety of climatic and edaphic conditions. The commercial range includes the Lake States as well as parts of New England; it also includes Manitoba, Saskatchewan, and Alberta, Canada. Although many stands in...

Aspen [Chapter 3

Treesearch

Dale L. Bartos

2007-01-01

Quaking aspen (Populus tremuloides Michx.) is the most widely distributed broadleaf tree in North American (Little 1971; Sargent 1890). Aspen forests occur from Labrador on the east coast to Alaska in the north to Mexico in the south. In its eastern range, aspen is relatively continuously distributed. In the western United States, however, it occurs on the more...

Regression analysis using dependent Polya trees.

PubMed

Schörgendorfer, Angela; Branscum, Adam J

2013-11-30

Many commonly used models for linear regression analysis force overly simplistic shape and scale constraints on the residual structure of data. We propose a semiparametric Bayesian model for regression analysis that produces data-driven inference by using a new type of dependent Polya tree prior to model arbitrary residual distributions that are allowed to evolve across increasing levels of an ordinal covariate (e.g., time, in repeated measurement studies). By modeling residual distributions at consecutive covariate levels or time points using separate, but dependent Polya tree priors, distributional information is pooled while allowing for broad pliability to accommodate many types of changing residual distributions. We can use the proposed dependent residual structure in a wide range of regression settings, including fixed-effects and mixed-effects linear and nonlinear models for cross-sectional, prospective, and repeated measurement data. A simulation study illustrates the flexibility of our novel semiparametric regression model to accurately capture evolving residual distributions. In an application to immune development data on immunoglobulin G antibodies in children, our new model outperforms several contemporary semiparametric regression models based on a predictive model selection criterion. Copyright © 2013 John Wiley & Sons, Ltd.

Growing stock levels in even-aged ponderosa pine

Treesearch

Clifford A. Myers

1967-01-01

Growth of the most widely distributed pine in North America is under joint study by the western Forest and Range Experiment Stations of the U. S. Forest Service. Young, even-aged ponderosa pine (Pinus ponderosa Laws.) stands are being examined over a wide range of tree sizes, stand densities, and site index. The single plan that co-...

Betweenness centrality in a weighted network

NASA Astrophysics Data System (ADS)

Wang, Huijuan; Hernandez, Javier Martin; van Mieghem, Piet

2008-04-01

When transport in networks follows the shortest paths, the union of all shortest path trees G∪SPT can be regarded as the “transport overlay network.” Overlay networks such as peer-to-peer networks or virtual private networks can be considered as a subgraph of G∪SPT . The traffic through the network is examined by the betweenness Bl of links in the overlay G∪SPT . The strength of disorder can be controlled by, e.g., tuning the extreme value index α of the independent and identically distributed polynomial link weights. In the strong disorder limit (α→0) , all transport flows over a critical backbone, the minimum spanning tree (MST). We investigate the betweenness distributions of wide classes of trees, such as the MST of those well-known network models and of various real-world complex networks. All these trees with different degree distributions (e.g., uniform, exponential, or power law) are found to possess a power law betweenness distribution Pr[Bl=j]˜j-c . The exponent c seems to be positively correlated with the degree variance of the tree and to be insensitive of the size N of a network. In the weak disorder regime, transport in the network traverses many links. We show that a link with smaller link weight tends to carry more traffic. This negative correlation between link weight and betweenness depends on α and the structure of the underlying topology.

Treelink: data integration, clustering and visualization of phylogenetic trees.

PubMed

Allende, Christian; Sohn, Erik; Little, Cedric

2015-12-29

Phylogenetic trees are central to a wide range of biological studies. In many of these studies, tree nodes need to be associated with a variety of attributes. For example, in studies concerned with viral relationships, tree nodes are associated with epidemiological information, such as location, age and subtype. Gene trees used in comparative genomics are usually linked with taxonomic information, such as functional annotations and events. A wide variety of tree visualization and annotation tools have been developed in the past, however none of them are intended for an integrative and comparative analysis. Treelink is a platform-independent software for linking datasets and sequence files to phylogenetic trees. The application allows an automated integration of datasets to trees for operations such as classifying a tree based on a field or showing the distribution of selected data attributes in branches and leafs. Genomic and proteonomic sequences can also be linked to the tree and extracted from internal and external nodes. A novel clustering algorithm to simplify trees and display the most divergent clades was also developed, where validation can be achieved using the data integration and classification function. Integrated geographical information allows ancestral character reconstruction for phylogeographic plotting based on parsimony and likelihood algorithms. Our software can successfully integrate phylogenetic trees with different data sources, and perform operations to differentiate and visualize those differences within a tree. File support includes the most popular formats such as newick and csv. Exporting visualizations as images, cluster outputs and genomic sequences is supported. Treelink is available as a web and desktop application at http://www.treelinkapp.com .

Distribution maps for Midsouth tree species

Treesearch

Roy C. Beltz; Daniel F. Bertelson

1990-01-01

The Midsouth is an important timber-producing region, with a wide variety of sites and species. In addition to timber production, increasing demands for non-timber amenities are placed on the region’s forests. These maps indicate the distribution of individual species recorded in surveys of the Midsouth conducted by the U.S. Department of Agriculture, Forest Service....

Flowering phenology and its implications for management of big-leaf mahogany Swietenia macrophylla in Brazilian Amazonia.

PubMed

Grogan, James; Loveless, Marilyn D

2013-11-01

Flowering phenology is a crucial determinant of reproductive success and offspring genetic diversity in plants. We measure the flowering phenology of big-leaf mahogany (Swietenia macrophylla, Meliaceae), a widely distributed neotropical tree, and explore how disturbance from logging impacts its reproductive biology. We use a crown scoring system to estimate the timing and duration of population-level flowering at three forest sites in the Brazilian Amazon over a five-year period. We combine this information with data on population structure and spatial distribution to consider the implications of logging for population flowering patterns and reproductive success. Mahogany trees as small as 14 cm diam flowered, but only trees > 30 cm diam flowered annually or supra-annually. Mean observed flowering periods by focal trees ranged from 18-34 d, and trees flowered sequentially during 3-4 mo beginning in the dry season. Focal trees demonstrated significant interannual correlation in flowering order. Estimated population-level flowering schedules resembled that of the focal trees, with temporal isolation between early and late flowering trees. At the principal study site, conventional logging practices eliminated 87% of mahogany trees > 30 cm diam and an estimated 94% of annual pre-logging floral effort. Consistent interannual patterns of sequential flowering among trees create incompletely isolated subpopulations, constraining pollen flow. After harvests, surviving subcommercial trees will have fewer, more distant, and smaller potential partners, with probable consequences for post-logging regeneration. These results have important implications for the sustainability of harvesting systems for tropical timber species.

Multisites Coordination in Shared Multicast Trees

DTIC Science & Technology

1999-01-01

conferencing, distributed interactive simulations, and collaborative systems. We de- scribe a novel protocol to coordinate multipoint groupwork in the IP...multicast framework. The pro- tocol supports Internet-wide coordination for large and highly-interactive groupwork , relying on trans- mission of

7 CFR 301.45 - Notice of quarantine; restriction on interstate movement of specified regulated articles.

Code of Federal Regulations, 2010 CFR

2010-01-01

... prevent the spread of the gypsy moth, Lymantria dispar (Linnaeus), a dangerous insect injurious to forests and shade trees and not theretofore widely prevalent or distributed within or throughout the United...

7 CFR 301.45 - Notice of quarantine; restriction on interstate movement of specified regulated articles.

Code of Federal Regulations, 2012 CFR

2012-01-01

... prevent the spread of the gypsy moth, Lymantria dispar (Linnaeus), a dangerous insect injurious to forests and shade trees and not theretofore widely prevalent or distributed within or throughout the United...

7 CFR 301.45 - Notice of quarantine; restriction on interstate movement of specified regulated articles.

Code of Federal Regulations, 2011 CFR

2011-01-01

... prevent the spread of the gypsy moth, Lymantria dispar (Linnaeus), a dangerous insect injurious to forests and shade trees and not theretofore widely prevalent or distributed within or throughout the United...

7 CFR 301.45 - Notice of quarantine; restriction on interstate movement of specified regulated articles.

Code of Federal Regulations, 2014 CFR

2014-01-01

... prevent the spread of the gypsy moth, Lymantria dispar (Linnaeus), a dangerous insect injurious to forests and shade trees and not theretofore widely prevalent or distributed within or throughout the United...

7 CFR 301.45 - Notice of quarantine; restriction on interstate movement of specified regulated articles.

Code of Federal Regulations, 2013 CFR

2013-01-01

... prevent the spread of the gypsy moth, Lymantria dispar (Linnaeus), a dangerous insect injurious to forests and shade trees and not theretofore widely prevalent or distributed within or throughout the United...

The capacity to cope with climate warming declines from temperate to tropical latitudes in two widely distributed Eucalyptus species.

PubMed

Drake, John E; Aspinwall, Michael J; Pfautsch, Sebastian; Rymer, Paul D; Reich, Peter B; Smith, Renee A; Crous, Kristine Y; Tissue, David T; Ghannoum, Oula; Tjoelker, Mark G

2015-01-01

As rapid climate warming creates a mismatch between forest trees and their home environment, the ability of trees to cope with warming depends on their capacity to physiologically adjust to higher temperatures. In widespread species, individual trees in cooler home climates are hypothesized to more successfully acclimate to warming than their counterparts in warmer climates that may approach thermal limits. We tested this prediction with a climate-shift experiment in widely distributed Eucalyptus tereticornis and E. grandis using provenances originating along a ~2500 km latitudinal transect (15.5-38.0°S) in eastern Australia. We grew 21 provenances in conditions approximating summer temperatures at seed origin and warmed temperatures (+3.5 °C) using a series of climate-controlled glasshouse bays. The effects of +3.5 °C warming strongly depended on home climate. Cool-origin provenances responded to warming through an increase in photosynthetic capacity and total leaf area, leading to enhanced growth of 20-60%. Warm-origin provenances, however, responded to warming through a reduction in photosynthetic capacity and total leaf area, leading to reduced growth of approximately 10%. These results suggest that there is predictable intraspecific variation in the capacity of trees to respond to warming; cool-origin taxa are likely to benefit from warming, while warm-origin taxa may be negatively affected. © 2014 John Wiley & Sons Ltd.

Aspen restoration in the Blue Mountains of northeast Oregon

Treesearch

Diane M. Shirley; Vicky Erickson

2001-01-01

In the Blue Mountains of northeast Oregon, quaking aspen is on the western fringe of its range. It exists as small, scattered, remnant stands of rapidly declining trees. Although little is known about the historic distribution of aspen in Oregon, it is believed that stands were once larger and more widely distributed. Decline of the species is attributed to fire...

Tree edit distance for leaf-labelled trees on free leafset and its comparison with frequent subsplit dissimilarity and popular distance measures

PubMed Central

2011-01-01

Background This paper is devoted to distance measures for leaf-labelled trees on free leafset. A leaf-labelled tree is a data structure which is a special type of a tree where only leaves (terminal) nodes are labelled. This data structure is used in bioinformatics for modelling of evolution history of genes and species and also in linguistics for modelling of languages evolution history. Many domain specific problems occur and need to be solved with help of tree postprocessing techniques such as distance measures. Results Here we introduce the tree edit distance designed for leaf labelled trees on free leafset, which occurs to be a metric. It is presented together with tree edit consensus tree notion. We provide statistical evaluation of provided measure with respect to R-F, MAST and frequent subsplit based dissimilarity measures as the reference measures. Conclusions The tree edit distance was proven to be a metric and has the advantage of using different costs for contraction and pruning, therefore their properties can be tuned depending on the needs of the user. Two of the presented methods carry the most interesting properties. E(3,1) is very discriminative (having a wide range of values) and has a very regular distance distribution which is similar to a normal distribution in its shape and is good both for similar and non-similar trees. NFC(2,1) on the other hand is proportional or nearly proportional to the number of mutation operations used, irrespective of their type. PMID:21612645

Disparity in elevational shifts of European trees in response to recent climate warming.

PubMed

Rabasa, Sonia G; Granda, Elena; Benavides, Raquel; Kunstler, Georges; Espelta, Josep M; Ogaya, Romá; Peñuelas, Josep; Scherer-Lorenzen, Michael; Gil, Wojciech; Grodzki, Wojciech; Ambrozy, Slawomir; Bergh, Johan; Hódar, José A; Zamora, Regino; Valladares, Fernando

2013-08-01

Predicting climate-driven changes in plant distribution is crucial for biodiversity conservation and management under recent climate change. Climate warming is expected to induce movement of species upslope and towards higher latitudes. However, the mechanisms and physiological processes behind the altitudinal and latitudinal distribution range of a tree species are complex and depend on each tree species features and vary over ontogenetic stages. We investigated the altitudinal distribution differences between juvenile and adult individuals of seven major European tree species along elevational transects covering a wide latitudinal range from southern Spain (37°N) to northern Sweden (67°N). By comparing juvenile and adult distributions (shifts on the optimum position and the range limits) we assessed the response of species to present climate conditions in relation to previous conditions that prevailed when adults were established. Mean temperature increased by 0.86 °C on average at our sites during the last decade compared with previous 30-year period. Only one of the species studied, Abies alba, matched the expected predictions under the observed warming, with a maximum abundance of juveniles at higher altitudes than adults. Three species, Fagus sylvatica, Picea abies and Pinus sylvestris, showed an opposite pattern while for other three species, such as Quercus ilex, Acer pseudoplatanus and Q. petraea, we were no able to detect changes in distribution. These findings are in contrast with theoretical predictions and show that tree responses to climate change are complex and are obscured not only by other environmental factors but also by internal processes related to ontogeny and demography. © 2013 John Wiley & Sons Ltd.

Calibrated tree priors for relaxed phylogenetics and divergence time estimation.

PubMed

Heled, Joseph; Drummond, Alexei J

2012-01-01

The use of fossil evidence to calibrate divergence time estimation has a long history. More recently, Bayesian Markov chain Monte Carlo has become the dominant method of divergence time estimation, and fossil evidence has been reinterpreted as the specification of prior distributions on the divergence times of calibration nodes. These so-called "soft calibrations" have become widely used but the statistical properties of calibrated tree priors in a Bayesian setting hashave not been carefully investigated. Here, we clarify that calibration densities, such as those defined in BEAST 1.5, do not represent the marginal prior distribution of the calibration node. We illustrate this with a number of analytical results on small trees. We also describe an alternative construction for a calibrated Yule prior on trees that allows direct specification of the marginal prior distribution of the calibrated divergence time, with or without the restriction of monophyly. This method requires the computation of the Yule prior conditional on the height of the divergence being calibrated. Unfortunately, a practical solution for multiple calibrations remains elusive. Our results suggest that direct estimation of the prior induced by specifying multiple calibration densities should be a prerequisite of any divergence time dating analysis.

Habitone analysis of quaking aspen in the Utah Book Cliffs: Effects of site water demand and conifer cover

Treesearch

Joseph O. Sexton; R. Douglas Ramsey; Dale L. Bartos

2006-01-01

Quaking aspen (Populus tremuloides Michx.) is the most widely distributed tree species in North America, but its presence is declining across much of the Western United States. Aspen decline is complex, but results largely from two factors widely divergent in temporal scale: (1) Holocene climatic drying of the region has led to water limitation of aspen seedling...

Rooting and foraging effects of wild pigs on tree regeneration and acorn survival in California's oak woodland ecosystems

Treesearch

Rick A. Sweitzer; Dirk H. Van Vuren

2002-01-01

Wild pigs (Sus scrofa) have been widely distributed by humans and significant populations now occur in oak-dominated ecosystems in California. Because they are omnivorous and forage by rooting, wild pigs have the potential to impact a wide variety of plants and animals directly by consumption and indirectly through disturbance. In 1998, we initiated...

Flexible programmable logic module

DOEpatents

Robertson, Perry J.; Hutchinson, Robert L.; Pierson, Lyndon G.

2001-01-01

The circuit module of this invention is a VME board containing a plurality of programmable logic devices (PLDs), a controlled impedance clock tree, and interconnecting buses. The PLDs are arranged to permit systolic processing of a problem by offering wide data buses and a plurality of processing nodes. The board contains a clock reference and clock distribution tree that can drive each of the PLDs with two critically timed clock references. External clock references can be used to drive additional circuit modules all operating from the same synchronous clock reference.

The Spatial Pattern and Interactions of Woody Plants on the Temperate Savanna of Inner Mongolia, China: The Effects of Alternating Seasonal Grazing-Mowing Regimes

PubMed Central

2015-01-01

Ulmus pumila tree-dominated temperate savanna, which is distributed widely throughout the forest-steppe ecotone on the Mongolian Plateau, is a relatively stable woody-herbaceous complex ecosystem in northern China. Relatively more attention has been paid to the degradation of typical steppe areas, whereas less focus has been placed on the succession of this typical temperate savanna under the present management regime. In this study, we established 3 sample plots 100 m×100 m in size along a gradient of fixed distances from one herder’s stationary site and then surveyed all the woody plants in these plots. A spatial point pattern analysis was employed to clarify the spatial distribution and interaction of these woody plants. The results indicated that old U. pumila trees (DBH ≥ 20 cm) showed a random distribution and that medium U. pumila trees (5 cm ≤ DBH < 20 cm) showed an aggregated distribution at a smaller scale and a random distribution at a larger scale; few or no juvenile trees (DBH < 5 cm) were present, and seedlings (without DBH) formed aggregations in all 3 plots. These findings can be explained by an alternate seasonal grazing-mowing regime (exclosure in summer, mowing in autumn and grazing in winter and spring); the shrubs in all 3 plots exist along a grazing gradient that harbors xerophytic and mesophytic shrubs. Of these shrubs, xerophytic shrubs show significant aggregation at a smaller scale (0-5.5 m), whereas mesophytic shrubs show significant aggregation at a larger scale (0-25 m), which may be the result of the dual effects of grazing pressure and climate change. Medium trees and seedlings significantly facilitate the distributions of xerophytic shrubs and compete significantly with mesophytic shrubs due to differences in water use strategies. We conclude that the implementation of an alternative grazing-mowing regime results in xerophytic shrub encroachment or existence, breaking the chain of normal succession in a U. pumila tree community in this typical temperate savanna ecosystem. This might eventually result in the degradation of the original tree-dominated savanna to a xerophytic shrub-dominated savanna. PMID:26196956

Growing trees in internet news groups and forums

NASA Astrophysics Data System (ADS)

Kujawski, B.; Hołyst, J.; Rodgers, G. J.

2007-09-01

We present an empirical study of the networks created by users within internet news groups and forums and show that they organize themselves into scale-free trees. The structure of these trees depends on the topic under discussion; specialist topics have trees with a short shallow structure whereas more universal topics are discussed widely and have a deeper tree structure. For news groups we find that the distribution of the time intervals between when a message is posted and when it receives a response exhibits a composite power-law behavior. From our statistics we can see if the news group or forum is free or is overseen by a moderator. The correlation function of activity, the number of messages posted in a given time, shows long-range correlations connected with the users’ daily routines. The distribution of distances between each message and its root is exponential for most news groups and power law for the forums. For both formats we find that the relation between the supremacy (the total number of nodes that are under the node i , including node i ) and the degree is linear s(k)˜k , in contrast to the analytical relation for the Barabási-Albert network.

Climate Warming Threatens Semi-arid Forests in Inner Asia

NASA Astrophysics Data System (ADS)

WU, X.; Liu, H.; Qi, Z.; Li, X.

2014-12-01

A line of evidences reveal an increasing tree growth decline and tree mortality mainly attributable to climate warming and the warming-mediated changes in drought and other processes (such as fire and insect dynamics) in many parts of world tropical, temperate and boreal forests. However, the growth responses to climate change of the widely distributed semi-arid forests are unclear. Here, we synthetically investigate the tree growth patterns during past decades and its interannual response to climate variations in Inner Asia combining the ground truth field survey and samplings, remote sensing observations and climate data. We identified a pervasive tree growth decline since mid-1990s in semi-arid forests in Inner Asia. The widely observed tree growth decline is dominantly attributable to warming-induced water stress during pre- and early growing season. Tree growth of semi-arid forests in Inner Asia is particularly susceptible to spring warming and has been suffering a prolonged growth limitation in recent decades due to spring warming-mediated water conditions. Additionally, we identified a much slower growth rate in younger trees and a lack of tree regeneration in these semi-arid forests. The widely observed forest growth reduction and lack of tree regeneration over semi-arid forests in Inner Asia could predictably exert great effects on forest structure, regionally/globally biophysical and biochemical processes and the feedbacks between biosphere and atmosphere. Notably, further increases in forest stress and tree mortality could be reasonably expected, especially in context of the increase frequency and severity of high temperature and heat waves and changes in forest disturbances, potentially driving the eventual regional loss of current semi-arid forests. Given the potential risks of climate induced forest dieback, increased management attention to adaptation options for enhancing forest resistance and resilience to projected climate stress can be expected. However, the functionally realistic mechanisms beneath the pervasively climate-induced forest decline/dieback still remain unclear. Network-based long-term surveys and experiment studies are urgently needed for further understandings regarding the responses of forest/tree growth to climate warming/variations.

Species distribution models predict temporal but not spatial variation in forest growth.

PubMed

van der Maaten, Ernst; Hamann, Andreas; van der Maaten-Theunissen, Marieke; Bergsma, Aldo; Hengeveld, Geerten; van Lammeren, Ron; Mohren, Frits; Nabuurs, Gert-Jan; Terhürne, Renske; Sterck, Frank

2017-04-01

Bioclimate envelope models have been widely used to illustrate the discrepancy between current species distributions and their potential habitat under climate change. However, the realism and correct interpretation of such projections has been the subject of considerable discussion. Here, we investigate whether climate suitability predictions correlate to tree growth, measured in permanent inventory plots and inferred from tree-ring records. We use the ensemble classifier RandomForest and species occurrence data from ~200,000 inventory plots to build species distribution models for four important European forestry species: Norway spruce, Scots pine, European beech, and pedunculate oak. We then correlate climate-based habitat suitability with volume measurements from ~50-year-old stands, available from ~11,000 inventory plots. Secondly, habitat projections based on annual historical climate are compared with ring width from ~300 tree-ring chronologies. Our working hypothesis is that habitat suitability projections from species distribution models should to some degree be associated with temporal or spatial variation in these growth records. We find that the habitat projections are uncorrelated with spatial growth records (inventory plot data), but they do predict interannual variation in tree-ring width, with an average correlation of .22. Correlation coefficients for individual chronologies range from values as high as .82 or as low as -.31. We conclude that tree responses to projected climate change are highly site-specific and that local suitability of a species for reforestation is difficult to predict. That said, projected increase or decrease in climatic suitability may be interpreted as an average expectation of increased or reduced growth over larger geographic scales.

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.

Tall shrub and tree expansion in Siberian tundra ecotones since the 1960s.

PubMed

Frost, Gerald V; Epstein, Howard E

2014-04-01

Circumpolar expansion of tall shrubs and trees into Arctic tundra is widely thought to be occurring as a result of recent climate warming, but little quantitative evidence exists for northern Siberia, which encompasses the world's largest forest-tundra ecotonal belt. We quantified changes in tall shrub and tree canopy cover in 11, widely distributed Siberian ecotonal landscapes by comparing very high-resolution photography from the Cold War-era 'Gambit' and 'Corona' satellite surveillance systems (1965-1969) with modern imagery. We also analyzed within-landscape patterns of vegetation change to evaluate the susceptibility of different landscape components to tall shrub and tree increase. The total cover of tall shrubs and trees increased in nine of 11 ecotones. In northwest Siberia, alder (Alnus) shrubland cover increased 5.3-25.9% in five ecotones. In Taymyr and Yakutia, larch (Larix) cover increased 3.0-6.7% within three ecotones, but declined 16.8% at a fourth ecotone due to thaw of ice-rich permafrost. In Chukotka, the total cover of alder and dwarf pine (Pinus) increased 6.1% within one ecotone and was little changed at a second ecotone. Within most landscapes, shrub and tree increase was linked to specific geomorphic settings, especially those with active disturbance regimes such as permafrost patterned-ground, floodplains, and colluvial hillslopes. Mean summer temperatures increased at most ecotones since the mid-1960s, but rates of shrub and tree canopy cover expansion were not strongly correlated with temperature trends and were better correlated with mean annual precipitation. We conclude that shrub and tree cover is increasing in tundra ecotones across most of northern Siberia, but rates of increase vary widely regionally and at the landscape scale. Our results indicate that extensive changes can occur within decades in moist, shrub-dominated ecotones, as in northwest Siberia, while changes are likely to occur much more slowly in the highly continental, larch-dominated ecotones of central and eastern Siberia. © 2013 John Wiley & Sons Ltd.

Estimating urban trees and carbon stock potentials for mitigating climate change in Lagos: Case of Ikeja Government Reserved Area (GRA)

NASA Astrophysics Data System (ADS)

Elias, P. O.; Faderin, A.

2014-12-01

Urban trees are a component of the urban infrastructure which offers diverse services including environmental, aesthetic and economic. The accumulation of carbon in the atmosphere resulting from the indiscriminate distribution of human populations and urban activities with the unsustainable consumption of natural resources contributes to global environmental change especially in coastal cities like Lagos. Carbon stocks and sequestration by urban trees are increasingly recognized to play significant roles for mitigating climate change. This paper focuses on the estimation of carbon stock and sequestration through biomass estimation and quantification in Ikeja GRA, Lagos. Ikeja possesses a characteristic feature as a microcosm of Lagos due to the wide range of land uses. A canopy assessment of tree population was carried out using itree canopy software. A GPS survey was used to collect an inventory of all trees showing their location, spatial distribution and other attributes. The analysis of the carbon storage and sequestration potential of both actual and potential tree planting sites involved biomass estimations from tree allometry equations. Trees were identified at species level and measurements of their dendrometric values were recorded and integrated into the GIS database to estimate biomass of trees and carbon storage. The trees in the study area were estimated to have a biomass of 441.9 mg and carbon storage of 221.395 kg/tree. By considering the potential tree planting sites the estimated carbon stored increased to 11,352.73 kg. Carbon sequestration value in the study area was found to be 1.6790 tonnes for the existing trees and 40.707 tonnes for the potential tree planting sites (PTPS). The estimation of carbon storage and sequestration values of trees are important incentives for carbon accounting/footprints and monitoring of climate change mitigation which has implications for evaluation and monitoring of urban ecosystem.

Advances in ecological genomics in forest trees and applications to genetic resources conservation and breeding.

PubMed

Holliday, Jason A; Aitken, Sally N; Cooke, Janice E K; Fady, Bruno; González-Martínez, Santiago C; Heuertz, Myriam; Jaramillo-Correa, Juan-Pablo; Lexer, Christian; Staton, Margaret; Whetten, Ross W; Plomion, Christophe

2017-02-01

Forest trees are an unparalleled group of organisms in their combined ecological, economic and societal importance. With widespread distributions, predominantly random mating systems and large population sizes, most tree species harbour extensive genetic variation both within and among populations. At the same time, demographic processes associated with Pleistocene climate oscillations and land-use change have affected contemporary range-wide diversity and may impinge on the potential for future adaptation. Understanding how these adaptive and neutral processes have shaped the genomes of trees species is therefore central to their management and conservation. As for many other taxa, the advent of high-throughput sequencing methods is expected to yield an understanding of the interplay between the genome and environment at a level of detail and depth not possible only a few years ago. An international conference entitled 'Genomics and Forest Tree Genetics' was held in May 2016, in Arcachon (France), and brought together forest geneticists with a wide range of research interests to disseminate recent efforts that leverage contemporary genomic tools to probe the population, quantitative and evolutionary genomics of trees. An important goal of the conference was to discuss how such data can be applied to both genome-enabled breeding and the conservation of forest genetic resources under land use and climate change. Here, we report discoveries presented at the meeting and discuss how the ecological genomic toolkit can be used to address both basic and applied questions in tree biology. © 2016 John Wiley & Sons Ltd.

Species trees for the tree swallows (Genus Tachycineta): an alternative phylogenetic hypothesis to the mitochondrial gene tree.

PubMed

Dor, Roi; Carling, Matthew D; Lovette, Irby J; Sheldon, Frederick H; Winkler, David W

2012-10-01

The New World swallow genus Tachycineta comprises nine species that collectively have a wide geographic distribution and remarkable variation both within- and among-species in ecologically important traits. Existing phylogenetic hypotheses for Tachycineta are based on mitochondrial DNA sequences, thus they provide estimates of a single gene tree. In this study we sequenced multiple individuals from each species at 16 nuclear intron loci. We used gene concatenated approaches (Bayesian and maximum likelihood) as well as coalescent-based species tree inference to reconstruct phylogenetic relationships of the genus. We examined the concordance and conflict between the nuclear and mitochondrial trees and between concatenated and coalescent-based inferences. Our results provide an alternative phylogenetic hypothesis to the existing mitochondrial DNA estimate of phylogeny. This new hypothesis provides a more accurate framework in which to explore trait evolution and examine the evolution of the mitochondrial genome in this group. Copyright © 2012 Elsevier Inc. All rights reserved.

Response of spectral reflectances and vegetation indices on varying Juniper cone densities

USDA-ARS?s Scientific Manuscript database

Juniper trees are widely distributed throughout the world and are common sources of allergies when microscopic pollen grains are transported by wind and inhaled. In this study, we investigated the spectral influences of pollen discharging male juniper cones within a juniper canopy. This was done thr...

Managing Eastern Redceder

Treesearch

E.R. Ferguson; E.R. Lawson; W.R. Maple; C. Mesavage

1968-01-01

Eastern redcedar (Juniperus virginiana L.) is the most widely distributed conifer of tree size in the Eastern United States (48). Its range also extends into southeastern Canada. The wood was once favored for domestic use and export because of its exceptional cutting qualities, durability, rich color, and aroma. It has now lost much of its...

Analysing Amazonian forest productivity using a new individual and trait-based model (TFS v.1)

NASA Astrophysics Data System (ADS)

Fyllas, N. M.; Gloor, E.; Mercado, L. M.; Sitch, S.; Quesada, C. A.; Domingues, T. F.; Galbraith, D. R.; Torre-Lezama, A.; Vilanova, E.; Ramírez-Angulo, H.; Higuchi, N.; Neill, D. A.; Silveira, M.; Ferreira, L.; Aymard C., G. A.; Malhi, Y.; Phillips, O. L.; Lloyd, J.

2014-07-01

Repeated long-term censuses have revealed large-scale spatial patterns in Amazon basin forest structure and dynamism, with some forests in the west of the basin having up to a twice as high rate of aboveground biomass production and tree recruitment as forests in the east. Possible causes for this variation could be the climatic and edaphic gradients across the basin and/or the spatial distribution of tree species composition. To help understand causes of this variation a new individual-based model of tropical forest growth, designed to take full advantage of the forest census data available from the Amazonian Forest Inventory Network (RAINFOR), has been developed. The model allows for within-stand variations in tree size distribution and key functional traits and between-stand differences in climate and soil physical and chemical properties. It runs at the stand level with four functional traits - leaf dry mass per area (Ma), leaf nitrogen (NL) and phosphorus (PL) content and wood density (DW) varying from tree to tree - in a way that replicates the observed continua found within each stand. We first applied the model to validate canopy-level water fluxes at three eddy covariance flux measurement sites. For all three sites the canopy-level water fluxes were adequately simulated. We then applied the model at seven plots, where intensive measurements of carbon allocation are available. Tree-by-tree multi-annual growth rates generally agreed well with observations for small trees, but with deviations identified for larger trees. At the stand level, simulations at 40 plots were used to explore the influence of climate and soil nutrient availability on the gross (ΠG) and net (ΠN) primary production rates as well as the carbon use efficiency (CU). Simulated ΠG, ΠN and CU were not associated with temperature. On the other hand, all three measures of stand level productivity were positively related to both mean annual precipitation and soil nutrient status. Sensitivity studies showed a clear importance of an accurate parameterisation of within- and between-stand trait variability on the fidelity of model predictions. For example, when functional tree diversity was not included in the model (i.e. with just a single plant functional type with mean basin-wide trait values) the predictive ability of the model was reduced. This was also the case when basin-wide (as opposed to site-specific) trait distributions were applied within each stand. We conclude that models of tropical forest carbon, energy and water cycling should strive to accurately represent observed variations in functionally important traits across the range of relevant scales.

Beyond Flory theory: Distribution functions for interacting lattice trees

NASA Astrophysics Data System (ADS)

Rosa, Angelo; Everaers, Ralf

2017-01-01

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

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

PubMed

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

2016-01-01

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

Living on the Edges: Spatial Niche Occupation of Asian Citrus Psyllid, Diaphorina citri Kuwayama (Hemiptera: Liviidae), in Citrus Groves.

PubMed

Sétamou, Mamoudou; Bartels, David W

2015-01-01

The spatial niche occupation of the Asian citrus psyllid, Diaphorina citri Kuwayama, 1908, was evaluated to determine its field colonization and food resource exploitation strategies in citrus groves. Mature grapefruit and sweet orange groves were surveyed as part of an area-wide program in 2009-2010 to determine D. citri population densities and between-tree distribution. In both cultivars, significantly more psyllids were found on perimeter trees throughout the study period suggesting a strong edge effect in D. citri distribution in the groves. D. citri densities and infestation levels gradually declined from the edge to the center of grove. Higher numbers of D. citri were recorded on trees located on the east and south sides of the groves than those on the west and north sides. Citrus groves located at the outer edge of the study with at least one side non-surrounded to other citrus groves harbored significantly more D. citri than groves located within the block cluster and entirely surrounded by other groves. In detailed field studies during 2012, infestation of D. citri started from border trees in the grove where possibly one generation is completed before inner trees become infested. In addition, psyllid densities decreased significantly with increasing distance from the grove edge. Using the selection index, D citri exhibited a strong niche occupation preference for border trees.

Living on the Edges: Spatial Niche Occupation of Asian Citrus Psyllid, Diaphorina citri Kuwayama (Hemiptera: Liviidae), in Citrus Groves

PubMed Central

2015-01-01

The spatial niche occupation of the Asian citrus psyllid, Diaphorina citri Kuwayama, 1908, was evaluated to determine its field colonization and food resource exploitation strategies in citrus groves. Mature grapefruit and sweet orange groves were surveyed as part of an area-wide program in 2009–2010 to determine D. citri population densities and between-tree distribution. In both cultivars, significantly more psyllids were found on perimeter trees throughout the study period suggesting a strong edge effect in D. citri distribution in the groves. D. citri densities and infestation levels gradually declined from the edge to the center of grove. Higher numbers of D. citri were recorded on trees located on the east and south sides of the groves than those on the west and north sides. Citrus groves located at the outer edge of the study with at least one side non-surrounded to other citrus groves harbored significantly more D. citri than groves located within the block cluster and entirely surrounded by other groves. In detailed field studies during 2012, infestation of D. citri started from border trees in the grove where possibly one generation is completed before inner trees become infested. In addition, psyllid densities decreased significantly with increasing distance from the grove edge. Using the selection index, D citri exhibited a strong niche occupation preference for border trees. PMID:26193111

An Isometric Mapping Based Co-Location Decision Tree Algorithm

NASA Astrophysics Data System (ADS)

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

2018-05-01

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

A Laser Photoacoustic Analysis of Residual CO2 and H2O in Larch Stems

PubMed Central

Ageev, Boris; Ponomarev, Yurii; Sapozhnikova, Valeria; Savchuk, Dmitry

2014-01-01

Every so often, the results obtained from investigations into the effects of varying environmental conditions on the tree growth rate at the same sites and on the change in the carbon balance in plants, using traditional methods, are found to differ widely. We believe that the reason for the ambiguity of the data has to do with failure to account for the role of the residual CO2 (and H2O) in the tree wood exhibiting a climate response. In our earlier work, the results of a laser photoacoustic gas analysis of CO2 and H2O vacuum-desorbed from disc tree rings of evergreen conifer trees were presented. In this paper, laser photoacoustic measurements of tree ring gases in deciduous conifer trees and CO2 carbon isotope composition determined by means of a mass spectrometer are given. Conclusions are made regarding the response of annual larch CO2 disc tree ring distributions to climatic parameters (temperatures and precipitation). The data about the CO2 disc content for different sites are compared. PMID:25808838

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

PubMed Central

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

2016-01-01

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

Comparison of modeling methods to predict the spatial distribution of deep-sea coral and sponge in the Gulf of Alaska

NASA Astrophysics Data System (ADS)

Rooper, Christopher N.; Zimmermann, Mark; Prescott, Megan M.

2017-08-01

Deep-sea coral and sponge ecosystems are widespread throughout most of Alaska's marine waters, and are associated with many different species of fishes and invertebrates. These ecosystems are vulnerable to the effects of commercial fishing activities and climate change. We compared four commonly used species distribution models (general linear models, generalized additive models, boosted regression trees and random forest models) and an ensemble model to predict the presence or absence and abundance of six groups of benthic invertebrate taxa in the Gulf of Alaska. All four model types performed adequately on training data for predicting presence and absence, with regression forest models having the best overall performance measured by the area under the receiver-operating-curve (AUC). The models also performed well on the test data for presence and absence with average AUCs ranging from 0.66 to 0.82. For the test data, ensemble models performed the best. For abundance data, there was an obvious demarcation in performance between the two regression-based methods (general linear models and generalized additive models), and the tree-based models. The boosted regression tree and random forest models out-performed the other models by a wide margin on both the training and testing data. However, there was a significant drop-off in performance for all models of invertebrate abundance ( 50%) when moving from the training data to the testing data. Ensemble model performance was between the tree-based and regression-based methods. The maps of predictions from the models for both presence and abundance agreed very well across model types, with an increase in variability in predictions for the abundance data. We conclude that where data conforms well to the modeled distribution (such as the presence-absence data and binomial distribution in this study), the four types of models will provide similar results, although the regression-type models may be more consistent with biological theory. For data with highly zero-inflated distributions and non-normal distributions such as the abundance data from this study, the tree-based methods performed better. Ensemble models that averaged predictions across the four model types, performed better than the GLM or GAM models but slightly poorer than the tree-based methods, suggesting ensemble models might be more robust to overfitting than tree methods, while mitigating some of the disadvantages in predictive performance of regression methods.

Climate-growth relationships along a black spruce toposequence in Interior Alaska

Treesearch

Jane M. Wolken; Daniel H. Mann; Thomas A. Grant; Andrea H. Lloyd; T. Scott Rupp; Teresa N. Hollingsworth

2016-01-01

Despite its wide geographic distribution and important role in boreal forest fire regimes, little is known about the climate-growth relationships of black spruce (Picea mariana [Mill.] B.S.P.). We used site- and tree-level analyses to evaluate the radial growth responses to climate of black spruce growing...

Cercocarpus Kunth: mountain-mahogany

Treesearch

Stanley G. Kitchen

2008-01-01

The mountain mahoganies - genus Cercocarpus - are 8 to 10 species of moderately to intricately branched shrubs or small trees that are endemic to dry coastal and interior mountains of the western United States and Mexico (Stutz 1990). Leaves are generally persistent and stems are unarmed. Two of the most widely distributed and utilized species are described here.

Underplanting to sustain future stocking of oak (Quercus) in temperate deciduous forests

Treesearch

Daniel C. Dey; Emile S. Gardiner; Callie J. Schweitzer; John M. Kabrick; Douglass F. Jacobs

2012-01-01

Oaks (Quercus spp.) are one of the most important tree taxa in the northern hemisphere. Although they are dominant in mixed species forests and widely distributed, there are frequent reports of regeneration failures. An adequate population of large oak advance reproduction is a critical prerequisite to successful oak regeneration, and hence...

Soil compaction and chestnut ink disease

Treesearch

T.F. Fonseca; C.G. Abreu; B.R. Parresol

2004-01-01

Chestnut ink disease caused by the oomycete Phytophthora cinnamomi, a soil-borne pathogen of world-wide distribution, accounts for the majority of disease problems on chestnuts in Portugal, limiting yield in a large number of stands and impeding establishment of trees in new areas. A survey was carried out in 32 chestnut stands in the Padrela...

Silvical characteristics of white fir

Treesearch

David C. Maul

1958-01-01

White fir (Abies concolor Gord. and Glend.) Lindl.) is an economically important native tree in western United States and parts of Mexico. In the United States it is widely distributed in the Rocky Mountain and Pacific Coast regions, extending from New Mexico and Wyoming, westward to Oregon and California. It attains best development in California...

Anomalous dismeter distribution shifts estimated from FIA inventories through time

Treesearch

Francis A. Roesch; Paul C. Van Deusen

2010-01-01

In the past decade, the United States Department of Agriculture Forest Service’s Forest Inventory and Analysis Program (FIA) has replaced regionally autonomous, periodic, state-wide forest inventories using various probability proportional to tree size sampling designs with a nationally consistent annual forest inventory design utilizing systematically spaced clusters...

Pines

Treesearch

C. Plomion; D. Chagne; D. Pot; S. Kumar; P.L. Wilcox; R.D. Burdon; D. Prat; D.G. Peterson; J. Paiva; P. Chaumeil; G.G. Vendramin; F. Sebastiani; C.D. Nelson; C.S. Echt; O. Savolainen; T.L. Kubisiak; M.T. Cervera; N. de Maria; M.N. Islam-Faridi

2007-01-01

Pinus is the most important genus within the Family Pinaceae and also within the gymnosperms by the number of species (109 species recognized by Farjon 2001) and by its contribution to forest ecosystems. All pine species are evergreen trees or shrubs. They are widely distributed in the northern hemisphere, from tropical areas to northern areas in America and Eurasia....

Arbutus menziesii Pursh. Pacific madrone

Treesearch

Philip M. McDonald

1990-01-01

Pacific madrone (Arbutus menziesii) is one of the most widely distributed tree species native to the Pacific coast. Named for its discoverer, Archibald Menzies, a 19th century Scottish physician and naturalist, the species is called arbutus in Canada, and madrone, madroña, or madroño in the United States. The latter name is...

Spatial Patterns of Soil Organic Carbon Relative to Tree Size and Canopy Distribution in a Semi-Desert Grassland

NASA Astrophysics Data System (ADS)

Throop, H. L.; Archer, S.

2004-12-01

The abundance of woody species in grasslands and savannas has increased globally over the past century. Recent estimates suggest that this proliferation of woody plants may account for a significant fraction of the Northern Hemisphere C sink, although a large degree of uncertainty exists in the magnitude and spatial distribution of these plant and soil pools. While field-based inventories have made progress in assessing the role of aboveground woody growth in ecosystem C inventories, the effect of woody proliferation on soil organic carbon (SOC) remains controversial, despite the fact that the majority of ecosystem C in these systems is typically belowground. Elevated levels of SOC underneath woody plant canopies have been widely reported, but little is known about the spatial distribution of SOC relative to tree canopies. Understanding the spatial distribution of SOC is critical, however, to developing accurate landscape-scale assessments of woody proliferation impacts on ecosystem C pools. We quantified the influence of encroaching mesquite trees (Fabaceae: Prosopis velutina) on the concentration of SOC and total nitrogen (TN) in a semi-desert grassland in southern Arizona. SOC concentrations near the boles of large trees (basal diameter 85-102 cm) were approximately double that of SOC in intercanopy zones (0.9% vs. 0.4% SOC by weight). SOC declined moving out from the bole to the canopy edge, at which point it was equivalent to inter-canopy spaces. Small to medium-sized trees (basal diameters less than 85 cm) had minimal influence on SOC concentrations. Patterns of TN values mirrored those of SOC in all cases, although TN values were roughly an order of magnitude lower than SOC values. These data suggest that accurate accounting of landscape-level SOC stocks will require developing area-weighting algorithms that account for tree size and bole-to-canopy gradients.

Tree cover in Central Africa: determinants and sensitivity under contrasted scenarios of global change.

PubMed

Aleman, Julie C; Blarquez, Olivier; Gourlet-Fleury, Sylvie; Bremond, Laurent; Favier, Charly

2017-01-30

Tree cover is a key variable for ecosystem functioning, and is widely used to study tropical ecosystems. But its determinants and their relative importance are still a matter of debate, especially because most regional and global analyses have not considered the influence of agricultural practices. More information is urgently needed regarding how human practices influence vegetation structure. Here we focused in Central Africa, a region still subjected to traditional agricultural practices with a clear vegetation gradient. Using remote sensing data and global databases, we calibrated a Random Forest model to correlatively link tree cover with climatic, edaphic, fire and agricultural practices data. We showed that annual rainfall and accumulated water deficit were the main drivers of the distribution of tree cover and vegetation classes (defined by the modes of tree cover density), but agricultural practices, especially pastoralism, were also important in determining tree cover. We simulated future tree cover with our model using different scenarios of climate and land-use (agriculture and population) changes. Our simulations suggest that tree cover may respond differently regarding the type of scenarios, but land-use change was an important driver of vegetation change even able to counterbalance the effect of climate change in Central Africa.

Tree cover in Central Africa: determinants and sensitivity under contrasted scenarios of global change

NASA Astrophysics Data System (ADS)

Aleman, Julie C.; Blarquez, Olivier; Gourlet-Fleury, Sylvie; Bremond, Laurent; Favier, Charly

2017-01-01

Tree cover is a key variable for ecosystem functioning, and is widely used to study tropical ecosystems. But its determinants and their relative importance are still a matter of debate, especially because most regional and global analyses have not considered the influence of agricultural practices. More information is urgently needed regarding how human practices influence vegetation structure. Here we focused in Central Africa, a region still subjected to traditional agricultural practices with a clear vegetation gradient. Using remote sensing data and global databases, we calibrated a Random Forest model to correlatively link tree cover with climatic, edaphic, fire and agricultural practices data. We showed that annual rainfall and accumulated water deficit were the main drivers of the distribution of tree cover and vegetation classes (defined by the modes of tree cover density), but agricultural practices, especially pastoralism, were also important in determining tree cover. We simulated future tree cover with our model using different scenarios of climate and land-use (agriculture and population) changes. Our simulations suggest that tree cover may respond differently regarding the type of scenarios, but land-use change was an important driver of vegetation change even able to counterbalance the effect of climate change in Central Africa.

Architecture of the wood-wide web: Rhizopogon spp. genets link multiple Douglas-fir cohorts.

PubMed

Beiler, Kevin J; Durall, Daniel M; Simard, Suzanne W; Maxwell, Sheri A; Kretzer, Annette M

2010-01-01

*The role of mycorrhizal networks in forest dynamics is poorly understood because of the elusiveness of their spatial structure. We mapped the belowground distribution of the fungi Rhizopogon vesiculosus and Rhizopogon vinicolor and interior Douglas-fir trees (Pseudotsuga menziesii var. glauca) to determine the architecture of a mycorrhizal network in a multi-aged old-growth forest. *Rhizopogon spp. mycorrhizas were collected within a 30 x 30 m plot. Trees and fungal genets were identified using multi-locus microsatellite DNA analysis. Tree genotypes from mycorrhizas were matched to reference trees aboveground. Two trees were considered linked if they shared the same fungal genet(s). *The two Rhizopogon species each formed 13-14 genets, each colonizing up to 19 trees in the plot. Rhizopogon vesiculosus genets were larger, occurred at greater depths, and linked more trees than genets of R. vinicolor. Multiple tree cohorts were linked, with young saplings established within the mycorrhizal network of Douglas-fir veterans. A strong positive relationship was found between tree size and connectivity, resulting in a scale-free network architecture with small-world properties. *This mycorrhizal network architecture suggests an efficient and robust network, where large trees play a foundational role in facilitating conspecific regeneration and stabilizing the ecosystem.

Rapid decay of tree-community composition in Amazonian forest fragments

PubMed Central

Laurance, William F.; Nascimento, Henrique E. M.; Laurance, Susan G.; Andrade, Ana; Ribeiro, José E. L. S.; Giraldo, Juan Pablo; Lovejoy, Thomas E.; Condit, Richard; Chave, Jerome; Harms, Kyle E.; D'Angelo, Sammya

2006-01-01

Forest fragmentation is considered a greater threat to vertebrates than to tree communities because individual trees are typically long-lived and require only small areas for survival. Here we show that forest fragmentation provokes surprisingly rapid and profound alterations in Amazonian tree-community composition. Results were derived from a 22-year study of exceptionally diverse tree communities in 40 1-ha plots in fragmented and intact forests, which were sampled repeatedly before and after fragment isolation. Within these plots, trajectories of change in abundance were assessed for 267 genera and 1,162 tree species. Abrupt shifts in floristic composition were driven by sharply accelerated tree mortality and recruitment within ≈100 m of fragment margins, causing rapid species turnover and population declines or local extinctions of many large-seeded, slow-growing, and old-growth taxa; a striking increase in a smaller set of disturbance-adapted and abiotically dispersed species; and significant shifts in tree size distributions. Even among old-growth trees, species composition in fragments is being restructured substantially, with subcanopy species that rely on animal seed-dispersers and have obligate outbreeding being the most strongly disadvantaged. These diverse changes in tree communities are likely to have wide-ranging impacts on forest architecture, canopy-gap dynamics, plant–animal interactions, and forest carbon storage. PMID:17148598

Phylogeography of Quercus variabilis Based on Chloroplast DNA Sequence in East Asia: Multiple Glacial Refugia and Mainland-Migrated Island Populations

PubMed Central

Kang, Hongzhang; Sun, Xiao; Yin, Shan; Du, Hongmei; Yamanaka, Norikazu; Gapare, Washington; Wu, Harry X.; Liu, Chunjiang

2012-01-01

The biogeographical relationships between far-separated populations, in particular, those in the mainland and islands, remain unclear for widespread species in eastern Asia where the current distribution of plants was greatly influenced by the Quaternary climate. Deciduous Oriental oak (Quercus variabilis) is one of the most widely distributed species in eastern Asia. In this study, leaf material of 528 Q. variabilis trees from 50 populations across the whole distribution (Mainland China, Korea Peninsular as well as Japan, Zhoushan and Taiwan Islands) was collected, and three cpDNA intergenic spacer fragments were sequenced using universal primers. A total of 26 haplotypes were detected, and it showed a weak phylogeographical structure in eastern Asia populations at species level, however, in the central-eastern region of Mainland China, the populations had more haplotypes than those in other regions, with a significant phylogeographical structure (N ST = 0.751> G ST = 0.690, P<0.05). Q. variabilis displayed high interpopulation and low intrapopulation genetic diversity across the distribution range. Both unimodal mismatch distribution and significant negative Fu’s FS indicated a demographic expansion of Q. variabilis populations in East Asia. A fossil calibrated phylogenetic tree showed a rapid speciation during Pleistocene, with a population augment occurred in Middle Pleistocene. Both diversity patterns and ecological niche modelling indicated there could be multiple glacial refugia and possible bottleneck or founder effects occurred in the southern Japan. We dated major spatial expansion of Q. variabilis population in eastern Asia to the last glacial cycle(s), a period with sea-level fluctuations and land bridges in East China Sea as possible dispersal corridors. This study showed that geographical heterogeneity combined with climate and sea-level changes have shaped the genetic structure of this wide-ranging tree species in East Asia. PMID:23115642

Life stage, not climate change, explains observed tree range shifts.

PubMed

Máliš, František; Kopecký, Martin; Petřík, Petr; Vladovič, Jozef; Merganič, Ján; Vida, Tomáš

2016-05-01

Ongoing climate change is expected to shift tree species distribution and therefore affect forest biodiversity and ecosystem services. To assess and project tree distributional shifts, researchers may compare the distribution of juvenile and adult trees under the assumption that differences between tree life stages reflect distributional shifts triggered by climate change. However, the distribution of tree life stages could differ within the lifespan of trees, therefore, we hypothesize that currently observed distributional differences could represent shifts over ontogeny as opposed to climatically driven changes. Here, we test this hypothesis with data from 1435 plots resurveyed after more than three decades across the Western Carpathians. We compared seedling, sapling and adult distribution of 12 tree species along elevation, temperature and precipitation gradients. We analyzed (i) temporal shifts between the surveys and (ii) distributional differences between tree life stages within both surveys. Despite climate warming, tree species distribution of any life stage did not shift directionally upward along elevation between the surveys. Temporal elevational shifts were species specific and an order of magnitude lower than differences among tree life stages within the surveys. Our results show that the observed range shifts among tree life stages are more consistent with ontogenetic differences in the species' environmental requirements than with responses to recent climate change. The distribution of seedlings substantially differed from saplings and adults, while the distribution of saplings did not differ from adults, indicating a critical transition between seedling and sapling tree life stages. Future research has to take ontogenetic differences among life stages into account as we found that distributional differences recently observed worldwide may not reflect climate change but rather the different environmental requirements of tree life stages. © 2016 John Wiley & Sons Ltd.

Life-stage, not climate change, explains observed tree range shifts

PubMed Central

Máliš, František; Kopecký, Martin; Petřík, Petr; Vladovič, Jozef; Merganič, Ján; Vida, Tomáš

2017-01-01

Ongoing climate change is expected to shift tree species distribution and therefore affect forest biodiversity and ecosystem services. To assess and project tree distributional shifts, researchers may compare the distribution of juvenile and adult trees under the assumption that differences between tree life-stages reflect distributional shifts triggered by climate change. However, the distribution of tree life-stages could differ within the lifespan of trees, therefore we hypothesize that currently observed distributional differences could represent shifts over ontogeny as opposed to climatically driven changes. Here we test this hypothesis with data from 1435 plots resurveyed after more than three decades across the Western Carpathians. We compared seedling, sapling and adult distribution of 12 tree species along elevation, temperature and precipitation gradients. We analyzed i) temporal shifts between the surveys and ii) distributional differences between tree life-stages within both surveys. Despite climate warming, tree species distribution of any life-stage did not shift directionally upward along elevation between the surveys. Temporal elevational shifts were species-specific and an order of magnitude lower than differences among tree life-stages within the surveys. Our results show that the observed range shifts among tree life-stages are more consistent with ontogenetic differences in the species’ environmental requirements than with responses to recent climate change. The distribution of seedlings substantially differed from saplings and adults, while the distribution of saplings did not differ from adults, indicating a critical transition between seedling and sapling tree life-stages. Future research has to take ontogenetic differences among life-stages into account as we found that distributional differences recently observed worldwide may not reflect climate change but rather the different environmental requirements of tree life-stages. PMID:26725258

A multilocus perspective on the speciation history of a North American aridland toad (Anaxyrus punctatus).

PubMed

Bryson, Robert W; Jaeger, Jef R; Lemos-Espinal, Julio A; Lazcano, David

2012-09-01

Interpretations of phylogeographic patterns can change when analyses shift from single gene-tree to multilocus coalescent analyses. Using multilocus coalescent approaches, a species tree and divergence times can be estimated from a set of gene trees while accounting for gene-tree stochasticity. We utilized the conceptual strengths of a multilocus coalescent approach coupled with complete range-wide sampling to examine the speciation history of a broadly distributed, North American warm-desert toad, Anaxyrus punctatus. Phylogenetic analyses provided strong support for three major lineages within A. punctatus. Each lineage broadly corresponded to one of three desert regions. Early speciation in A. punctatus appeared linked to late Miocene-Pliocene development of the Baja California peninsula. This event was likely followed by a Pleistocene divergence associated with the separation of the Chihuahuan and Sonoran Deserts. Our multilocus coalescent-based reconstruction provides an informative contrast to previous single gene-tree estimates of the evolutionary history of A. punctatus. Copyright © 2012 Elsevier Inc. All rights reserved.

The behavior of Metropolis-coupled Markov chains when sampling rugged phylogenetic distributions.

PubMed

Brown, Jeremy M; Thomson, Robert C

2018-02-15

Bayesian phylogenetic inference involves sampling from posterior distributions of trees, which sometimes exhibit local optima, or peaks, separated by regions of low posterior density. Markov chain Monte Carlo (MCMC) algorithms are the most widely used numerical method for generating samples from these posterior distributions, but they are susceptible to entrapment on individual optima in rugged distributions when they are unable to easily cross through or jump across regions of low posterior density. Ruggedness of posterior distributions can result from a variety of factors, including unmodeled variation in evolutionary processes and unrecognized variation in the true topology across sites or genes. Ruggedness can also become exaggerated when constraints are placed on topologies that require the presence or absence of particular bipartitions (often referred to as positive or negative constraints, respectively). These types of constraints are frequently employed when conducting tests of topological hypotheses (Bergsten et al. 2013; Brown and Thomson 2017). Negative constraints can lead to particularly rugged distributions when the data strongly support a forbidden clade, because monophyly of the clade can be disrupted by inserting outgroup taxa in many different ways. However, topological moves between the alternative disruptions are very difficult, because they require swaps between the inserted outgroup taxa while the data constrain taxa from the forbidden clade to remain close together on the tree. While this precise form of ruggedness is particular to negative constraints, trees with high posterior density can be separated by similarly complicated topological rearrangements, even in the absence of constraints.

The Effects of Tree Species on Soil Organic Carbon Content and Distribution in South Korea.

NASA Astrophysics Data System (ADS)

Oh, N. H.; Cha, J. Y.; Cha, Y. K.

2016-12-01

Soil organic carbon (SOC) content of forests is controlled by the dynamic balance between photosynthesis and respiration. Changes of tree species can affect the SOC content both directly by alteration in quantity and quality of newly photosynthesized inputs, and indirectly by changes in soil conditions such as root distribution and soil microbial communities. Although many studies have been conducted on the effects of tree species on SOC, the results are mixed possibly due to the locality and the scales of the studies. This can be overcome by systematic analysis on extensively collected samples of forest floors and soils. We investigated the impacts of tree species, dominantly pines (Pinus) and oaks (Quercus), on SOC stock and distribution in South Korea by conducting ANOVA and GLM analyses using the Korean National Forest Inventory data collected from 640 plots during 2007-2010. The trees used in the data were relatively young with 67% of them being less than 40 years old because of a nation-wide reforestation program started in the 1970s. The results demonstrated a clear contrast between Pinus and Quercus, depending on soil horizons. Forest floor SOC under Pinus was 6.98 ton C/ha, significantly higher than 5.30 ton C/ha under Quercus. In contrast, SOC in mineral soils was 51.31 ton C/ha under Pinus, significantly lower than 64.76 ton C/ha under Quercus. The total SOC content including both forest floor and mineral soils was significantly higher under Quercus than Pinus, suggesting that Quercus has a potential to sequester more atmospheric CO2 in the forests in Korea.

Past climate changes explain the phylogeography of Vitellaria paradoxa over Africa

PubMed Central

Allal, F; Sanou, H; Millet, L; Vaillant, A; Camus-Kulandaivelu, L; Logossa, Z A; Lefèvre, F; Bouvet, J-M

2011-01-01

The evolution of the savanna biome has been deeply marked by repeated contraction/expansion phases due to climate perturbations during the Quaternary period. In this study, we investigated the impact of the last glacial maximum (LGM) on the present genetic pattern of Vitellaria paradoxa (shea tree), a major African savanna tree. A range-wide sampling of the species enabled us to sample 374 individuals from 71 populations distributed throughout sub-Sahelian Africa. Trees were genotyped using 3 chloroplasts and 12 nuclear microsatellites, and were sequenced for 2 polymorphic chloroplast intergenic spacers. Analyses of genetic diversity and structure were based on frequency-based and Bayesian methods. Potential distributions of V. paradoxa at present, during the LGM and the last interglacial period, were examined using DIVA-GIS ecological niche modelling (ENM). Haplotypic and allelic richness varied significantly across the range according to chloroplast and nuclear microsatellites, which pointed to higher diversity in West Africa. A high but contrasted level of differentiation was revealed among populations with a clear phylogeographic signal, with both nuclear (FST=0.21; RST=0.28; RST>RST (permuted)) and chloroplast simple sequence repeats (SSRs) (GST=0.81; NST=0.90; NST>NST (permuted)). We identified a strong geographically related structure separating western and eastern populations, and a substructure in the eastern part of the area consistent with subspecies distinction. Using ENM, we deduced that perturbations during the LGM fragmented the potential eastern distribution of shea tree, but not its distribution in West Africa. Our main results suggest that climate variations are the major factor explaining the genetic pattern of V. paradoxa. PMID:21407253

A Survey of Avian Influenza in Tree Sparrows in China in 2011

PubMed Central

Han, Chunhua; Liu, Shuo; Chen, Jie; Li, Jinping; Zhang, Peng; Huang, Baoxu; Liu, Yuehuan; Chen, Jiming

2012-01-01

Tree sparrows (Passer montanus) are widely distributed in all seasons in many countries. In this study, a survey and relevant experiments on avian influenza (AI) in tree sparrows were conducted. The results suggested that the receptor for avian influenza viruses (AIVs), SAα2,3Gal, is abundant in the respiratory tract of tree sparrows, and most of the tree sparrows infected experimentally with two H5 subtype highly pathogenic avian influenza (HPAI) viruses died within five days after inoculation. Furthermore, no AIVs were isolated from the rectum eluate of 1300 tree sparrows, but 94 serological positives of AI were found in 800 tree sparrows. The serological positives were more prevalent for H5 subtype HPAI (94/800) than for H7 subtype AI (0/800), more prevalent for clade 2.3.2.1 H5 subtype HPAI (89/800) than for clade 2.3.4 (1/800) and clade 7.2 (4/800) H5 subtype HPAI, more prevalent for clade 2.3.2.1 H5 subtype HPAI in a city in southern China (82/800) than in a city in northern China (8/800). The serological data are all consistent with the distribution of the subtypes or clades of AI in poultry in China. Previously, sparrows or other passerine birds were often found to be pathogenically negative for AIVs, except when an AIV was circulating in the local poultry, or the tested passerine birds were from a region near waterfowl-rich bodies of water. Taken together, the data suggest that tree sparrows are susceptible to infection of AIVs, and surveys targeting sparrows can provide good serological data about the circulation of AIVs in relevant regions. PMID:22496742

A lognormal distribution of the lengths of terminal twigs on self-similar branches of elm trees.

PubMed

Koyama, Kohei; Yamamoto, Ken; Ushio, Masayuki

2017-01-11

Lognormal distributions and self-similarity are characteristics associated with a wide range of biological systems. The sequential breakage model has established a link between lognormal distributions and self-similarity and has been used to explain species abundance distributions. To date, however, there has been no similar evidence in studies of multicellular organismal forms. We tested the hypotheses that the distribution of the lengths of terminal stems of Japanese elm trees (Ulmus davidiana), the end products of a self-similar branching process, approaches a lognormal distribution. We measured the length of the stem segments of three elm branches and obtained the following results: (i) each occurrence of branching caused variations or errors in the lengths of the child stems relative to their parent stems; (ii) the branches showed statistical self-similarity; the observed error distributions were similar at all scales within each branch and (iii) the multiplicative effect of these errors generated variations of the lengths of terminal twigs that were well approximated by a lognormal distribution, although some statistically significant deviations from strict lognormality were observed for one branch. Our results provide the first empirical evidence that statistical self-similarity of an organismal form generates a lognormal distribution of organ sizes. © 2017 The Author(s).

Forcasting Shortleaf Pine Seed Crops in the Ouachita Mountains

Treesearch

Michael G. Shelton; Robert F. Wittwer

2004-01-01

We field tested a cone-rating system to forecast seed crops from 1993 to 1996 in 28 shortleaf pine (Pinus echinata Mill.) stands, which represented a wide range of stand conditions. Sample trees were visually assigned to one of three cone-density classes based on cone spacing, occurrence of cones in clusters, and distribution of cones within the...

Status of Sassafras albidum (Nutt.) Nees in the presence of laurel wilt disease and throughout the eastern United States

Treesearch

KaDonna C. Randolph

2017-01-01

Sassafras albidum (Sassafras) is an ecologically important tree species that is widely distributed throughout the eastern United States. Sassafras is presently threatened by Raffaelea lauricola, a fungus vectored by Xyleborus glabratus (Coleoptera: Curculionidae: Scolytinae; Redbay Ambrosia Beetle), which...

Historical and contemporary lessons from ponderosa pine genetic studies at the Fort Valley Experimental Forest, Arizona

Treesearch

Laura E. DeWald; Mary Frances Mahalovich

2008-01-01

Forest management will protect genetic integrity of tree species only if their genetic diversity is understood and considered in decision-making. Genetic knowledge is particularly important for species such as ponderosa pine (Pinus ponderosa Dougl. ex Laws.) that are distributed across wide geographic distances and types of climates. A ponderosa pine...

Fraxinus nigra (black ash) dieback in Minnesota: Regional variation and potential contributing factors

Treesearch

Brian J. Palik; Michael E. Ostry; Robert C. Venette; Ebrahim Abdela

2011-01-01

Extensive tree dieback is a recurrent issue in many regions. Crown dieback of Fraxinus nigra Marsh. (black ash; brown ash) in the northeastern and north central United States is an example. F. nigra is a widely distributed hardwood that is often the dominant species in wetland forests from Manitoba to Newfoundland and West...

Gap-phase regeneration inlongleaf pine wiregrass ecosystems

Treesearch

D.G. Brockway; K.W. Outcalt

1998-01-01

Naturally regenerated seedlings of longleaf pine are typically observed to cluster in the center of tree fall canopy gaps and be encircled by a wide zone from which they are generally excluded. Twelve representative canopy gaps distributed across 600 ha of a naturally regenerated uneven-agedlongleaf pine forest in the sandhills of north central Florida were examined to...

Effects of light acclimation on photosynthesis, growth, and biomass allocation in america chestnut seedlings

Treesearch

G. Geoff Wang; William L. Bauerle; Bryan T. Mudder

2006-01-01

American chestnut [Castanea dentate(Marshall) Borkh.] was a widely distributed tree species in the Eastern U.S., comprising an estimated 25 percent of native eastern hardwood forests. Chestnut blight eradicated American chestnut from the forest canopy by the 1950s, and now it only persists as understory sprouts. However, blight-resistant hybrids with...

Predictive mapping of soil organic carbon in wet cultivated lands using classification-tree based models: the case study of Denmark.

PubMed

Bou Kheir, Rania; Greve, Mogens H; Bøcher, Peder K; Greve, Mette B; Larsen, René; McCloy, Keith

2010-05-01

Soil organic carbon (SOC) is one of the most important carbon stocks globally and has large potential to affect global climate. Distribution patterns of SOC in Denmark constitute a nation-wide baseline for studies on soil carbon changes (with respect to Kyoto protocol). This paper predicts and maps the geographic distribution of SOC across Denmark using remote sensing (RS), geographic information systems (GISs) and decision-tree modeling (un-pruned and pruned classification trees). Seventeen parameters, i.e. parent material, soil type, landscape type, elevation, slope gradient, slope aspect, mean curvature, plan curvature, profile curvature, flow accumulation, specific catchment area, tangent slope, tangent curvature, steady-state wetness index, Normalized Difference Vegetation Index (NDVI), Normalized Difference Wetness Index (NDWI) and Soil Color Index (SCI) were generated to statistically explain SOC field measurements in the area of interest (Denmark). A large number of tree-based classification models (588) were developed using (i) all of the parameters, (ii) all Digital Elevation Model (DEM) parameters only, (iii) the primary DEM parameters only, (iv), the remote sensing (RS) indices only, (v) selected pairs of parameters, (vi) soil type, parent material and landscape type only, and (vii) the parameters having a high impact on SOC distribution in built pruned trees. The best constructed classification tree models (in the number of three) with the lowest misclassification error (ME) and the lowest number of nodes (N) as well are: (i) the tree (T1) combining all of the parameters (ME=29.5%; N=54); (ii) the tree (T2) based on the parent material, soil type and landscape type (ME=31.5%; N=14); and (iii) the tree (T3) constructed using parent material, soil type, landscape type, elevation, tangent slope and SCI (ME=30%; N=39). The produced SOC maps at 1:50,000 cartographic scale using these trees are highly matching with coincidence values equal to 90.5% (Map T1/Map T2), 95% (Map T1/Map T3) and 91% (Map T2/Map T3). The overall accuracies of these maps once compared with field observations were estimated to be 69.54% (Map T1), 68.87% (Map T2) and 69.41% (Map T3). The proposed tree models are relatively simple, and may be also applied to other areas. Copyright 2010 Elsevier Ltd. All rights reserved.

The discovery of the Amazonian tree flora with an updated checklist of all known tree taxa

PubMed Central

ter Steege, Hans; Vaessen, Rens W.; Cárdenas-López, Dairon; Sabatier, Daniel; Antonelli, Alexandre; de Oliveira, Sylvia Mota; Pitman, Nigel C. A.; Jørgensen, Peter Møller; Salomão, Rafael P.

2016-01-01

Amazonia is the most biodiverse rainforest on Earth, and the debate over how many tree species grow there remains contentious. Here we provide a checklist of all tree species collected to date, and describe spatial and temporal trends in data accumulation. We report 530,025 unique collections of trees in Amazonia, dating between 1707 and 2015, for a total of 11,676 species in 1225 genera and 140 families. These figures support recent estimates of 16,000 total Amazonian tree species based on ecological plot data from the Amazonian Tree Diversity Network. Botanical collection in Amazonia is characterized by three major peaks, centred around 1840, 1920, and 1980, which are associated with flora projects and the establishment of inventory plots. Most collections were made in the 20th century. The number of collections has increased exponentially, but shows a slowdown in the last two decades. We find that a species’ range size is a better predictor of the number of times it has been collected than the species’ estimated basin-wide population size. Finding, describing, and documenting the distribution of the remaining species will require coordinated efforts at under-collected sites. PMID:27406027

The discovery of the Amazonian tree flora with an updated checklist of all known tree taxa.

PubMed

Ter Steege, Hans; Vaessen, Rens W; Cárdenas-López, Dairon; Sabatier, Daniel; Antonelli, Alexandre; de Oliveira, Sylvia Mota; Pitman, Nigel C A; Jørgensen, Peter Møller; Salomão, Rafael P

2016-07-13

Amazonia is the most biodiverse rainforest on Earth, and the debate over how many tree species grow there remains contentious. Here we provide a checklist of all tree species collected to date, and describe spatial and temporal trends in data accumulation. We report 530,025 unique collections of trees in Amazonia, dating between 1707 and 2015, for a total of 11,676 species in 1225 genera and 140 families. These figures support recent estimates of 16,000 total Amazonian tree species based on ecological plot data from the Amazonian Tree Diversity Network. Botanical collection in Amazonia is characterized by three major peaks, centred around 1840, 1920, and 1980, which are associated with flora projects and the establishment of inventory plots. Most collections were made in the 20th century. The number of collections has increased exponentially, but shows a slowdown in the last two decades. We find that a species' range size is a better predictor of the number of times it has been collected than the species' estimated basin-wide population size. Finding, describing, and documenting the distribution of the remaining species will require coordinated efforts at under-collected sites.

The discovery of the Amazonian tree flora with an updated checklist of all known tree taxa

NASA Astrophysics Data System (ADS)

Ter Steege, Hans; Vaessen, Rens W.; Cárdenas-López, Dairon; Sabatier, Daniel; Antonelli, Alexandre; de Oliveira, Sylvia Mota; Pitman, Nigel C. A.; Jørgensen, Peter Møller; Salomão, Rafael P.

2016-07-01

Amazonia is the most biodiverse rainforest on Earth, and the debate over how many tree species grow there remains contentious. Here we provide a checklist of all tree species collected to date, and describe spatial and temporal trends in data accumulation. We report 530,025 unique collections of trees in Amazonia, dating between 1707 and 2015, for a total of 11,676 species in 1225 genera and 140 families. These figures support recent estimates of 16,000 total Amazonian tree species based on ecological plot data from the Amazonian Tree Diversity Network. Botanical collection in Amazonia is characterized by three major peaks, centred around 1840, 1920, and 1980, which are associated with flora projects and the establishment of inventory plots. Most collections were made in the 20th century. The number of collections has increased exponentially, but shows a slowdown in the last two decades. We find that a species’ range size is a better predictor of the number of times it has been collected than the species’ estimated basin-wide population size. Finding, describing, and documenting the distribution of the remaining species will require coordinated efforts at under-collected sites.

False discovery rate control incorporating phylogenetic tree increases detection power in microbiome-wide multiple testing.

PubMed

Xiao, Jian; Cao, Hongyuan; Chen, Jun

2017-09-15

Next generation sequencing technologies have enabled the study of the human microbiome through direct sequencing of microbial DNA, resulting in an enormous amount of microbiome sequencing data. One unique characteristic of microbiome data is the phylogenetic tree that relates all the bacterial species. Closely related bacterial species have a tendency to exhibit a similar relationship with the environment or disease. Thus, incorporating the phylogenetic tree information can potentially improve the detection power for microbiome-wide association studies, where hundreds or thousands of tests are conducted simultaneously to identify bacterial species associated with a phenotype of interest. Despite much progress in multiple testing procedures such as false discovery rate (FDR) control, methods that take into account the phylogenetic tree are largely limited. We propose a new FDR control procedure that incorporates the prior structure information and apply it to microbiome data. The proposed procedure is based on a hierarchical model, where a structure-based prior distribution is designed to utilize the phylogenetic tree. By borrowing information from neighboring bacterial species, we are able to improve the statistical power of detecting associated bacterial species while controlling the FDR at desired levels. When the phylogenetic tree is mis-specified or non-informative, our procedure achieves a similar power as traditional procedures that do not take into account the tree structure. We demonstrate the performance of our method through extensive simulations and real microbiome datasets. We identified far more alcohol-drinking associated bacterial species than traditional methods. R package StructFDR is available from CRAN. chen.jun2@mayo.edu. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Quantifying in situ phenotypic variability in the hydraulic properties of four tree species across their distribution range in Europe

PubMed Central

Sterck, F.; Torres-Ruiz, J. M.; Petit, G.; Cochard, H.; von Arx, G.; Lintunen, A.; Caldeira, M. C.; Capdeville, G.; Copini, P.; Gebauer, R.; Grönlund, L.; Hölttä, T.; Lobo-do-Vale, R.; Peltoniemi, M.; Stritih, A.; Urban, J.; Delzon, S.

2018-01-01

Many studies have reported that hydraulic properties vary considerably between tree species, but little is known about their intraspecific variation and, therefore, their capacity to adapt to a warmer and drier climate. Here, we quantify phenotypic divergence and clinal variation for embolism resistance, hydraulic conductivity and branch growth, in four tree species, two angiosperms (Betula pendula, Populus tremula) and two conifers (Picea abies, Pinus sylvestris), across their latitudinal distribution in Europe. Growth and hydraulic efficiency varied widely within species and between populations. The variability of embolism resistance was in general weaker than that of growth and hydraulic efficiency, and very low for all species but Populus tremula. In addition, no and weak support for a safety vs. efficiency trade-off was observed for the angiosperm and conifer species, respectively. The limited variability of embolism resistance observed here for all species except Populus tremula, suggests that forest populations will unlikely be able to adapt hydraulically to drier conditions through the evolution of embolism resistance. PMID:29715289

Tree cover in Central Africa: determinants and sensitivity under contrasted scenarios of global change

PubMed Central

Aleman, Julie C.; Blarquez, Olivier; Gourlet-Fleury, Sylvie; Bremond, Laurent; Favier, Charly

2017-01-01

Tree cover is a key variable for ecosystem functioning, and is widely used to study tropical ecosystems. But its determinants and their relative importance are still a matter of debate, especially because most regional and global analyses have not considered the influence of agricultural practices. More information is urgently needed regarding how human practices influence vegetation structure. Here we focused in Central Africa, a region still subjected to traditional agricultural practices with a clear vegetation gradient. Using remote sensing data and global databases, we calibrated a Random Forest model to correlatively link tree cover with climatic, edaphic, fire and agricultural practices data. We showed that annual rainfall and accumulated water deficit were the main drivers of the distribution of tree cover and vegetation classes (defined by the modes of tree cover density), but agricultural practices, especially pastoralism, were also important in determining tree cover. We simulated future tree cover with our model using different scenarios of climate and land-use (agriculture and population) changes. Our simulations suggest that tree cover may respond differently regarding the type of scenarios, but land-use change was an important driver of vegetation change even able to counterbalance the effect of climate change in Central Africa. PMID:28134259

A microwave scattering model for layered vegetation

NASA Technical Reports Server (NTRS)

Karam, Mostafa A.; Fung, Adrian K.; Lang, Roger H.; Chauhan, Narinder S.

1992-01-01

A microwave scattering model was developed for layered vegetation based on an iterative solution of the radiative transfer equation up to the second order to account for multiple scattering within the canopy and between the ground and the canopy. The model is designed to operate over a wide frequency range for both deciduous and coniferous forest and to account for the branch size distribution, leaf orientation distribution, and branch orientation distribution for each size. The canopy is modeled as a two-layered medium above a rough interface. The upper layer is the crown containing leaves, stems, and branches. The lower layer is the trunk region modeled as randomly positioned cylinders with a preferred orientation distribution above an irregular soil surface. Comparisons of this model with measurements from deciduous and coniferous forests show good agreements at several frequencies for both like and cross polarizations. Major features of the model needed to realize the agreement include allowance for: (1) branch size distribution, (2) second-order effects, and (3) tree component models valid over a wide range of frequencies.

GOTHIC: Gravitational oct-tree code accelerated by hierarchical time step controlling

NASA Astrophysics Data System (ADS)

Miki, Yohei; Umemura, Masayuki

2017-04-01

The tree method is a widely implemented algorithm for collisionless N-body simulations in astrophysics well suited for GPU(s). Adopting hierarchical time stepping can accelerate N-body simulations; however, it is infrequently implemented and its potential remains untested in GPU implementations. We have developed a Gravitational Oct-Tree code accelerated by HIerarchical time step Controlling named GOTHIC, which adopts both the tree method and the hierarchical time step. The code adopts some adaptive optimizations by monitoring the execution time of each function on-the-fly and minimizes the time-to-solution by balancing the measured time of multiple functions. Results of performance measurements with realistic particle distribution performed on NVIDIA Tesla M2090, K20X, and GeForce GTX TITAN X, which are representative GPUs of the Fermi, Kepler, and Maxwell generation of GPUs, show that the hierarchical time step achieves a speedup by a factor of around 3-5 times compared to the shared time step. The measured elapsed time per step of GOTHIC is 0.30 s or 0.44 s on GTX TITAN X when the particle distribution represents the Andromeda galaxy or the NFW sphere, respectively, with 224 = 16,777,216 particles. The averaged performance of the code corresponds to 10-30% of the theoretical single precision peak performance of the GPU.

A comparison of ground-based air-blast sprayer and aircraft application of fungicides to manage scab in tall pecan trees

USDA-ARS?s Scientific Manuscript database

Scab (caused by Venturia effusa) is the most destructive disease of pecan in the southeastern USA. The most widely used method to apply fungicide is air-blast (AB) sprayers. Aerially (A) applied sprays are also used, but the disease distribution and spray coverage of these two methods has not been c...

Distribution of tree species in Kentucky

Treesearch

Lake F. Compton; Robert K. Winters

1952-01-01

The Forest Survey is a Nation-wide activity of the Forest Service. The fivefold purpose of the Forest Survey is: (1) to make a field inventory of the present supply of standing timber; (2) to find out how fast this supply is being increased through growth; (3) to find out how fast it is being diminished through industrial and domestic uses, windfall, fire, disease, and...

Moderate-scale mapping methods of aspen stand types: a case study for Cedar Mountain in southern Utah

Treesearch

Chad M. Oukrop; David M. Evans; Dale L. Bartos; R. Douglas Ramsey; Ronald J. Ryel

2011-01-01

Quaking aspen (Populus tremuloides Michx.) are the most widely distributed tree species across North America, but its dominance is declining in many areas of the western United States, with certain areas experiencing rapid mortality events over the past decade. The loss of aspen from western landscapes will continue to profoundly impact biological, commercial, and...

Condensed tannins: Quinone methide intermediates in procyanidin synthesis

Treesearch

Richard W. Hemingway; L. Y. Foo

1983-01-01

Proanthocyanidins (condensed tanruns) are widely distributed in plants and are found in sufficiently high concentration in some tree barks to encourage their industrial utilization. These polymers consist of flavanoid units linked through the C-4 of the pyran ring to the C-6 or C-8 carbons of the aromatic A-ring. Recent advances in the chemistry of condensed tannins...

Oak decline in central hardwood forests: frequency, spatial extent, and scale

Treesearch

Steven W Oak; Marty Spetich; Randall S. Morin

2015-01-01

Oak decline is a widely distributed disease that results from an interacting set of factors in the Central Hardwood Region. Episodes of decline have been reported since before the turn of the twentieth century and from every state in the region. It is a stress-mediated disease that results from the interactions of physiologically mature trees, abiotic and biotic...

The identification of Douglas-fir wood

Treesearch

Forest Products Laboratory (U.S.)

1963-01-01

Douglas-fir is one of the largest, most abundant and widely distributed species of trees native to North America, and next to the southern yellow pines, it is cut in the greatest quantities of any wood of commercial importance. It belongs to the coniferous family and is, therefore, a softwood. Other names for Douglas -fir are red fir, yellow fir, Oregon pine, Puget...

Adapting nematode-based biological control systems to North American populations of Sirex noctilio

Treesearch

David W. Williams; Victor C. Mastro

2011-01-01

The European woodwasp, Sirex noctilio, was found in Oswego County, NY, in 2004. During the past 6 years, surveys have revealed that it is distributed over a wide area of eastern North America. Because S. noctilio kills relatively healthy trees, it poses a serious threat to pine forests and plantations in the United States and...

Flowering phenology and its implications for management of big-leaf mahogany Swietenia macrophylla in Brazilian Amazonia

Treesearch

J. Grogan; M. D. Loveless

2013-01-01

Premise of the study: Flowering phenology is a crucial determinant of reproductive success and offspring genetic diversity in plants. We measure the fl owering phenology of big-leaf mahogany ( Swietenia macrophylla , Meliaceae), a widely distributed neotropical tree, and explore how disturbance from logging impacts its reproductive biology. • Methods: We use a crown...

Widespread inbreeding and unexpected geographic patterns of genetic variation in eastern hemlock (Tsuga canadensis), an imperiled North American conifer

Treesearch

Kevin M. Potter; Robert M. Jetton; William S. Dvorak; Valerie D. Hipkins; Rusty Rhea; W. Andrew Whittier

2012-01-01

Eastern hemlock (Tsuga canadensis [L.] Carr.) is an ecologically important tree species experiencing severe mortality across much of its eastern North American distribution, caused by infestation of the exotic hemlock woolly adelgid (Adelges tsugae Annand). To guide gene conservation strategies for this imperiled conifer, we conducted a range-wide genetic variation...

Genetic and palaeo-climatic evidence for widespread persistence of the coastal tree species Eucalyptus gomphocephala (Myrtaceae) during the Last Glacial Maximum.

PubMed

Nevill, Paul G; Bradbury, Donna; Williams, Anna; Tomlinson, Sean; Krauss, Siegfried L

2014-01-01

Few phylogeographic studies have been undertaken of species confined to narrow, linear coastal systems where past sea level and geomorphological changes may have had a profound effect on species population sizes and distributions. In this study, a phylogeographic analysis was conducted of Eucalyptus gomphocephala (tuart), a tree species restricted to a 400 × 10 km band of coastal sand-plain in south west Australia. Here, there is little known about the response of coastal vegetation to glacial/interglacial climate change, and a test was made as to whether this species was likely to have persisted widely through the Last Glacial Maximum (LGM), or conforms to a post-LGM dispersal model of recovery from few refugia. The genetic structure over the entire range of tuart was assessed using seven nuclear (21 populations; n = 595) and four chloroplast (24 populations; n = 238) microsatellite markers designed for eucalypt species. Correlative palaeodistribution modelling was also conducted based on five climatic variables, within two LGM models. The chloroplast markers generated six haplotypes, which were strongly geographically structured (GST = 0·86 and RST = 0·75). Nuclear microsatellite diversity was high (overall mean HE 0·75) and uniformly distributed (FST = 0·05), with a strong pattern of isolation by distance (r(2) = 0·362, P = 0·001). Distribution models of E. gomphocephala during the LGM showed a wide distribution that extended at least 30 km westward from the current distribution to the palaeo-coastline. The chloroplast and nuclear data suggest wide persistence of E. gomphocephala during the LGM. Palaeodistribution modelling supports the conclusions drawn from genetic data and indicates a widespread westward shift of E. gomphocephala onto the exposed continental shelf during the LGM. This study highlights the importance of the inclusion of complementary, non-genetic data (information on geomorphology and palaeoclimate) to interpret phylogeographic patterns.

Genetic and palaeo-climatic evidence for widespread persistence of the coastal tree species Eucalyptus gomphocephala (Myrtaceae) during the Last Glacial Maximum

PubMed Central

Nevill, Paul G.; Bradbury, Donna; Williams, Anna; Tomlinson, Sean; Krauss, Siegfried L.

2014-01-01

Background and Aims Few phylogeographic studies have been undertaken of species confined to narrow, linear coastal systems where past sea level and geomorphological changes may have had a profound effect on species population sizes and distributions. In this study, a phylogeographic analysis was conducted of Eucalyptus gomphocephala (tuart), a tree species restricted to a 400 × 10 km band of coastal sand-plain in south west Australia. Here, there is little known about the response of coastal vegetation to glacial/interglacial climate change, and a test was made as to whether this species was likely to have persisted widely through the Last Glacial Maximum (LGM), or conforms to a post-LGM dispersal model of recovery from few refugia. Methods The genetic structure over the entire range of tuart was assessed using seven nuclear (21 populations; n = 595) and four chloroplast (24 populations; n = 238) microsatellite markers designed for eucalypt species. Correlative palaeodistribution modelling was also conducted based on five climatic variables, within two LGM models. Key Results The chloroplast markers generated six haplotypes, which were strongly geographically structured (GST = 0·86 and RST = 0·75). Nuclear microsatellite diversity was high (overall mean HE 0·75) and uniformly distributed (FST = 0·05), with a strong pattern of isolation by distance (r2 = 0·362, P = 0·001). Distribution models of E. gomphocephala during the LGM showed a wide distribution that extended at least 30 km westward from the current distribution to the palaeo-coastline. Conclusions The chloroplast and nuclear data suggest wide persistence of E. gomphocephala during the LGM. Palaeodistribution modelling supports the conclusions drawn from genetic data and indicates a widespread westward shift of E. gomphocephala onto the exposed continental shelf during the LGM. This study highlights the importance of the inclusion of complementary, non-genetic data (information on geomorphology and palaeoclimate) to interpret phylogeographic patterns. PMID:24284819

Development of microsatellite markers for Anadenanthera colubrina (Leguminosae), a neotropical tree species.

PubMed

Feres, Juliana Massimino; Monteiro, Mariza; Zucchi, Maria I; Pinheiro, José B; Mestriner, Moacyr A; Alzate-Marin, Ana Lilia

2012-04-01

We developed and characterized nuclear microsatellite markers for Anadenanthera colubrina, a tropical tree species widely distributed in South America. Leaf samples of mature A. colubrina trees, popularly called "angico," were collected from an area that is greatly impacted by agricultural practices in the region of Ribeirão Preto in São Paulo State in southeastern Brazil. Twenty simple sequence repeat (SSR) markers were developed, 14 of which had polymorphic loci. A total of 96 alleles were detected with an average of 6.86 alleles per polymorphic locus. The expected heterozygosity, calculated at polymorphic loci, ranged from 0.18 to 0.83. Finally, we demonstrated that 18 loci were cross-amplified in A. peregrina. A total of 14 polymorphic markers suggest a high potential for genetic diversity, gene flow, and mating system analyses in A. colubrina.

Coarse root topology of Norway spruce (Picea abies) and its effects on slope stability

NASA Astrophysics Data System (ADS)

Lith, Aniek; Schmaltz, Elmar; Bogaard, Thom; Keesstra, Saskia

2017-04-01

The structural distribution of coarse roots and its beneficial effects on soil reinforcement has widely been assessed. However, it is still not fully understood how topological features of coarse roots (e.g. branching patterns) are affected by slope inclination and further influence the ability of young trees to reinforce soil. This study aims to analyse empirically the impact of slope gradient on the topological development of coarse roots and thus to assess its effects on soil reinforcement. We performed root system excavations on two young Picea abies: tree A on a gently inclined plane (β ≈ 12°) where slope failures are not expected; tree B on a slope (β ≈ 35°) with failure potential. The diameter (d) of the segments between distinct root nodes (root ends, branching locations, direction changes and attachments to stem) of coarse roots (d > 2mm) were measured in situ. The spatial coordinates (x,y,z) of the nodes and surface were measured on a plane raster grid, from which segment length (ls), direction and inclination towards the surface (βr) were derived. Roots and segments were classified into laterals (βr < 10°), obliques (10° ≤ βr < 70°) and verticals (βr ≥ 70°), with βr,max = 90°. We assigned topological orders to the segments according to developmental (DSC) and functional segment classifications (FSC), to obtain quantitative relations between the topological order and number of segments, total and average ls. The maximal root cohesion (cr) of each segment was assessed using material specific tensile forces (Tr), root area ratio (RAR) and βr, assuming that a potential slip surface would cross the root system parallel to the slope. Laterals depicted the majority of roots (57 %) for tree A orientated rather in upslope direction (76.8 %), whereas tree B showed mostly obliques (54 %) orientated rather in downslope direction (55.4 %). Vertical roots were scarcely observable for both trees. DSC showed a high r2 (> 0.84) for the segments and ls. FSC showed high r2 (> 0.95) for the number of segments and the total length. RAR values of tree B are distributed rather upslope (76.8 % of RARtot), compared to 44.5 % of RARtot for tree A. The average cr (0.15) of each segment of tree B was remarkably higher than of tree A (0.10), leading to the conclusion that the slope has a strong influence on cr itself. This is supported by comparing the distribution of cr for both trees, where tree B tends to produce a higher cr in upslope direction (68.7 % of total cr) than tree A (37.7 %). In contrast to our expectations, tree B shows generally a higher cr compared to tree A, despite lower subsurface biomass. The findings indicate that the distinct branching patterns of coarse roots might determine the distribution of the RAR and thus lead to a higher reinforcement potential of young Picea abies on slopes.

Branching out to residential lands: Missions and strategies of five tree distribution programs in the U.S.

Treesearch

Vi D. Nguyen; Lara A. Roman; Dexter H. Locke; Sarah K. Mincey; Jessica R. Sanders; Erica Smith Fichman; Mike Duran-Mitchell; Sarah Lumban Tobing

2017-01-01

Residential lands constitute a major component of existing and possible tree canopy in many cities in the United States. To expand the urban forest on these lands, some municipalities and nonprofit organizations have launched residential yard tree distribution programs, also known as tree giveaway programs. This paper describes the operations of five tree distribution...

Periodical cicadas use light for oviposition site selection.

PubMed

Yang, Louie H

2006-12-07

Organisms use incomplete information from local experience to assess the suitability of potential habitat sites over a wide range of spatial and temporal scales. Although ecologists have long recognized the importance of spatial scales in habitat selection, few studies have investigated the temporal scales of habitat selection. In particular, cues in the immediate environment may commonly provide indirect information about future habitat quality. In periodical cicadas (Magicicada spp.), oviposition site selection represents a very long-term habitat choice. Adult female cicadas insert eggs into tree branches during a few weeks in the summer of emergence, but their oviposition choices determine the underground habitats of root-feeding nymphs over the following 13 or 17 years. Here, field experiments are used to show that female cicadas use the local light environment of host trees during the summer of emergence to select long-term host trees. Light environments may also influence oviposition microsite selection within hosts, suggesting a potential behavioural mechanism for associating solar cues with host trees. In contrast, experimental nutrient enrichment of host trees did not influence cicada oviposition densities. These findings suggest that the light environments around host trees may provide a robust predictor of host tree quality in the near future. This habitat selection may influence the spatial distribution of several cicada-mediated ecological processes in eastern North American forests.

Periodical cicadas use light for oviposition site selection

PubMed Central

Yang, Louie H

2006-01-01

Organisms use incomplete information from local experience to assess the suitability of potential habitat sites over a wide range of spatial and temporal scales. Although ecologists have long recognized the importance of spatial scales in habitat selection, few studies have investigated the temporal scales of habitat selection. In particular, cues in the immediate environment may commonly provide indirect information about future habitat quality. In periodical cicadas (Magicicada spp.), oviposition site selection represents a very long-term habitat choice. Adult female cicadas insert eggs into tree branches during a few weeks in the summer of emergence, but their oviposition choices determine the underground habitats of root-feeding nymphs over the following 13 or 17 years. Here, field experiments are used to show that female cicadas use the local light environment of host trees during the summer of emergence to select long-term host trees. Light environments may also influence oviposition microsite selection within hosts, suggesting a potential behavioural mechanism for associating solar cues with host trees. In contrast, experimental nutrient enrichment of host trees did not influence cicada oviposition densities. These findings suggest that the light environments around host trees may provide a robust predictor of host tree quality in the near future. This habitat selection may influence the spatial distribution of several cicada-mediated ecological processes in eastern North American forests. PMID:17015354

Distribution of the cone insect, Dioryctria disclusa, in red pine.

Treesearch

William J. Mattson

1976-01-01

Within the crowns of red pine, Pinus resinosa Ait., trees, larvae of the cone insect, Dioryctria disclusa Heinrich, tended to follow the distributions of their foods. Between-tree distributions of larvae, however, were relatable to food distributions in only two of five years. Cone damage/tree by D. disclusa increased linearly with cone abundance per tree when insect...

Phylogenetic tree construction using trinucleotide usage profile (TUP).

PubMed

Chen, Si; Deng, Lih-Yuan; Bowman, Dale; Shiau, Jyh-Jen Horng; Wong, Tit-Yee; Madahian, Behrouz; Lu, Henry Horng-Shing

2016-10-06

It has been a challenging task to build a genome-wide phylogenetic tree for a large group of species containing a large number of genes with long nucleotides sequences. The most popular method, called feature frequency profile (FFP-k), finds the frequency distribution for all words of certain length k over the whole genome sequence using (overlapping) windows of the same length. For a satisfactory result, the recommended word length (k) ranges from 6 to 15 and it may not be a multiple of 3 (codon length). The total number of possible words needed for FFP-k can range from 4 6 =4096 to 4 15 . We propose a simple improvement over the popular FFP method using only a typical word length of 3. A new method, called Trinucleotide Usage Profile (TUP), is proposed based only on the (relative) frequency distribution using non-overlapping windows of length 3. The total number of possible words needed for TUP is 4 3 =64, which is much less than the total count for the recommended optimal "resolution" for FFP. To build a phylogenetic tree, we propose first representing each of the species by a TUP vector and then using an appropriate distance measure between pairs of the TUP vectors for the tree construction. In particular, we propose summarizing a DNA sequence by a matrix of three rows corresponding to three reading frames, recording the frequency distribution of the non-overlapping words of length 3 in each of the reading frame. We also provide a numerical measure for comparing trees constructed with various methods. Compared to the FFP method, our empirical study showed that the proposed TUP method is more capable of building phylogenetic trees with a stronger biological support. We further provide some justifications on this from the information theory viewpoint. Unlike the FFP method, the TUP method takes the advantage that the starting of the first reading frame is (usually) known. Without this information, the FFP method could only rely on the frequency distribution of overlapping words, which is the average (or mixture) of the frequency distributions of three possible reading frames. Consequently, we show (from the entropy viewpoint) that the FFP procedure could dilute important gene information and therefore provides less accurate classification.

Northward migration under a changing climate: a case study of blackgum (Nyssa Sylvatica)

Treesearch

Johanna Desprez; Basil V. Iannone III; Peilin Yang; Christopher M. Oswalt; Songlin Fei

2014-01-01

Species are predicted to shift their distribution ranges in response to climate change. Region-wide, empirically-based studies, however, are still limited to support these predictions. We used a model tree species, blackgum (Nyssa sylvatica), to study climate-induced range shift. Data collected from two separate sampling periods (1980s and 2007) by the USDA’s Forestry...

Historical and contemporary lessons from ponderosa pine genetic studies at the Fort Valley Experimental Forest, Arizona (P-53)

Treesearch

Laura E. DeWald; Mary Frances Mahalovich

2008-01-01

Forest management will protect genetic integrity of tree species only if their genetic diversity is understood and considered in decision-making. Genetic knowledge is particularly important for species such as ponderosa pine (Pinus ponderosa Dougl. ex Laws.) that are distributed across wide geographic distances and types of climates. A ponderosa pine study initiated in...

The Seeley Lake larch: Living link to indian and frontier history

Treesearch

Stephen F. Arno

2010-01-01

Western Montana’s Big Blackfoot River was once the gateway to a magnificent forest and the conduit that fed an immense sawmill. Epic log drives once choked the waterway full of timber each spring. The Big Blackfoot drainage was known for its majestic, centuries-old ponderosa pine and western larch trees. Although stately old ponderosas were widely distributed across...

Allozyme and microsatellite data reveal small clone size and high genetic diversity in aspen in the southern Cascade Mountains

Treesearch

Jennifer DeWoody; Thomas H. Rickman; Bobette E. Jones; Valerie D. Hipkins

2009-01-01

The most widely distributed tree in North America, quaking aspen (Populus tremuloides, Michx.), reproduces sexually via seed and clonally via suckers. The size of aspen clones varies geographically, generally smaller in the east and large in the arid Intermountain West. In order to describe clone size and genetic structure of aspen in the southern Cascade...

New host record for the Asian Ambrosia beetle, Xylosandrus crassiusculus (Motschulsky) (Coleoptera: Curculionidae)

Treesearch

Scott Horn; George N. Horn

2006-01-01

The Asian ambrosia beetle, Xylosandrus crassiusculus (Motchulsky), is a widely distributed beetie found in southern Asia, Africa, Indonesia, Australia, Islands of the Pacific, Europe, and the U.S. (Wood 1982, Great Basin Naturalist Memoirs No. 6, BYU; Solot3on 1995, insect Borers in N. Am. broadleaf Trees and Shrubs, AH-706; Pennacchio et al. 2003, Redia 86: 77-80). It...

Effects of dwarf mistletoe on stand structure of lodgepole pine forests 21-28 years post-mountain pine beetle epidemic in central Oregon

Treesearch

Michelle C. Agne; David C. Shaw; Travis J. Woolley; Mónica E. Queijeiro-Bolaños; Mai-He. Li

2014-01-01

Lodgepole pine (Pinus contorta) forests are widely distributed throughout North America and are subject to mountain pine beetle (Dendroctonus ponderosae) epidemics, which have caused mortality over millions of hectares of mature trees in recent decades. Mountain pine beetle is known to influence stand structure, and has the ability to impact many forest processes....

Climate change effects on the geographic distribution of specialist tree species of the Brazilian tropical dry forests.

PubMed

Rodrigues, P M S; Silva, J O; Eisenlohr, P V; Schaefer, C E G R

2015-08-01

The aim of this study was to evaluate the ecological niche models (ENMs) for three specialist trees (Anadenanthera colubrina, Aspidosperma pyrifolium and Myracrodruon urundeuva) in seasonally dry tropical forests (SDTFs) in Brazil, considering present and future pessimist scenarios (2080) of climate change. These three species exhibit typical deciduousness and are widely distributed by SDTF in South America, being important in studies of the historical and evolutionary processes experienced by this ecosystem. The modeling of the potential geographic distribution of species was done by the method of maximum entropy (Maxent).We verified a general expansion of suitable areas for occurrence of the three species in future (c.a., 18%), although there was reduction of areas with high environmental suitability in Caatinga region. Precipitation of wettest quarter and temperature seasonality were the predictor variables that most contributed to our models. Climatic changes can provide more severe and longer dry season with increasing temperature and tree mortality in tropics. On this scenario, areas currently occupied by rainforest and savannas could become more suitable for occurrence of the SDTF specialist trees, whereas regions occupied by Caatinga could not support the future level of unsustainable (e.g., aridity). Long-term multidisciplinary studies are necessary to make reliable predictions of the plant's adaptation strategies and responses to climate changes in dry forest at community level. Based on the high deforestation rate, endemism and threat, public policies to minimize the effects of climate change on the biodiversity found within SDTFs must be undertaken rapidly.

Widespread Amazon forest tree mortality from a single cross-basin squall line event

NASA Astrophysics Data System (ADS)

Negrón-Juárez, Robinson I.; Chambers, Jeffrey Q.; Guimaraes, Giuliano; Zeng, Hongcheng; Raupp, Carlos F. M.; Marra, Daniel M.; Ribeiro, Gabriel H. P. M.; Saatchi, Sassan S.; Nelson, Bruce W.; Higuchi, Niro

2010-08-01

Climate change is expected to increase the intensity of extreme precipitation events in Amazonia that in turn might produce more forest blowdowns associated with convective storms. Yet quantitative tree mortality associated with convective storms has never been reported across Amazonia, representing an important additional source of carbon to the atmosphere. Here we demonstrate that a single squall line (aligned cluster of convective storm cells) propagating across Amazonia in January, 2005, caused widespread forest tree mortality and may have contributed to the elevated mortality observed that year. Forest plot data demonstrated that the same year represented the second highest mortality rate over a 15-year annual monitoring interval. Over the Manaus region, disturbed forest patches generated by the squall followed a power-law distribution (scaling exponent α = 1.48) and produced a mortality of 0.3-0.5 million trees, equivalent to 30% of the observed annual deforestation reported in 2005 over the same area. Basin-wide, potential tree mortality from this one event was estimated at 542 ± 121 million trees, equivalent to 23% of the mean annual biomass accumulation estimated for these forests. Our results highlight the vulnerability of Amazon trees to wind-driven mortality associated with convective storms. Storm intensity is expected to increase with a warming climate, which would result in additional tree mortality and carbon release to the atmosphere, with the potential to further warm the climate system.

Spatial Distribution Patterns in the Very Rare and Species-Rich Picea chihuahuana Tree Community (Mexico).

PubMed

Wehenkel, Christian; Brazão-Protázio, João Marcelo; Carrillo-Parra, Artemio; Martínez-Guerrero, José Hugo; Crecente-Campo, Felipe

2015-01-01

The very rare Mexican Picea chihuahuana tree community covers an area of no more than 300 ha in the Sierra Madre Occidental. This special tree community has been the subject of several studies aimed at learning more about the genetic structure and ecology of the species and the potential effects of climate change. The spatial distribution of trees is a result of many ecological processes and can affect the degree of competition between neighbouring trees, tree density, variability in size and distribution, regeneration, survival, growth, mortality, crown formation and the biological diversity within forest communities. Numerous scale-dependent measures have been established in order to describe spatial forest structure. The overall aim of most of these studies has been to obtain data to help design preservation and conservation strategies. In this study, we examined the spatial distribution pattern of trees in the P. chihuahuana tree community in 12 localities, in relation to i) tree stand density, ii) diameter distribution (vertical structure), iii) tree species diversity, iv) geographical latitude and v) tree dominance at a fine scale (in 0.25 ha plots), with the aim of obtaining a better understanding of the complex ecosystem processes and biological diversity. Because of the strongly mixed nature of this tree community, which often produces low population densities of each tree species and random tree fall gaps caused by tree death, we expect aggregated patterns in individual Picea chihuahuana trees and in the P. chihuahuana tree community, repulsive Picea patterns to other tree species and repulsive patterns of young to adult trees. Each location was represented by one plot of 50 x 50 m (0.25 ha) established in the centre of the tree community. The findings demonstrate that the hypothesis of aggregated tree pattern is not applicable to the mean pattern measured by Clark-Evans index, Uniform Angle index and Mean Directional index of the uneven-aged P. chihuahuana trees and P. chihuahuana tree community and but to specific spatial scales measured by the univariate L-function. The spatial distribution pattern of P. chihuahuana trees was found to be independent of patches of other tree species measured by the bivariate L-function. The spatial distribution was not significantly related to tree density, diameter distribution or tree species diversity. The index of Clark and Evans decreased significantly from the southern to northern plots containing all tree species. Self-thinning due to intra and inter-specific competition-induced mortality is probably the main cause of the decrease in aggregation intensity during the course of population development in this tree community. We recommend the use of larger sampling plots (> 0.25 ha) in uneven-aged and species-rich forest ecosystems to detect less obvious, but important, relationships between spatial tree pattern and functioning and diversity in these forests.

Spatial Distribution Patterns in the Very Rare and Species-Rich Picea chihuahuana Tree Community (Mexico)

PubMed Central

Wehenkel, Christian; Brazão-Protázio, João Marcelo; Carrillo-Parra, Artemio; Martínez-Guerrero, José Hugo; Crecente-Campo, Felipe

2015-01-01

The very rare Mexican Picea chihuahuana tree community covers an area of no more than 300 ha in the Sierra Madre Occidental. This special tree community has been the subject of several studies aimed at learning more about the genetic structure and ecology of the species and the potential effects of climate change. The spatial distribution of trees is a result of many ecological processes and can affect the degree of competition between neighbouring trees, tree density, variability in size and distribution, regeneration, survival, growth, mortality, crown formation and the biological diversity within forest communities. Numerous scale-dependent measures have been established in order to describe spatial forest structure. The overall aim of most of these studies has been to obtain data to help design preservation and conservation strategies. In this study, we examined the spatial distribution pattern of trees in the P. chihuahuana tree community in 12 localities, in relation to i) tree stand density, ii) diameter distribution (vertical structure), iii) tree species diversity, iv) geographical latitude and v) tree dominance at a fine scale (in 0.25 ha plots), with the aim of obtaining a better understanding of the complex ecosystem processes and biological diversity. Because of the strongly mixed nature of this tree community, which often produces low population densities of each tree species and random tree fall gaps caused by tree death, we expect aggregated patterns in individual Picea chihuahuana trees and in the P. chihuahuana tree community, repulsive Picea patterns to other tree species and repulsive patterns of young to adult trees. Each location was represented by one plot of 50 x 50 m (0.25 ha) established in the centre of the tree community. The findings demonstrate that the hypothesis of aggregated tree pattern is not applicable to the mean pattern measured by Clark-Evans index, Uniform Angle index and Mean Directional index of the uneven-aged P. chihuahuana trees and P. chihuahuana tree community and but to specific spatial scales measured by the univariate L-function. The spatial distribution pattern of P. chihuahuana trees was found to be independent of patches of other tree species measured by the bivariate L-function. The spatial distribution was not significantly related to tree density, diameter distribution or tree species diversity. The index of Clark and Evans decreased significantly from the southern to northern plots containing all tree species. Self-thinning due to intra and inter-specific competition-induced mortality is probably the main cause of the decrease in aggregation intensity during the course of population development in this tree community. We recommend the use of larger sampling plots (> 0.25 ha) in uneven-aged and species-rich forest ecosystems to detect less obvious, but important, relationships between spatial tree pattern and functioning and diversity in these forests. PMID:26496189

Calibration of the Diameter Distribution Derived from the Area-based Approach with Individual Tree-based Diameter Estimates Using the Airborne Laser Scanning

NASA Astrophysics Data System (ADS)

Xu, Q.; Hou, Z.; Maltamo, M.; Tokola, T.

2015-12-01

Diameter distributions of trees are important indicators of current forest stand structure and future dynamics. A new method was proposed in the study to combine the diameter distributions derived from the area-based approach (ABA) and the diameter distribution derived from the individual tree detection (ITD) in order to obtain more accurate forest stand attributes. Since dominant trees can be reliably detected and measured by the Lidar data via the ITD, the focus of the study is to retrieve the suppressed trees (trees that were missed by the ITD) from the ABA. Replacement and histogram matching were respectively employed at the plot level to retrieve the suppressed trees. Cut point was detected from the ITD-derived diameter distribution for each sample plot to distinguish dominant trees from the suppressed trees. The results showed that calibrated diameter distributions were more accurate in terms of error index and the entire growing stock estimates. Compared with the best performer between the ABA and the ITD, calibrated diameter distributions decreased the relative RMSE of the estimated entire growing stock, saw log and pulpwood fractions by 2.81%, 3.05% and 7.73% points respectively. Calibration improved the estimation of pulpwood fraction significantly, resulting in a negligible bias of the estimated entire growing stock.

Density-dependent vulnerability of forest ecosystems to drought

USGS Publications Warehouse

Bottero, Alessandra; D'Amato, Anthony W.; Palik, Brian J.; Bradford, John B.; Fraver, Shawn; Battaglia, Mike A.; Asherin, Lance A.

2017-01-01

1. Climate models predict increasing drought intensity and frequency for many regions, which may have negative consequences for tree recruitment, growth and mortality, as well as forest ecosystem services. Furthermore, practical strategies for minimizing vulnerability to drought are limited. Tree population density, a metric of tree abundance in a given area, is a primary driver of competitive intensity among trees, which influences tree growth and mortality. Manipulating tree population density may be a mechanism for moderating drought-induced stress and growth reductions, although the relationship between tree population density and tree drought vulnerability remains poorly quantified, especially across climatic gradients.2. In this study, we examined three long-term forest ecosystem experiments in two widely distributed North American pine species, ponderosa pine Pinus ponderosa (Lawson & C. Lawson) and red pine Pinus resinosa (Aiton), to better elucidate the relationship between tree population density, growth and drought. These experiments span a broad latitude and aridity range and include tree population density treatments that have been purposefully maintained for several decades. We investigated how tree population density influenced resistance (growth during drought) and resilience (growth after drought compared to pre-drought growth) of stand-level growth during and after documented drought events.3. Our results show that relative tree population density was negatively related to drought resistance and resilience, indicating that trees growing at lower densities were less vulnerable to drought. This result was apparent in all three forest ecosystems, and was consistent across species, stand age and drought intensity.4. Synthesis and applications. Our results highlighted that managing pine forest ecosystems at low tree population density represents a promising adaptive strategy for reducing the adverse impacts of drought on forest growth in coming decades. Nonetheless, the broader applicability of our findings to other types of forest ecosystems merits additional investigation.

Where to nest? Ecological determinants of chimpanzee nest abundance and distribution at the habitat and tree species scale.

PubMed

Carvalho, Joana S; Meyer, Christoph F J; Vicente, Luis; Marques, Tiago A

2015-02-01

Conversion of forests to anthropogenic land-uses increasingly subjects chimpanzee populations to habitat changes and concomitant alterations in the plant resources available to them for nesting and feeding. Based on nest count surveys conducted during the dry season, we investigated nest tree species selection and the effect of vegetation attributes on nest abundance of the western chimpanzee, Pan troglodytes verus, at Lagoas de Cufada Natural Park (LCNP), Guinea-Bissau, a forest-savannah mosaic widely disturbed by humans. Further, we assessed patterns of nest height distribution to determine support for the anti-predator hypothesis. A zero-altered generalized linear mixed model showed that nest abundance was negatively related to floristic diversity (exponential form of the Shannon index) and positively with the availability of smaller-sized trees, reflecting characteristics of dense-canopy forest. A positive correlation between nest abundance and floristic richness (number of plant species) and composition indicated that species-rich open habitats are also important in nest site selection. Restricting this analysis to feeding trees, nest abundance was again positively associated with the availability of smaller-sized trees, further supporting the preference for nesting in food tree species from dense forest. Nest tree species selection was non-random, and oil palms were used at a much lower proportion (10%) than previously reported from other study sites in forest-savannah mosaics. While this study suggests that human disturbance may underlie the exclusive arboreal nesting at LCNP, better quantitative data are needed to determine to what extent the construction of elevated nests is in fact a response to predators able to climb trees. Given the importance of LCNP as refuge for Pan t. verus our findings can improve conservation decisions for the management of this important umbrella species as well as its remaining suitable habitats. © 2014 Wiley Periodicals, Inc.

Compact 0-complete trees: A new method for searching large files

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

Orlandic, R.; Pfaltz, J.L.

1988-01-26

In this report, a novel approach to ordered retrieval in very large files is developed. The method employs a B-tree like search algorithm that is independent of key type or key length because all keys in index blocks are encoded by a 1 byte surrogate. The replacement of actual key sequences by the 1 byte surrogate ensures a maximal possible fan out and greatly reduces the storage overhead of maintaining access indices. Initially, retrieval in binary trie structure is developed. With the aid of a fairly complex recurrence relation, the rather scraggly binary trie is transformed into compact multi-way searchmore » tree. Then the recurrence relation itself is replaced by an unusually simple search algorithm. Then implementation details and empirical performance results are presented. Reduction of index size by 50%--75% opens up the possibility of replicating system-wide indices for parallel access in distributed databases. 23 figs.« less

Ants inhabiting myrmecophytic ferns regulate the distribution of lianas on emergent trees in a Bornean tropical rainforest.

PubMed

Tanaka, Hiroshi O; Itioka, Takao

2011-10-23

Little is known about the spatial distribution of lianas on emergent trees in tropical rainforests and the factors affecting this distribution. The present study investigated the effects of an arboreal ant species, Crematogaster difformis, which forms myrmecophytic symbioses with two epiphytic ferns, Lecanopteris sp. and Platycerium sp., on the spatial distribution of lianas associated with emergent trees. Living lianas were placed onto trunk surfaces inside and outside the territories of the ants in the canopy, to examine their ability to remove them. The number of leaves pruned by the ants was significantly higher on lianas inside than outside their territories. The spatial overlap of the distributions of lianas and the two ferns on emergent trees were then examined. The frequency of liana colonization of tree crowns was found to be significantly lower on trees with than without ferns. Under the natural conditions, C. difformis workers were observed biting and pruning the lianas. These results suggest that C. difformis regulates the distribution of lianas on emergent trees.

Use of classification trees to apportion single echo detections to species: Application to the pelagic fish community of Lake Superior

USGS Publications Warehouse

Yule, Daniel L.; Adams, Jean V.; Hrabik, Thomas R.; Vinson, Mark R.; Woiak, Zebadiah; Ahrenstroff, Tyler D.

2013-01-01

Acoustic methods are used to estimate the density of pelagic fish in large lakes with results of midwater trawling used to assign species composition. Apportionment in lakes having mixed species can be challenging because only a small fraction of the water sampled acoustically is sampled with trawl gear. Here we describe a new method where single echo detections (SEDs) are assigned to species based on classification tree models developed from catch data that separate species based on fish size and the spatial habitats they occupy. During the summer of 2011, we conducted a spatially-balanced lake-wide acoustic and midwater trawl survey of Lake Superior. A total of 51 sites in four bathymetric depth strata (0–30 m, 30–100 m, 100–200 m, and >200 m) were sampled. We developed classification tree models for each stratum and found fish length was the most important variable for separating species. To apply these trees to the acoustic data, we needed to identify a target strength to length (TS-to-L) relationship appropriate for all abundant Lake Superior pelagic species. We tested performance of 7 general (i.e., multi-species) relationships derived from three published studies. The best-performing relationship was identified by comparing predicted and observed catch compositions using a second independent Lake Superior data set. Once identified, the relationship was used to predict lengths of SEDs from the lake-wide survey, and the classification tree models were used to assign each SED to a species. Exotic rainbow smelt (Osmerus mordax) were the most common species at bathymetric depths 100 m (384 million; 6.0 kt). Cisco (Coregonus artedi) were widely distributed over all strata with their population estimated at 182 million (44 kt). The apportionment method we describe should be transferable to other large lakes provided fish are not tightly aggregated, and an appropriate TS-to-L relationship for abundant pelagic fish species can be determined.

Method for estimating potential tree-grade distributions for northeastern forest species

Treesearch

Daniel A. Yaussy; Daniel A. Yaussy

1993-01-01

Generalized logistic regression was used to distribute trees into four potential tree grades for 20 northeastern species groups. The potential tree grade is defined as the tree grade based on the length and amount of clear cuttings and defects only, disregarding minimum grading diameter. The algorithms described use site index and tree diameter as the predictive...

The Spatial Distribution of Dead Trees across Arkansas Timberlands

Treesearch

Martin A. Spetich; James M. Guldin

1999-01-01

Abstract -- Dead trees are an important part of the forest ecosystem and their attributes have been studied at the stand scale. However, their distribution over a large region has rarely been examined. In this study, the distribution and dynamics of sound wood in dead trees and the ratio of dead to live trees across the Arkansas landscape were...

Identifying the rooted species tree from the distribution of unrooted gene trees under the coalescent.

PubMed

Allman, Elizabeth S; Degnan, James H; Rhodes, John A

2011-06-01

Gene trees are evolutionary trees representing the ancestry of genes sampled from multiple populations. Species trees represent populations of individuals-each with many genes-splitting into new populations or species. The coalescent process, which models ancestry of gene copies within populations, is often used to model the probability distribution of gene trees given a fixed species tree. This multispecies coalescent model provides a framework for phylogeneticists to infer species trees from gene trees using maximum likelihood or Bayesian approaches. Because the coalescent models a branching process over time, all trees are typically assumed to be rooted in this setting. Often, however, gene trees inferred by traditional phylogenetic methods are unrooted. We investigate probabilities of unrooted gene trees under the multispecies coalescent model. We show that when there are four species with one gene sampled per species, the distribution of unrooted gene tree topologies identifies the unrooted species tree topology and some, but not all, information in the species tree edges (branch lengths). The location of the root on the species tree is not identifiable in this situation. However, for 5 or more species with one gene sampled per species, we show that the distribution of unrooted gene tree topologies identifies the rooted species tree topology and all its internal branch lengths. The length of any pendant branch leading to a leaf of the species tree is also identifiable for any species from which more than one gene is sampled.

Proceedings of the Symposium on Ponderosa Pine: Issues, Trends, and Management, 2004 October 18-21, Klamath Falls, OR

Treesearch

Martin W. Ritchie; Douglas A. Maguire; Andrew Youngblood

2005-01-01

Ponderosa pine is one of the most widely distributed tree species in western North America. It is highly-valued as a source of lumber, but also is key to the health and social value western forests, whether growing in pure stands or in mixture with other conifer and hardwood species. In recent years, management objectives for forests containing this species have...

Status of black walnut (Juglans nigra L.) in the Eastern United States in light of the discovery of thousand cankers disease

Treesearch

KaDonna Randolph; Anita Rose; Christopher Oswalt; Mark Brown

2013-01-01

Juglans nigra (black walnut) is widely distributed throughout the US eastern forest, with high concentrations occurring in Missouri and the Ohio and Tennessee River basins. It is an extremely desirable tree for wildlife forage and timber production on forest land, and for shade, aesthetics, and wildlife forage in urban areas. Current (2009–2010)...

Stomata open at night in pole-sized and mature ponderosa pine: implications for O3 exposure metrics

Treesearch

Nancy Grulke; R. Alonso; T. Nguyen; C. Cascio; W. Dobrowolski

2004-01-01

Ponderosa pine (Pinus ponderosa Dougl. exLaws.) is widely distributed in the western USA.We report the lack of stomatal closure at night in early summer for ponderosa pine at two of three sites investigated. Trees at a third site with lower nitrogen dioxide and nitric acid exposure, but greater drought stress, had slightly open stomata at night in...

Genome wide in silico characterization of Dof gene families of pigeonpea (Cajanus cajan (L) Millsp.).

PubMed

Malviya, N; Gupta, S; Singh, V K; Yadav, M K; Bisht, N C; Sarangi, B K; Yadav, D

2015-02-01

The DNA binding with One Finger (Dof) protein is a plant specific transcription factor involved in the regulation of wide range of processes. The analysis of whole genome sequence of pigeonpea has identified 38 putative Dof genes (CcDof) distributed on 8 chromosomes. A total of 17 out of 38 CcDof genes were found to be intronless. A comprehensive in silico characterization of CcDof gene family including the gene structure, chromosome location, protein motif, phylogeny, gene duplication and functional divergence has been attempted. The phylogenetic analysis resulted in 3 major clusters with closely related members in phylogenetic tree revealed common motif distribution. The in silico cis-regulatory element analysis revealed functional diversity with predominance of light responsive and stress responsive elements indicating the possibility of these CcDof genes to be associated with photoperiodic control and biotic and abiotic stress. The duplication pattern showed that tandem duplication is predominant over segmental duplication events. The comparative phylogenetic analysis of these Dof proteins along with 78 soybean, 36 Arabidopsis and 30 rice Dof proteins revealed 7 major clusters. Several groups of orthologs and paralogs were identified based on phylogenetic tree constructed. Our study provides useful information for functional characterization of CcDof genes.

Widespread crown condition decline, food web disruption, and amplified tree mortality with increased climate change-type drought

PubMed Central

Carnicer, Jofre; Coll, Marta; Ninyerola, Miquel; Pons, Xavier; Sánchez, Gerardo; Peñuelas, Josep

2011-01-01

Climate change is progressively increasing severe drought events in the Northern Hemisphere, causing regional tree die-off events and contributing to the global reduction of the carbon sink efficiency of forests. There is a critical lack of integrated community-wide assessments of drought-induced responses in forests at the macroecological scale, including defoliation, mortality, and food web responses. Here we report a generalized increase in crown defoliation in southern European forests occurring during 1987–2007. Forest tree species have consistently and significantly altered their crown leaf structures, with increased percentages of defoliation in the drier parts of their distributions in response to increased water deficit. We assessed the demographic responses of trees associated with increased defoliation in southern European forests, specifically in the Iberian Peninsula region. We found that defoliation trends are paralleled by significant increases in tree mortality rates in drier areas that are related to tree density and temperature effects. Furthermore, we show that severe drought impacts are associated with sudden changes in insect and fungal defoliation dynamics, creating long-term disruptive effects of drought on food webs. Our results reveal a complex geographical mosaic of species-specific responses to climate change–driven drought pressures on the Iberian Peninsula, with an overwhelmingly predominant trend toward increased drought damage. PMID:21220333

Widespread crown condition decline, food web disruption, and amplified tree mortality with increased climate change-type drought.

PubMed

Carnicer, Jofre; Coll, Marta; Ninyerola, Miquel; Pons, Xavier; Sánchez, Gerardo; Peñuelas, Josep

2011-01-25

Climate change is progressively increasing severe drought events in the Northern Hemisphere, causing regional tree die-off events and contributing to the global reduction of the carbon sink efficiency of forests. There is a critical lack of integrated community-wide assessments of drought-induced responses in forests at the macroecological scale, including defoliation, mortality, and food web responses. Here we report a generalized increase in crown defoliation in southern European forests occurring during 1987-2007. Forest tree species have consistently and significantly altered their crown leaf structures, with increased percentages of defoliation in the drier parts of their distributions in response to increased water deficit. We assessed the demographic responses of trees associated with increased defoliation in southern European forests, specifically in the Iberian Peninsula region. We found that defoliation trends are paralleled by significant increases in tree mortality rates in drier areas that are related to tree density and temperature effects. Furthermore, we show that severe drought impacts are associated with sudden changes in insect and fungal defoliation dynamics, creating long-term disruptive effects of drought on food webs. Our results reveal a complex geographical mosaic of species-specific responses to climate change-driven drought pressures on the Iberian Peninsula, with an overwhelmingly predominant trend toward increased drought damage.

Conservation of the Ethiopian church forests: Threats, opportunities and implications for their management.

PubMed

Aerts, Raf; Van Overtveld, Koen; November, Eva; Wassie, Alemayehu; Abiyu, Abrham; Demissew, Sebsebe; Daye, Desalegn D; Giday, Kidane; Haile, Mitiku; TewoldeBerhan, Sarah; Teketay, Demel; Teklehaimanot, Zewge; Binggeli, Pierre; Deckers, Jozef; Friis, Ib; Gratzer, Georg; Hermy, Martin; Heyn, Moïra; Honnay, Olivier; Paris, Maxim; Sterck, Frank J; Muys, Bart; Bongers, Frans; Healey, John R

2016-05-01

In the central and northern highlands of Ethiopia, native forest and forest biodiversity is almost confined to sacred groves associated with churches. Local communities rely on these 'church forests' for essential ecosystem services including shade and fresh water but little is known about their region-wide distribution and conservation value. We (1) performed the first large-scale spatially-explicit assessment of church forests, combining remote-sensing and field data, to assess the number of forests, their size, shape, isolation and woody plant species composition, (2) determined their plant communities and related these to environmental variables and potential natural vegetation, (3) identified the main challenges to biodiversity conservation in view of plant population dynamics and anthropogenic disturbances, and (4) present guidelines for management and policy. The 394 forests identified in satellite images were on average ~2ha in size and generally separated by ~2km from the nearest neighboring forest. Shape complexity, not size, decreased from the northern to the central highlands. Overall, 148 indigenous tree, shrub and liana species were recorded across the 78 surveyed forests. Patch α-diversity increased with mean annual precipitation, but typically only 25 woody species occurred per patch. The combined results showed that >50% of tree species present in tropical northeast Africa were still present in the 78 studied church forests, even though individual forests were small and relatively species-poor. Tree species composition of church forests varied with elevation and precipitation, and resembled the potential natural vegetation. With a wide distribution over the landscape, these church forests have high conservation value. However, long-term conservation of biodiversity of individual patches and evolutionary potential of species may be threatened by isolation, small sizes of tree species populations and disturbance, especially when considering climate change. Forest management interventions are essential and should be supported by environmental education and other forms of public engagement. Copyright © 2016 Elsevier B.V. All rights reserved.

Warming-Induced Decline of Picea crassifolia Growth in the Qilian Mountains in Recent Decades.

PubMed

Yu, Li; Huang, Lei; Shao, Xuemei; Xiao, Fengjing; Wilmking, Martin; Zhang, Yongxiang

2015-01-01

Warming-induced drought has widely affected forest dynamics in most places of the northern hemisphere. In this study, we assessed how climate warming has affected Picea crassifolia (Qinghai spruce) forests using tree growth-climate relationships and the normalized difference vegetation index (NDVI) along the Qilian Mountains, northeastern Tibet Plateau (the main range of Picea crassifolia). Based on the analysis on trees radial growth data from the upper tree line and the regional NDVI data, we identified a pervasive growth decline in recent decades, most likely caused by warming-induced droughts. The drought stress on Picea crassifolia radial growth were expanding from northeast to southwest and the favorable moisture conditions for tree growth were retreating along the identical direction in the study area over the last half century. Compared to the historical drought stress on tree radial growth in the 1920s, recent warming-induced droughts display a longer-lasting stress with a broader spatial distribution on regional forest growth. If the recent warming continues without the effective moisture increasing, then a notable challenge is developed for Picea crassifolia in the Qilian Mountains. Elaborate forest management is necessary to counteract the future risk of climate change effects in this region.

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.

Uncertainty in sap flow-based transpiration due to xylem properties

NASA Astrophysics Data System (ADS)

Looker, N. T.; Hu, J.; Martin, J. T.; Jencso, K. G.

2014-12-01

Transpiration, the evaporative loss of water from plants through their stomata, is a key component of the terrestrial water balance, influencing streamflow as well as regional convective systems. From a plant physiological perspective, transpiration is both a means of avoiding destructive leaf temperatures through evaporative cooling and a consequence of water loss through stomatal uptake of carbon dioxide. Despite its hydrologic and ecological significance, transpiration remains a notoriously challenging process to measure in heterogeneous landscapes. Sap flow methods, which estimate transpiration by tracking the velocity of a heat pulse emitted into the tree sap stream, have proven effective for relating transpiration dynamics to climatic variables. To scale sap flow-based transpiration from the measured domain (often <5 cm of tree cross-sectional area) to the whole-tree level, researchers generally assume constancy of scale factors (e.g., wood thermal diffusivity (k), radial and azimuthal distributions of sap velocity, and conducting sapwood area (As)) through time, across space, and within species. For the widely used heat-ratio sap flow method (HRM), we assessed the sensitivity of transpiration estimates to uncertainty in k (a function of wood moisture content and density) and As. A sensitivity analysis informed by distributions of wood moisture content, wood density and As sampled across a gradient of water availability indicates that uncertainty in these variables can impart substantial error when scaling sap flow measurements to the whole tree. For species with variable wood properties, the application of the HRM assuming a spatially constant k or As may systematically over- or underestimate whole-tree transpiration rates, resulting in compounded error in ecosystem-scale estimates of transpiration.

Node degree distribution in spanning trees

NASA Astrophysics Data System (ADS)

Pozrikidis, C.

2016-03-01

A method is presented for computing the number of spanning trees involving one link or a specified group of links, and excluding another link or a specified group of links, in a network described by a simple graph in terms of derivatives of the spanning-tree generating function defined with respect to the eigenvalues of the Kirchhoff (weighted Laplacian) matrix. The method is applied to deduce the node degree distribution in a complete or randomized set of spanning trees of an arbitrary network. An important feature of the proposed method is that the explicit construction of spanning trees is not required. It is shown that the node degree distribution in the spanning trees of the complete network is described by the binomial distribution. Numerical results are presented for the node degree distribution in square, triangular, and honeycomb lattices.

Intraspecies variation in a widely distributed tree species regulates the responses of soil microbiome to different temperature regimes.

PubMed

Zhang, Cui-Jing; Delgado-Baquerizo, Manuel; Drake, John E; Reich, Peter B; Tjoelker, Mark G; Tissue, David T; Wang, Jun-Tao; He, Ji-Zheng; Singh, Brajesh K

2018-04-01

Plant characteristics in different provenances within a single species may vary in response to climate change, which might alter soil microbial communities and ecosystem functions. We conducted a glasshouse experiment and grew seedlings of three provenances (temperate, subtropical and tropical origins) of a tree species (i.e., Eucalyptus tereticornis) at different growth temperatures (18, 21.5, 25, 28.5, 32 and 35.5°C) for 54 days. At the end of the experiment, bacterial and fungal community composition, diversity and abundance were characterized. Measured soil functions included surrogates of microbial respiration, enzyme activities and nutrient cycling. Using Permutation multivariate analysis of variance (PerMANOVA) and network analysis, we found that the identity of tree provenances regulated both structure and function of soil microbiomes. In some cases, tree provenances substantially affected the response of microbial communities to the temperature treatments. For example, we found significant interactions of temperature and tree provenance on bacterial community and relative abundances of Chloroflexi and Zygomycota, and inorganic nitrogen. Microbial abundance was altered in response to increasing temperature, but was not affected by tree provenances. Our study provides novel evidence that even a small variation in biotic components (i.e., intraspecies tree variation) can significantly influence the response of soil microbial community composition and specific soil functions to global warming. © 2018 Society for Applied Microbiology and John Wiley & Sons Ltd.

Ants inhabiting myrmecophytic ferns regulate the distribution of lianas on emergent trees in a Bornean tropical rainforest

PubMed Central

Tanaka, Hiroshi O.; Itioka, Takao

2011-01-01

Little is known about the spatial distribution of lianas on emergent trees in tropical rainforests and the factors affecting this distribution. The present study investigated the effects of an arboreal ant species, Crematogaster difformis, which forms myrmecophytic symbioses with two epiphytic ferns, Lecanopteris sp. and Platycerium sp., on the spatial distribution of lianas associated with emergent trees. Living lianas were placed onto trunk surfaces inside and outside the territories of the ants in the canopy, to examine their ability to remove them. The number of leaves pruned by the ants was significantly higher on lianas inside than outside their territories. The spatial overlap of the distributions of lianas and the two ferns on emergent trees were then examined. The frequency of liana colonization of tree crowns was found to be significantly lower on trees with than without ferns. Under the natural conditions, C. difformis workers were observed biting and pruning the lianas. These results suggest that C. difformis regulates the distribution of lianas on emergent trees. PMID:21508025

The effects of sampling bias and model complexity on the predictive performance of MaxEnt species distribution models.

PubMed

Syfert, Mindy M; Smith, Matthew J; Coomes, David A

2013-01-01

Species distribution models (SDMs) trained on presence-only data are frequently used in ecological research and conservation planning. However, users of SDM software are faced with a variety of options, and it is not always obvious how selecting one option over another will affect model performance. Working with MaxEnt software and with tree fern presence data from New Zealand, we assessed whether (a) choosing to correct for geographical sampling bias and (b) using complex environmental response curves have strong effects on goodness of fit. SDMs were trained on tree fern data, obtained from an online biodiversity data portal, with two sources that differed in size and geographical sampling bias: a small, widely-distributed set of herbarium specimens and a large, spatially clustered set of ecological survey records. We attempted to correct for geographical sampling bias by incorporating sampling bias grids in the SDMs, created from all georeferenced vascular plants in the datasets, and explored model complexity issues by fitting a wide variety of environmental response curves (known as "feature types" in MaxEnt). In each case, goodness of fit was assessed by comparing predicted range maps with tree fern presences and absences using an independent national dataset to validate the SDMs. We found that correcting for geographical sampling bias led to major improvements in goodness of fit, but did not entirely resolve the problem: predictions made with clustered ecological data were inferior to those made with the herbarium dataset, even after sampling bias correction. We also found that the choice of feature type had negligible effects on predictive performance, indicating that simple feature types may be sufficient once sampling bias is accounted for. Our study emphasizes the importance of reducing geographical sampling bias, where possible, in datasets used to train SDMs, and the effectiveness and essentialness of sampling bias correction within MaxEnt.

Spatial properties of snow cover in the Upper Merced River Basin: implications for a distributed snow measurement network

NASA Astrophysics Data System (ADS)

Bouffon, T.; Rice, R.; Bales, R.

2006-12-01

The spatial distributions of snow water equivalent (SWE) and snow depth within a 1, 4, and 16 km2 grid element around two automated snow pillows in a forested and open- forested region of the Upper Merced River Basin (2,800 km2) of Yosemite National Park were characterized using field observations and analyzed using binary regression trees. Snow surveys occurred at the forested site during the accumulation and ablation seasons, while at the open-forest site a survey was performed only during the accumulation season. An average of 130 snow depth and 7 snow density measurements were made on each survey, within the 4 km2 grid. Snow depth was distributed using binary regression trees and geostatistical methods using the physiographic parameters (e.g. elevation, slope, vegetation, aspect). Results in the forest region indicate that the snow pillow overestimated average SWE within the 1, 4, and 16 km2 areas by 34 percent during ablation, but during accumulation the snow pillow provides a good estimate of the modeled mean SWE grid value, however it is suspected that the snow pillow was underestimating SWE. However, at the open forest site, during accumulation, the snow pillow was 28 percent greater than the mean modeled grid element. In addition, the binary regression trees indicate that the independent variables of vegetation, slope, and aspect are the most influential parameters of snow depth distribution. The binary regression tree and multivariate linear regression models explain about 60 percent of the initial variance for snow depth and 80 percent for density, respectively. This short-term study provides motivation and direction for the installation of a distributed snow measurement network to fill the information gap in basin-wide SWE and snow depth measurements. Guided by these results, a distributed snow measurement network was installed in the Fall 2006 at Gin Flat in the Upper Merced River Basin with the specific objective of measuring accumulation and ablation across topographic variables with the aim of providing guidance for future larger scale observation network designs.

Predicting the potential future distribution of four tree species in Ohio using current habitat availability and climatic forcing

Treesearch

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

2001-01-01

We investigated the effect of habitat loss on the ability of trees to shift in distribution across a landscape dominated by agriculture. The potential distribution shifts of four tree species (Diospyros virginiana, Oxydendron arboreum, Pinus virginiana, Quercus falcata var. falcata) whose northern distribution limits fall in the...

The Efficacy of Consensus Tree Methods for Summarizing Phylogenetic Relationships from a Posterior Sample of Trees Estimated from Morphological Data.

PubMed

O'Reilly, Joseph E; Donoghue, Philip C J

2018-03-01

Consensus trees are required to summarize trees obtained through MCMC sampling of a posterior distribution, providing an overview of the distribution of estimated parameters such as topology, branch lengths, and divergence times. Numerous consensus tree construction methods are available, each presenting a different interpretation of the tree sample. The rise of morphological clock and sampled-ancestor methods of divergence time estimation, in which times and topology are coestimated, has increased the popularity of the maximum clade credibility (MCC) consensus tree method. The MCC method assumes that the sampled, fully resolved topology with the highest clade credibility is an adequate summary of the most probable clades, with parameter estimates from compatible sampled trees used to obtain the marginal distributions of parameters such as clade ages and branch lengths. Using both simulated and empirical data, we demonstrate that MCC trees, and trees constructed using the similar maximum a posteriori (MAP) method, often include poorly supported and incorrect clades when summarizing diffuse posterior samples of trees. We demonstrate that the paucity of information in morphological data sets contributes to the inability of MCC and MAP trees to accurately summarise of the posterior distribution. Conversely, majority-rule consensus (MRC) trees represent a lower proportion of incorrect nodes when summarizing the same posterior samples of trees. Thus, we advocate the use of MRC trees, in place of MCC or MAP trees, in attempts to summarize the results of Bayesian phylogenetic analyses of morphological data.

The Efficacy of Consensus Tree Methods for Summarizing Phylogenetic Relationships from a Posterior Sample of Trees Estimated from Morphological Data

PubMed Central

O’Reilly, Joseph E; Donoghue, Philip C J

2018-01-01

Abstract Consensus trees are required to summarize trees obtained through MCMC sampling of a posterior distribution, providing an overview of the distribution of estimated parameters such as topology, branch lengths, and divergence times. Numerous consensus tree construction methods are available, each presenting a different interpretation of the tree sample. The rise of morphological clock and sampled-ancestor methods of divergence time estimation, in which times and topology are coestimated, has increased the popularity of the maximum clade credibility (MCC) consensus tree method. The MCC method assumes that the sampled, fully resolved topology with the highest clade credibility is an adequate summary of the most probable clades, with parameter estimates from compatible sampled trees used to obtain the marginal distributions of parameters such as clade ages and branch lengths. Using both simulated and empirical data, we demonstrate that MCC trees, and trees constructed using the similar maximum a posteriori (MAP) method, often include poorly supported and incorrect clades when summarizing diffuse posterior samples of trees. We demonstrate that the paucity of information in morphological data sets contributes to the inability of MCC and MAP trees to accurately summarise of the posterior distribution. Conversely, majority-rule consensus (MRC) trees represent a lower proportion of incorrect nodes when summarizing the same posterior samples of trees. Thus, we advocate the use of MRC trees, in place of MCC or MAP trees, in attempts to summarize the results of Bayesian phylogenetic analyses of morphological data. PMID:29106675

Landscape genomics reveals altered genome wide diversity within revegetated stands of Eucalyptus microcarpa (Grey Box).

PubMed

Jordan, Rebecca; Dillon, Shannon K; Prober, Suzanne M; Hoffmann, Ary A

2016-12-01

In order to contribute to evolutionary resilience and adaptive potential in highly modified landscapes, revegetated areas should ideally reflect levels of genetic diversity within and across natural stands. Landscape genomic analyses enable such diversity patterns to be characterized at genome and chromosomal levels. Landscape-wide patterns of genomic diversity were assessed in Eucalyptus microcarpa, a dominant tree species widely used in revegetation in Southeastern Australia. Trees from small and large patches within large remnants, small isolated remnants and revegetation sites were assessed across the now highly fragmented distribution of this species using the DArTseq genomic approach. Genomic diversity was similar within all three types of remnant patches analysed, although often significantly but only slightly lower in revegetation sites compared with natural remnants. Differences in diversity between stand types varied across chromosomes. Genomic differentiation was higher between small, isolated remnants, and among revegetated sites compared with natural stands. We conclude that small remnants and revegetated sites of our E. microcarpa samples largely but not completely capture patterns in genomic diversity across the landscape. Genomic approaches provide a powerful tool for assessing restoration efforts across the landscape. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

A Hybrid Key Management Scheme for WSNs Based on PPBR and a Tree-Based Path Key Establishment Method

PubMed Central

Zhang, Ying; Liang, Jixing; Zheng, Bingxin; Chen, Wei

2016-01-01

With the development of wireless sensor networks (WSNs), in most application scenarios traditional WSNs with static sink nodes will be gradually replaced by Mobile Sinks (MSs), and the corresponding application requires a secure communication environment. Current key management researches pay less attention to the security of sensor networks with MS. This paper proposes a hybrid key management schemes based on a Polynomial Pool-based key pre-distribution and Basic Random key pre-distribution (PPBR) to be used in WSNs with MS. The scheme takes full advantages of these two kinds of methods to improve the cracking difficulty of the key system. The storage effectiveness and the network resilience can be significantly enhanced as well. The tree-based path key establishment method is introduced to effectively solve the problem of communication link connectivity. Simulation clearly shows that the proposed scheme performs better in terms of network resilience, connectivity and storage effectiveness compared to other widely used schemes. PMID:27070624

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.

Tree Species Composition and Harvest Intensity Affect Herbivore Density and Leaf Damage on Beech, Fagus sylvatica, in Different Landscape Contexts

PubMed Central

Mangels, Jule; Blüthgen, Nico; Frank, Kevin; Grassein, Fabrice; Hilpert, Andrea; Mody, Karsten

2015-01-01

Most forests are exposed to anthropogenic management activities that affect tree species composition and natural ecosystem processes. Changes in ecosystem processes such as herbivory depend on management intensity, and on regional environmental conditions and species pools. Whereas influences of specific forest management measures have already been addressed for different herbivore taxa on a local scale, studies considering effects of different aspects of forest management across different regions are rare. We assessed the influence of tree species composition and intensity of harvesting activities on arthropod herbivores and herbivore-related damage to beech trees, Fagus sylvatica, in 48 forest plots in three regions of Germany. We found that herbivore abundance and damage to beech trees differed between regions and that – despite the regional differences - density of tree-associated arthropod taxa and herbivore damage were consistently affected by tree species composition and harvest intensity. Specifically, overall herbivore damage to beech trees increased with increasing dominance of beech trees – suggesting the action of associational resistance processes – and decreased with harvest intensity. The density of leaf chewers and mines was positively related to leaf damage, and several arthropod groups responded to beech dominance and harvest intensity. The distribution of damage patterns was consistent with a vertical shift of herbivores to higher crown layers during the season and with higher beech dominance. By linking quantitative data on arthropod herbivore abundance and herbivory with tree species composition and harvesting activity in a wide variety of beech forests, our study helps to better understand the influence of forest management on interactions between a naturally dominant deciduous forest tree and arthropod herbivores. PMID:25938417

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.

Anatomical, chemical, and ecological factors affecting tree species choice in dendrochemistry studies

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

Cutter, B.E.; Guyette, R.P.

1993-07-01

Recently, element concentrations in tree rings have been used to monitor metal contamination, fertilization, and the effects of acid precipitation on soils. This has stimulated interest in which tree species may be suitable for use in studies of long-term trends in environmental chemistry. Potential radial translocation of elements across living boundaries can be a confounding factor in assessing environmental change. The selection of species which minimizes radial translocation of elements can be critical to the success of dendrochemical research. Criteria for selection of species with characteristics favorable for dendrochemical analysis are categorized into (1) habitat-based factors, (2) xylem-based factors, andmore » (3) element-based factors. A wide geographic range and ecological amplitude provide an advantage in calibration and better controls on the effects of soil chemistry. The most important xylem-based criteria are heartwood moisture content, permeability, and the nature of the sapwood-heartwood transition. The element of interest is important in determining suitable tree species because all elements are not equally mobile or detectable in the xylem. Ideally, the tree species selected for dendrochemical study will be long-lived, grow on a wide range of sites over a large geographic distribution, have a distinct heartwood with a low number of rings in the sapwood, a low heartwood moisture content, and have low radial permeability. Recommended temperate zone North American species include white oak (Quercus alba L.), post oak (Q. stellate Wangenh.), eastern redcedar (funiperus virginiana L.), old-growth Douglas-fir [Pseudoaugu menziesii (Mirb.) Franco] and big sagebrush (Artemisia tridentata Nutt.). In addition, species such as bristlecone pine (Pinus aristata Engelm. syn. longaeva), old-growth redwood [Sequoia sempervirens (D. Don) Endl.], and giant sequoia [S. gigantea (Lindl.) Deene] may be suitable for local purposes. 118 refs., 2 tabs.« less

Regime Shifts and Weakened Environmental Gradients in Open Oak and Pine Ecosystems

PubMed Central

Hanberry, Brice B.; Dey, Dan C.; He, Hong S.

2012-01-01

Fire suppression allows tree species that are intolerant of fire stress to increase their distribution, potentially resulting in disruption of historical species-environmental relationships. To measure changes between historical General Land Office surveys (1815 to 1850) and current USDA Forest Inventory and Assessment surveys (2004 to 2008), we compared composition, distribution, and site factors of 21 tree species or species groups in the Missouri Ozarks. We used 24 environmental variables and random forests as a classification method to model distributions. Eastern redcedar, elms, maples, and other fire-sensitive species have increased in dominance in oak forests, with concurrent reductions by oak species; specific changes varied by ecological subsection. Ordinations displayed loss of separation between formerly distinctive oak and fire-sensitive tree species groups. Distribution maps showed decreased presence of disturbance-dependent oak and pine species and increased presence of fire-sensitive species that generally expanded from subsections protected from fire along rivers to upland areas, except for eastern redcedar, which expanded into these subsections. Large scale differences in spatial gradients between past and present communities paralleled reduced influence of local topographic gradients in the varied relief of the Missouri Ozarks, as fire-sensitive species have moved to higher, drier, and sunnier sites away from riverine corridors. Due to changes in land use, landscapes in the Missouri Ozarks, eastern United States, and world-wide are changing from open oak and pine-dominated ecosystems to novel oak-mixed species forests, although at fine scales, forests are becoming more diverse in tree species today. Fire suppression weakened the influence by environmental gradients over species dominance, allowing succession from disturbance-dependent oaks to an alternative state of fire-sensitive species. Current and future research and conservation that rely on historical relationships and ecological principles based on disturbance across the landscape will need to incorporate modern interactions among species for resources into management plans and projections. PMID:22848467

Regime shifts and weakened environmental gradients in open oak and pine ecosystems.

PubMed

Hanberry, Brice B; Dey, Dan C; He, Hong S

2012-01-01

Fire suppression allows tree species that are intolerant of fire stress to increase their distribution, potentially resulting in disruption of historical species-environmental relationships. To measure changes between historical General Land Office surveys (1815 to 1850) and current USDA Forest Inventory and Assessment surveys (2004 to 2008), we compared composition, distribution, and site factors of 21 tree species or species groups in the Missouri Ozarks. We used 24 environmental variables and random forests as a classification method to model distributions. Eastern redcedar, elms, maples, and other fire-sensitive species have increased in dominance in oak forests, with concurrent reductions by oak species; specific changes varied by ecological subsection. Ordinations displayed loss of separation between formerly distinctive oak and fire-sensitive tree species groups. Distribution maps showed decreased presence of disturbance-dependent oak and pine species and increased presence of fire-sensitive species that generally expanded from subsections protected from fire along rivers to upland areas, except for eastern redcedar, which expanded into these subsections. Large scale differences in spatial gradients between past and present communities paralleled reduced influence of local topographic gradients in the varied relief of the Missouri Ozarks, as fire-sensitive species have moved to higher, drier, and sunnier sites away from riverine corridors. Due to changes in land use, landscapes in the Missouri Ozarks, eastern United States, and world-wide are changing from open oak and pine-dominated ecosystems to novel oak-mixed species forests, although at fine scales, forests are becoming more diverse in tree species today. Fire suppression weakened the influence by environmental gradients over species dominance, allowing succession from disturbance-dependent oaks to an alternative state of fire-sensitive species. Current and future research and conservation that rely on historical relationships and ecological principles based on disturbance across the landscape will need to incorporate modern interactions among species for resources into management plans and projections.

Vertical and horizontal root distribution of mature aspen clones: mechanisms for resource acquisition

NASA Astrophysics Data System (ADS)

Landhäusser, S. M.; Snedden, J.; Silins, U.; Devito, K. J.

2012-04-01

Spatial root distribution, root morphology, and intra- and inter-clonal connections of mature boreal trembling aspen clones (Populus tremuloides Michx.) were explored to shed light on the functional relationships between vertical and horizontal distribution of roots and the variation in soil water availability along hill slopes. Root systems of mature aspen were hydraulically excavated in large plots (6 m wide and 12 m long) and to a depth of 30 cm. Most aspen roots were located in the upper 20 cm of the soil and fine and coarse root occupancy was highest in the lower slope positions and lowest towards the upper hill slope position likely because of soil moisture availability. Observation of the root system distribution along the hill slope correlated well with the observation of greater leaf area carried by trees growing at the lower portion of the hill slope. Interestingly, trees growing at the bottom of the slope required also less sapwood area to support the same amount of leaf area of trees growing at the top of a slope. These observations appear to be closely related to soil moisture availability and with that greater productivity at the bottom of the slope. However, trees growing on the upper slope tended to have long lateral roots extending downslope, which suggests long distance water transport through these lateral feeder roots. Genetic analysis indicated that both intra- and inter-clonal root connections occur in aspen, which can play a role in the sharing of resources along moisture gradients. Root systems of boreal aspen growing on upper slope positions exhibited a combination of three attributes (1) asymmetric lateral root systems, that are skewed downslope, (2) deeper taproots, and (3) intra and inter-clonal root connections, which can all be considered adaptive strategies to avoid drought stress in upper slope positions.

Modeling of air pollutant removal by dry deposition to urban trees using a WRF/CMAQ/i-Tree Eco coupled system.

PubMed

Cabaraban, Maria Theresa I; Kroll, Charles N; Hirabayashi, Satoshi; Nowak, David J

2013-05-01

A distributed adaptation of i-Tree Eco was used to simulate dry deposition in an urban area. This investigation focused on the effects of varying temperature, LAI, and NO2 concentration inputs on estimated NO2 dry deposition to trees in Baltimore, MD. A coupled modeling system is described, wherein WRF provided temperature and LAI fields, and CMAQ provided NO2 concentrations. A base case simulation was conducted using built-in distributed i-Tree Eco tools, and simulations using different inputs were compared against this base case. Differences in land cover classification and tree cover between the distributed i-Tree Eco and WRF resulted in changes in estimated LAI, which in turn resulted in variations in simulated NO2 dry deposition. Estimated NO2 removal decreased when CMAQ-derived concentration was applied to the distributed i-Tree Eco simulation. Discrepancies in temperature inputs did little to affect estimates of NO2 removal by dry deposition to trees in Baltimore. Copyright © 2013 Elsevier Ltd. All rights reserved.

Quantifying environmental limiting factors on tree cover using geospatial data.

PubMed

Greenberg, Jonathan A; Santos, Maria J; Dobrowski, Solomon Z; Vanderbilt, Vern C; Ustin, Susan L

2015-01-01

Environmental limiting factors (ELFs) are the thresholds that determine the maximum or minimum biological response for a given suite of environmental conditions. We asked the following questions: 1) Can we detect ELFs on percent tree cover across the eastern slopes of the Lake Tahoe Basin, NV? 2) How are the ELFs distributed spatially? 3) To what extent are unmeasured environmental factors limiting tree cover? ELFs are difficult to quantify as they require significant sample sizes. We addressed this by using geospatial data over a relatively large spatial extent, where the wall-to-wall sampling ensures the inclusion of rare data points which define the minimum or maximum response to environmental factors. We tested mean temperature, minimum temperature, potential evapotranspiration (PET) and PET minus precipitation (PET-P) as potential limiting factors on percent tree cover. We found that the study area showed system-wide limitations on tree cover, and each of the factors showed evidence of being limiting on tree cover. However, only 1.2% of the total area appeared to be limited by the four (4) environmental factors, suggesting other unmeasured factors are limiting much of the tree cover in the study area. Where sites were near their theoretical maximum, non-forest sites (tree cover < 25%) were primarily limited by cold mean temperatures, open-canopy forest sites (tree cover between 25% and 60%) were primarily limited by evaporative demand, and closed-canopy forests were not limited by any particular environmental factor. The detection of ELFs is necessary in order to fully understand the width of limitations that species experience within their geographic range.

Spacing, Thinning, and Pruning Practices for Young Cottonwood Plantations

Treesearch

Leon S. Minckler

1970-01-01

The 5-year growth of cottonwood trees planted at five spacing levels is summarized. Wide spacing resulted in better diameter and height growth, but less total wood production per acre than close spacing. Early thinning of closely spaced trees did not maintain diameter growth equal to that of trees with initial wide spacing.

Climatic-Induced Shifts in the Distribution of Teak ( Tectona grandis) in Tropical Asia: Implications for Forest Management and Planning

NASA Astrophysics Data System (ADS)

Deb, Jiban Chandra; Phinn, Stuart; Butt, Nathalie; McAlpine, Clive A.

2017-09-01

Modelling the future suitable climate space for tree species has become a widely used tool for forest management planning under global climate change. Teak ( Tectona grandis) is one of the most valuable tropical hardwood species in the international timber market, and natural teak forests are distributed from India through Myanmar, Laos and Thailand. The extents of teak forests are shrinking due to deforestation and the local impacts of global climate change. However, the direct impacts of climate changes on the continental-scale distributions of native and non-native teak have not been examined. In this study, we developed a species distribution model for teak across its entire native distribution in tropical Asia, and its non-native distribution in Bangladesh. We used presence-only records of trees and twelve environmental variables that were most representative for current teak distributions in South and Southeast Asia. MaxEnt (maximum entropy) models were used to model the distributions of teak under current and future climate scenarios. We found that land use/land cover change and elevation were the two most important variables explaining the current and future distributions of native and non-native teak in tropical Asia. Changes in annual precipitation, precipitation seasonality and annual mean actual evapotranspiration may result in shifts in the distributions of teak across tropical Asia. We discuss the implications for the conservation of critical teak habitats, forest management planning, and risks of biological invasion that may occur due to its cultivation in non-native ranges.

Declines in low-elevation subalpine tree populations outpace growth in high-elevation populations with warming

DOE PAGES

Conlisk, Erin; Castanha, Cristina; Germino, Matthew J.; ...

2017-02-08

Species distribution shifts in response to climate change require that recruitment increase beyond current range boundaries. For trees with long life spans, the importance of climate-sensitive seedling establishment to the pace of range shifts has not been demonstrated quantitatively. Using spatially explicit, stochastic population models combined with data from long-term forest surveys, we explored whether the climate-sensitivity of recruitment observed in climate manipulation experiments was sufficient to alter populations and elevation ranges of two widely distributed, high-elevation North American conifers. Empirically observed, warming-driven declines in recruitment led to rapid modelled population declines at the low-elevation, ‘warm edge’ of subalpine forestmore » and slow emergence of populations beyond the high-elevation, ‘cool edge’. Because population declines in the forest occurred much faster than population emergence in the alpine, we observed range contraction for both species. For Engelmann spruce, this contraction was permanent over the modelled time horizon, even in the presence of increased moisture. For limber pine, lower sensitivity to warming may facilitate persistence at low elevations – especially in the presence of increased moisture – and rapid establishment above tree line, and, ultimately, expansion into the alpine. Synthesis. Assuming 21st century warming and no additional moisture, population dynamics in high-elevation forests led to transient range contractions for limber pine and potentially permanent range contractions for Engelmann spruce. Thus, limitations to seedling recruitment with warming can constrain the pace of subalpine tree range shifts.« less

Declines in low-elevation subalpine tree populations outpace growth in high-elevation populations with warming

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

Conlisk, Erin; Castanha, Cristina; Germino, Matthew J.

Species distribution shifts in response to climate change require that recruitment increase beyond current range boundaries. For trees with long life spans, the importance of climate-sensitive seedling establishment to the pace of range shifts has not been demonstrated quantitatively. Using spatially explicit, stochastic population models combined with data from long-term forest surveys, we explored whether the climate-sensitivity of recruitment observed in climate manipulation experiments was sufficient to alter populations and elevation ranges of two widely distributed, high-elevation North American conifers. Empirically observed, warming-driven declines in recruitment led to rapid modelled population declines at the low-elevation, ‘warm edge’ of subalpine forestmore » and slow emergence of populations beyond the high-elevation, ‘cool edge’. Because population declines in the forest occurred much faster than population emergence in the alpine, we observed range contraction for both species. For Engelmann spruce, this contraction was permanent over the modelled time horizon, even in the presence of increased moisture. For limber pine, lower sensitivity to warming may facilitate persistence at low elevations – especially in the presence of increased moisture – and rapid establishment above tree line, and, ultimately, expansion into the alpine. Synthesis. Assuming 21st century warming and no additional moisture, population dynamics in high-elevation forests led to transient range contractions for limber pine and potentially permanent range contractions for Engelmann spruce. Thus, limitations to seedling recruitment with warming can constrain the pace of subalpine tree range shifts.« less

Declines in low-elevation subalpine tree populations outpace growth in high-elevation populations with warming

USGS Publications Warehouse

Conlisk, Erin; Castanha, Cristina; Germino, Matthew J.; Veblen, Thomas T; Smith, Jeremy M.; Kueppers, Lara M.

2017-01-01

Species distribution shifts in response to climate change require that recruitment increase beyond current range boundaries. For trees with long life spans, the importance of climate-sensitive seedling establishment to the pace of range shifts has not been demonstrated quantitatively.Using spatially explicit, stochastic population models combined with data from long-term forest surveys, we explored whether the climate-sensitivity of recruitment observed in climate manipulation experiments was sufficient to alter populations and elevation ranges of two widely distributed, high-elevation North American conifers.Empirically observed, warming-driven declines in recruitment led to rapid modelled population declines at the low-elevation, ‘warm edge’ of subalpine forest and slow emergence of populations beyond the high-elevation, ‘cool edge’. Because population declines in the forest occurred much faster than population emergence in the alpine, we observed range contraction for both species. For Engelmann spruce, this contraction was permanent over the modelled time horizon, even in the presence of increased moisture. For limber pine, lower sensitivity to warming may facilitate persistence at low elevations – especially in the presence of increased moisture – and rapid establishment above tree line, and, ultimately, expansion into the alpine.Synthesis. Assuming 21st century warming and no additional moisture, population dynamics in high-elevation forests led to transient range contractions for limber pine and potentially permanent range contractions for Engelmann spruce. Thus, limitations to seedling recruitment with warming can constrain the pace of subalpine tree range shifts.

The Estimation of Tree Posterior Probabilities Using Conditional Clade Probability Distributions

PubMed Central

Larget, Bret

2013-01-01

In this article I introduce the idea of conditional independence of separated subtrees as a principle by which to estimate the posterior probability of trees using conditional clade probability distributions rather than simple sample relative frequencies. I describe an algorithm for these calculations and software which implements these ideas. I show that these alternative calculations are very similar to simple sample relative frequencies for high probability trees but are substantially more accurate for relatively low probability trees. The method allows the posterior probability of unsampled trees to be calculated when these trees contain only clades that are in other sampled trees. Furthermore, the method can be used to estimate the total probability of the set of sampled trees which provides a measure of the thoroughness of a posterior sample. [Bayesian phylogenetics; conditional clade distributions; improved accuracy; posterior probabilities of trees.] PMID:23479066

Predicting the potential future distribution of four tree species in Ohio using current habitat availability and climatic forcing

Treesearch

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

2000-01-01

We investigated the effect of habitat loss on the ability of trees to shift in distribution across a landscape dominated by agriculture. The potential distribution shifts of four tree species (Diospyros virginiana, Oxydendron arboreum, Pinus virginiana, Quercus falcata var. falcata) whose northern distribution limits fall in the southern third of Ohio were used to...

Transpiration and stomatal conductance in a young secondary tropical montane forest: contrasts between native trees and invasive understorey shrubs.

PubMed

Ghimire, Chandra Prasad; Bruijnzeel, L Adrian; Lubczynski, Maciek W; Zwartendijk, Bob W; Odongo, Vincent Omondi; Ravelona, Maafaka; van Meerveld, H J Ilja

2018-04-21

It has been suggested that vigorous secondary tropical forests can have very high transpiration rates, but sap flow and stomatal conductance dynamics of trees and shrubs in these forests are understudied. In an effort to address this knowledge gap, sap flow (thermal dissipation method, 12 trees) and stomatal conductance (porometry, six trees) were measured for young (5-7 years) Psiadia altissima (DC.) Drake trees, a widely occurring species dominating young regrowth following abandonment of swidden agriculture in upland eastern Madagascar. In addition, stomatal conductance (gs) was determined for three individuals of two locally common invasive shrubs (Lantana camara L. and Rubus moluccanus L.) during three periods with contrasting soil moisture conditions. Values of gs for the three investigated species were significantly higher and more sensitive to climatic conditions during the wet period compared with the dry period. Further, gs of the understorey shrubs was much more sensitive to soil moisture content than that of the trees. Tree transpiration rates (Ec) were relatively stable during the dry season and were only affected somewhat by soil water content at the end of the dry season, suggesting the trees had continued access to soil water despite drying out of the topsoil. The Ec exhibited a plateau-shaped relation with vapour pressure deficit (VPD), which was attributed to stomatal closure at high VPD. Vapour pressure deficit was the major driver of variation in Ec, during both the wet and the dry season. Overall water use of the trees was modest, possibly reflecting low site fertility after three swidden cultivation cycles. The observed contrast in gs response to soil water and climatic conditions for the trees and shrubs underscores the need to take root distributions into account when modelling transpiration from regenerating tropical forests.

Water availability determines the richness and density of fig trees within Brazilian semideciduous forest landscapes

NASA Astrophysics Data System (ADS)

Coelho, Luís Francisco Mello; Ribeiro, Milton Cezar; Pereira, Rodrigo Augusto Santinelo

2014-05-01

The success of fig trees in tropical ecosystems is evidenced by the great diversity (+750 species) and wide geographic distribution of the genus. We assessed the contribution of environmental variables on the species richness and density of fig trees in fragments of seasonal semideciduous forest (SSF) in Brazil. We assessed 20 forest fragments in three regions in Sao Paulo State, Brazil. Fig tree richness and density was estimated in rectangular plots, comprising 31.4 ha sampled. Both richness and fig tree density were linearly modeled as function of variables representing (1) fragment metrics, (2) forest structure, and (3) landscape metrics expressing water drainage in the fragments. Model selection was performed by comparing the AIC values (Akaike Information Criterion) and the relative weight of each model (wAIC). Both species richness and fig tree density were better explained by the water availability in the fragment (meter of streams/ha): wAICrichness = 0.45, wAICdensity = 0.96. The remaining variables related to anthropic perturbation and forest structure were of little weight in the models. The rainfall seasonality in SSF seems to select for both establishment strategies and morphological adaptations in the hemiepiphytic fig tree species. In the studied SSF, hemiepiphytes established at lower heights in their host trees than reported for fig trees in evergreen rainforests. Some hemiepiphytic fig species evolved superficial roots extending up to 100 m from their trunks, resulting in hectare-scale root zones that allow them to efficiently forage water and soil nutrients. The community of fig trees was robust to variation in forest structure and conservation level of SSF fragments, making this group of plants an important element for the functioning of seasonal tropical forests.

Tree voles: an evaluation of their distribution and habitat relationships based on recent and historical studies, habitat models, and vegetation change

Treesearch

Eric D. Forsman; James K. Swingle; Raymond J. Davis; Brian L. Biswell; Lawrence S. Andrews

2016-01-01

We describe the historical and current distribution of tree voles (Arborimus longicaudus; A. pomo) and compare the minimum density of trees with tree vole nests in different forest age-classes based on museum records, field notes of previous collectors, tree vole nest surveys conducted by federal agencies, and our field studies in Oregon and...

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.

[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.

Large tree diameter distribution modelling using sparse airborne laser scanning data in a subtropical forest in Nepal

NASA Astrophysics Data System (ADS)

Rana, Parvez; Vauhkonen, Jari; Junttila, Virpi; Hou, Zhengyang; Gautam, Basanta; Cawkwell, Fiona; Tokola, Timo

2017-12-01

Large-diameter trees (taking DBH > 30 cm to define large trees) dominate the dynamics, function and structure of a forest ecosystem. The aim here was to employ sparse airborne laser scanning (ALS) data with a mean point density of 0.8 m-2 and the non-parametric k-most similar neighbour (k-MSN) to predict tree diameter at breast height (DBH) distributions in a subtropical forest in southern Nepal. The specific objectives were: (1) to evaluate the accuracy of the large-tree fraction of the diameter distribution; and (2) to assess the effect of the number of training areas (sample size, n) on the accuracy of the predicted tree diameter distribution. Comparison of the predicted distributions with empirical ones indicated that the large tree diameter distribution can be derived in a mixed species forest with a RMSE% of 66% and a bias% of -1.33%. It was also feasible to downsize the sample size without losing the interpretability capacity of the model. For large-diameter trees, even a reduction of half of the training plots (n = 250), giving a marginal increase in the RMSE% (1.12-1.97%) was reported compared with the original training plots (n = 500). To be consistent with these outcomes, the sample areas should capture the entire range of spatial and feature variability in order to reduce the occurrence of error.

Soil nutrients influence spatial distributions of tropical trees species

USGS Publications Warehouse

John, R.; Dalling, J.W.; Harms, K.E.; Yavitt, J.B.; Stallard, R.F.; Mirabello, M.; Hubbell, S.P.; Valencia, R.; Navarrete, H.; Vallejo, M.; Foster, R.B.

2007-01-01

The importance of niche vs. neutral assembly mechanisms in structuring tropical tree communities remains an important unsettled question in community ecology [Bell G (2005) Ecology 86:1757-1770]. There is ample evidence that species distributions are determined by soils and habitat factors at landscape (0.5 million individual trees of 1,400 species and 10 essential plant nutrients, we used Monte Carlo simulations of species distributions to test plant-soil associations against null expectations based on dispersal assembly. We found that the spatial distributions of 36-51% of tree species at these sites show strong associations to soil nutrient distributions. Neutral dispersal assembly cannot account for these plant-soil associations or the observed niche breadths of these species. These results indicate that belowground resource availability plays an important role in the assembly of tropical tree communities at local scales and provide the basis for future investigations on the mechanisms of resource competition among tropical tree species. ?? 2007 by The National Academy of Sciences of the USA.

Stomata open at night in pole-sized and mature ponderosa pine: implications for O3 exposure metrics.

PubMed

Grulke, N E; Alonso, R; Nguyen, T; Cascio, C; Dobrowolski, W

2004-09-01

Ponderosa pine (Pinus ponderosa Dougl. ex Laws.) is widely distributed in the western USA. We report the lack of stomatal closure at night in early summer for ponderosa pine at two of three sites investigated. Trees at a third site with lower nitrogen dioxide and nitric acid exposure, but greater drought stress, had slightly open stomata at night in early summer but closed stomata at night for the rest of the summer. The three sites had similar background ozone exposure during the summer of measurement (2001). Nighttime stomatal conductance (gs) ranged from one tenth to one fifth that of maximum daytime values. In general, pole-sized trees (< 40 years old) had greater nighttime gs than mature trees (> 250 years old). In late summer, nighttime gs was low (< 3.0 mmol H2O m(-2) s(-1)) for both tree size classes at all sites. Measurable nighttime gs has also been reported in other conifers, but the values we observed were higher. In June, nighttime ozone (O3) uptake accounted for 9, 5 and 3% of the total daily O3 uptake of pole-sized trees from west to east across the San Bernardino Mountains. In late summer, O3 uptake at night was < 2% of diel uptake at all sites. Nocturnal O3 uptake may contribute to greater oxidant injury development, especially in pole-sized trees in early summer.

Tree differences in primary and secondary growth drive convergent scaling in leaf area to sapwood area across Europe.

PubMed

Petit, Giai; von Arx, Georg; Kiorapostolou, Natasa; Lechthaler, Silvia; Prendin, Angela Luisa; Anfodillo, Tommaso; Caldeira, Maria C; Cochard, Hervé; Copini, Paul; Crivellaro, Alan; Delzon, Sylvain; Gebauer, Roman; Gričar, Jožica; Grönholm, Leila; Hölttä, Teemu; Jyske, Tuula; Lavrič, Martina; Lintunen, Anna; Lobo-do-Vale, Raquel; Peltoniemi, Mikko; Peters, Richard L; Robert, Elisabeth M R; Roig Juan, Sílvia; Senfeldr, Martin; Steppe, Kathy; Urban, Josef; Van Camp, Janne; Sterck, Frank

2018-06-01

Trees scale leaf (A L ) and xylem (A X ) areas to couple leaf transpiration and carbon gain with xylem water transport. Some species are known to acclimate in A L  : A X balance in response to climate conditions, but whether trees of different species acclimate in A L  : A X in similar ways over their entire (continental) distributions is unknown. We analyzed the species and climate effects on the scaling of A L vs A X in branches of conifers (Pinus sylvestris, Picea abies) and broadleaved (Betula pendula, Populus tremula) sampled across a continental wide transect in Europe. Along the branch axis, A L and A X change in equal proportion (isometric scaling: b ˜ 1) as for trees. Branches of similar length converged in the scaling of A L vs A X with an exponent of b = 0.58 across European climates irrespective of species. Branches of slow-growing trees from Northern and Southern regions preferentially allocated into new leaf rather than xylem area, with older xylem rings contributing to maintaining total xylem conductivity. In conclusion, trees in contrasting climates adjust their functional balance between water transport and leaf transpiration by maintaining biomass allocation to leaves, and adjusting their growth rate and xylem production to maintain xylem conductance. © 2018 The Authors. New Phytologist © 2018 New Phytologist Trust.

Biodiversity of Trichoderma (Hypocreaceae) in Southern Europe and Macaronesia

PubMed Central

Jaklitsch, W.M.; Voglmayr, H.

2015-01-01

The first large-scale survey of sexual and asexual Trichoderma morphs collected from plant and fungal materials conducted in Southern Europe and Macaronesia including a few collections from French islands east of Africa yielded more than 650 specimens identified to the species level. Routine sequencing of tef1 revealed a genetic variation among these isolates that exceeds previous experience and ca. 90 species were recognized, of which 74 are named and 17 species newly described. Aphysiostroma stercorarium is combined in Trichoderma. For the first time a sexual morph is described for T. hamatum. The hitherto most complete phylogenetic tree is presented for the entire genus Trichoderma, based on rpb2 sequences. For the first time also a genus-wide phylogenetic tree based on acl1 sequences is shown. Detailed phylogenetic analyses using tef1 sequences are presented in four separate trees representing major clades of Trichoderma. Discussions involve species composition of clades and ecological and biogeographic considerations including distribution of species. PMID:26955191

The Use of Binary Search Trees in External Distribution Sorting.

ERIC Educational Resources Information Center

Cooper, David; Lynch, Michael F.

1984-01-01

Suggests new method of external distribution called tree partitioning that involves use of binary tree to split incoming file into successively smaller partitions for internal sorting. Number of disc accesses during a tree-partitioning sort were calculated in simulation using files extracted from British National Bibliography catalog files. (19…

Tree canopy types constrain plant distributions in ponderosa pine-Gambel oak forests, northern Arizona

Treesearch

Scott R. Abella

2009-01-01

Trees in many forests affect the soils and plants below their canopies. In current high-density southwestern ponderosa pine (Pinus ponderosa) forests, managers have opportunities to enhance multiple ecosystem values by manipulating tree density, distribution, and canopy cover through tree thinning. I performed a study in northern Arizona ponderosa...

Tropical dendrochemistry: A novel approach to estimate age and growth from ringless trees

NASA Astrophysics Data System (ADS)

Poussart, P. M.; Myneni, S. C. B.; Lanzirotti, A.

2006-09-01

Although tropical forests play an active role in the global carbon cycle and climate, their growth history remains poorly characterized compared to other ecosystems on the planet. Trees are prime candidates for the extraction of paleoclimate archives as they can be probed sub-annually, are widely distributed and can live for over 1400 years [Chambers et al., 1998]. However, dendrochronological techniques have found limited applications in the tropics because trees often lack visible growth rings (Whitmore, 1990). Alternative methods exist (dendrometry (DaSilva et al., 2002), radio- and stable isotopes (Evans and Schrag, 2004; Poussart et al., 2004; Poussart and Schrag, 2005), but the derived records are either of short-duration, lack seasonal resolution or are prohibitively labor intensive to produce. Here, we show the first X-ray microprobe synchrotron record of calcium (Ca) from a ringless Miliusa velutina tree from Thailand and use it to estimate the tree's age and growth history. The Ca age model agrees within <=2 years of bomb-radiocarbon age estimates and confirms that the cycles are seasonal. The amplitude of the Ca annual cycle is correlated significantly with growth and annual Ca maxima correlate with the amount of dry season rainfall. Synchrotron measurements are fast and producing sufficient numbers of replicated multi-century tropical dendrochemical climate records now seems analytically feasible.

Survival of Norway spruce remains higher in mixed stands under a dryer and warmer climate.

PubMed

Neuner, Susanne; Albrecht, Axel; Cullmann, Dominik; Engels, Friedrich; Griess, Verena C; Hahn, W Andreas; Hanewinkel, Marc; Härtl, Fabian; Kölling, Christian; Staupendahl, Kai; Knoke, Thomas

2015-02-01

Shifts in tree species distributions caused by climatic change are expected to cause severe losses in the economic value of European forestland. However, this projection disregards potential adaptation options such as tree species conversion, shorter production periods, or establishment of mixed species forests. The effect of tree species mixture has, as yet, not been quantitatively investigated for its potential to mitigate future increases in production risks. For the first time, we use survival time analysis to assess the effects of climate, species mixture and soil condition on survival probabilities for Norway spruce and European beech. Accelerated Failure Time (AFT) models based on an extensive dataset of almost 65,000 trees from the European Forest Damage Survey (FDS)--part of the European-wide Level I monitoring network--predicted a 24% decrease in survival probability for Norway spruce in pure stands at age 120 when unfavorable changes in climate conditions were assumed. Increasing species admixture greatly reduced the negative effects of unfavorable climate conditions, resulting in a decline in survival probabilities of only 7%. We conclude that future studies of forest management under climate change as well as forest policy measures need to take this, as yet unconsidered, strongly advantageous effect of tree species mixture into account. © 2014 John Wiley & Sons Ltd.

Phylogeny and evolutionary histories of Pyrus L. revealed by phylogenetic trees and networks based on data from multiple DNA sequences.

PubMed

Zheng, Xiaoyan; Cai, Danying; Potter, Daniel; Postman, Joseph; Liu, Jing; Teng, Yuanwen

2014-11-01

Reconstructing the phylogeny of Pyrus has been difficult due to the wide distribution of the genus and lack of informative data. In this study, we collected 110 accessions representing 25 Pyrus species and constructed both phylogenetic trees and phylogenetic networks based on multiple DNA sequence datasets. Phylogenetic trees based on both cpDNA and nuclear LFY2int2-N (LN) data resulted in poor resolution, especially, only five primary species were monophyletic in the LN tree. A phylogenetic network of LN suggested that reticulation caused by hybridization is one of the major evolutionary processes for Pyrus species. Polytomies of the gene trees and star-like structure of cpDNA networks suggested rapid radiation is another major evolutionary process, especially for the occidental species. Pyrus calleryana and P. regelii were the earliest diverged Pyrus species. Two North African species, P. cordata, P. spinosa and P. betulaefolia were descendent of primitive stock Pyrus species and still share some common molecular characters. Southwestern China, where a large number of P. pashia populations are found, is probably the most important diversification center of Pyrus. More accessions and nuclear genes are needed for further understanding the evolutionary histories of Pyrus. Copyright © 2014 Elsevier Inc. All rights reserved.

The genus Machaerium (Fabaceae): taxonomy, phytochemistry, traditional uses and biological activities.

PubMed

Amen, Yhiya M; Marzouk, Amani M; Zaghloul, Mona G; Afifi, Mohamed S

2015-01-01

Machaerium, in the family Fabaceae, predominantly is a genus of a Neotropical distribution of trees, shrubs, and lianas occurring from southern Mexico to Brazil and northern Argentina and as far as South America. Several Machaerium species are widely used in traditional medicine and are considered to have multiple medicinal properties. This review aims to provide up-to-date and comprehensive information on the taxonomy, phytochemistry, traditional uses and biological activities of plants in the genus Machaerium.

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

NASA Astrophysics Data System (ADS)

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

2015-10-01

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

Student interpretations of phylogenetic trees in an introductory biology course.

PubMed

Dees, Jonathan; Momsen, Jennifer L; Niemi, Jarad; Montplaisir, Lisa

2014-01-01

Phylogenetic trees are widely used visual representations in the biological sciences and the most important visual representations in evolutionary biology. Therefore, phylogenetic trees have also become an important component of biology education. We sought to characterize reasoning used by introductory biology students in interpreting taxa relatedness on phylogenetic trees, to measure the prevalence of correct taxa-relatedness interpretations, and to determine how student reasoning and correctness change in response to instruction and over time. Counting synapomorphies and nodes between taxa were the most common forms of incorrect reasoning, which presents a pedagogical dilemma concerning labeled synapomorphies on phylogenetic trees. Students also independently generated an alternative form of correct reasoning using monophyletic groups, the use of which decreased in popularity over time. Approximately half of all students were able to correctly interpret taxa relatedness on phylogenetic trees, and many memorized correct reasoning without understanding its application. Broad initial instruction that allowed students to generate inferences on their own contributed very little to phylogenetic tree understanding, while targeted instruction on evolutionary relationships improved understanding to some extent. Phylogenetic trees, which can directly affect student understanding of evolution, appear to offer introductory biology instructors a formidable pedagogical challenge. © 2014 J. Dees et al. CBE—Life Sciences Education © 2014 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Evidence of tree species’ range shifts in a complex landscape

Treesearch

Vicente J. Monleon; Heather E. Lintz; Sylvain Delzon

2015-01-01

Climate change is expected to change the distribution of species. For long-lived, sessile species such as trees, tracking the warming climate depends on seedling colonization of newly favorable areas. We compare the distribution of seedlings and mature trees for all but the rarest tree species in California, Oregon and Washington, United States of America, a large,...

Woodland recovery following drought-induced tree mortality across an environmental stress gradient.

PubMed

Redmond, Miranda D; Cobb, Neil S; Clifford, Michael J; Barger, Nichole N

2015-10-01

Recent droughts and increasing temperatures have resulted in extensive tree mortality across the globe. Understanding the environmental controls on tree regeneration following these drought events will allow for better predictions of how these ecosystems may shift under a warmer, drier climate. Within the widely distributed piñon-juniper woodlands of the southwestern USA, a multiyear drought in 2002-2004 resulted in extensive adult piñon mortality and shifted adult woodland composition to a juniper-dominated, more savannah-type ecosystem. Here, we used pre- (1998-2001) and 10-year post- (2014) drought stand structure data of individually mapped trees at 42 sites to assess the effects of this drought on tree regeneration across a gradient of environmental stress. We found declines in piñon juvenile densities since the multiyear drought due to limited new recruitment and high (>50%) juvenile mortality. This is in contrast to juniper juvenile densities, which increased over this time period. Across the landscape, piñon recruitment was positively associated with live adult piñon densities and soil available water capacity, likely due to their respective effects on seed and water availability. Juvenile piñon survival was strongly facilitated by certain types of nurse trees and shrubs. These nurse plants also moderated the effects of environmental stress on piñon survival: Survival of interspace piñon juveniles was positively associated with soil available water capacity, whereas survival of nursed piñon juveniles was negatively associated with perennial grass cover. Thus, nurse plants had a greater facilitative effect on survival at sites with higher soil available water capacity and perennial grass cover. Notably, mean annual climatic water deficit and elevation were not associated with piñon recruitment or survival across the landscape. Our findings reveal a clear shift in successional trajectories toward a more juniper-dominated woodland and highlight the importance of incorporating biotic interactions and soil properties into species distribution modeling approaches. © 2015 John Wiley & Sons Ltd.

Species distributions in response to individual soil nutrients and seasonal drought across a community of tropical trees

PubMed Central

Condit, Richard; Engelbrecht, Bettina M. J.; Pino, Delicia; Pérez, Rolando; Turner, Benjamin L.

2013-01-01

Tropical forest vegetation is shaped by climate and by soil, but understanding how the distributions of individual tree species respond to specific resources has been hindered by high diversity and consequent rarity. To study species over an entire community, we surveyed trees and measured soil chemistry across climatic and geological gradients in central Panama and then used a unique hierarchical model of species occurrence as a function of rainfall and soil chemistry to circumvent analytical difficulties posed by rare species. The results are a quantitative assessment of the responses of 550 tree species to eight environmental factors, providing a measure of the importance of each factor across the entire tree community. Dry-season intensity and soil phosphorus were the strongest predictors, each affecting the distribution of more than half of the species. Although we anticipated clear-cut responses to dry-season intensity, the finding that many species have pronounced associations with either high or low phosphorus reveals a previously unquantified role for this nutrient in limiting tropical tree distributions. The results provide the data necessary for understanding distributional limits of tree species and predicting future changes in forest composition. PMID:23440213

Species distributions in response to individual soil nutrients and seasonal drought across a community of tropical trees.

PubMed

Condit, Richard; Engelbrecht, Bettina M J; Pino, Delicia; Pérez, Rolando; Turner, Benjamin L

2013-03-26

Tropical forest vegetation is shaped by climate and by soil, but understanding how the distributions of individual tree species respond to specific resources has been hindered by high diversity and consequent rarity. To study species over an entire community, we surveyed trees and measured soil chemistry across climatic and geological gradients in central Panama and then used a unique hierarchical model of species occurrence as a function of rainfall and soil chemistry to circumvent analytical difficulties posed by rare species. The results are a quantitative assessment of the responses of 550 tree species to eight environmental factors, providing a measure of the importance of each factor across the entire tree community. Dry-season intensity and soil phosphorus were the strongest predictors, each affecting the distribution of more than half of the species. Although we anticipated clear-cut responses to dry-season intensity, the finding that many species have pronounced associations with either high or low phosphorus reveals a previously unquantified role for this nutrient in limiting tropical tree distributions. The results provide the data necessary for understanding distributional limits of tree species and predicting future changes in forest composition.

Tree grade distribution in Allegheny hardwoods

Treesearch

Richard L. Ernst; David A. Marquis

1978-01-01

Estimates of the distribution of tree grades by diameter class were developed for six hardwood species on the Allegheny Plateau. These estimates can be used to calculate present and projected stand values when actual tree grade measurements are not available.

Demographic history and population structure of Anopheles pseudopunctipennis in Argentina based on the mitochondrial COI gene.

PubMed

Dantur Juri, María J; Moreno, Marta; Prado Izaguirre, Mónica J; Navarro, Juan C; Zaidenberg, Mario O; Almirón, Walter R; Claps, Guillermo L; Conn, Jan E

2014-09-04

Anopheles pseudopunctipennis is an important malaria vector in the Neotropical region and the only species involved in Plasmodium transmission in the Andean foothills. Its wide geographical distribution in America, high preference for biting humans and capacity to rest inside dwellings after feeding, are attributes contributing to its vector status. Previous reports have tried to elucidate its taxonomic status, distinguishing populations from North, Central and South America. In the present study we used a mitochondrial marker to examine the demographic history of An. pseudopunctipennis in northwestern Argentina. Twelve localities were selected across 550 km of the distribution of this species in Argentina, including two near the Bolivian border and several in South Tucumán, for sampling. A fragment of the cytochrome oxidase I (COI) gene was sequenced and haplotype relationships were analyzed by a statistical parsimony network and a Neighbor-Joining (NJ) tree. Genetic differentiation was estimated with FST. Historical demographic processes were evaluated using diversity measures, neutrality tests and mismatch distribution. Forty-one haplotypes were identified, of which haplotype A was the most common and widely distributed. Neither the network nor the NJ tree showed any geographic differentiation between northern and southern populations. Haplotype diversities, Tajima's DT and Fu & Li's F and D neutrality tests and mismatch distribution supported a scenario of Holocene demographic expansion. The demographic pattern suggests that An. pseudopunctipennis has undergone a single colonization process, and the ancestral haplotype is shared by specimens from all localities, indicating mitochondrial gene flow. Genetic differentiation was minimal, observed only between one northern and one southern locality. The estimated time of the population expansion of this species was during the Holocene. These data suggest that regional vector control measures would be equally effective in both northern and southern localities sampled, but also that insecticide resistant genes may spread rapidly within this region.

Phylogenetic Analysis of Local-Scale Tree Soil Associations in a Lowland Moist Tropical Forest

PubMed Central

Schreeg, Laura A.; Kress, W. John; Erickson, David L.; Swenson, Nathan G.

2010-01-01

Background Local plant-soil associations are commonly studied at the species-level, while associations at the level of nodes within a phylogeny have been less well explored. Understanding associations within a phylogenetic context, however, can improve our ability to make predictions across systems and can advance our understanding of the role of evolutionary history in structuring communities. Methodology/Principal Findings Here we quantified evolutionary signal in plant-soil associations using a DNA sequence-based community phylogeny and several soil variables (e.g., extractable phosphorus, aluminum and manganese, pH, and slope as a proxy for soil water). We used published plant distributional data from the 50-ha plot on Barro Colorado Island (BCI), Republic of Panamá. Our results suggest some groups of closely related species do share similar soil associations. Most notably, the node shared by Myrtaceae and Vochysiaceae was associated with high levels of aluminum, a potentially toxic element. The node shared by Apocynaceae was associated with high extractable phosphorus, a nutrient that could be limiting on a taxon specific level. The node shared by the large group of Laurales and Magnoliales was associated with both low extractable phosphorus and with steeper slope. Despite significant node-specific associations, this study detected little to no phylogeny-wide signal. We consider the majority of the ‘traits’ (i.e., soil variables) evaluated to fall within the category of ecological traits. We suggest that, given this category of traits, phylogeny-wide signal might not be expected while node-specific signals can still indicate phylogenetic structure with respect to the variable of interest. Conclusions Within the BCI forest dynamics plot, distributions of some plant taxa are associated with local-scale differences in soil variables when evaluated at individual nodes within the phylogenetic tree, but they are not detectable by phylogeny-wide signal. Trends highlighted in this analysis suggest how plant-soil associations may drive plant distributions and diversity at the local-scale. PMID:21060686

Epiphytes in wooded pastures: Isolation matters for lichen but not for bryophyte species richness

PubMed Central

Keller, Christine; Scheidegger, Christoph; Bergamini, Ariel

2017-01-01

Sylvo-pastoral systems are species-rich man-made landscapes that are currently often severely threatened by abandonment or management intensification. At low tree densities, single trees in these systems represent habitat islands for epiphytic cryptogams. Here, we focused on sycamore maple (Acer pseudoplatanus) wooded pastures in the northern European Alps. We assessed per tree species richness of bryophytes and lichens on 90 sycamore maple trees distributed across six study sites. We analysed the effects of a range of explanatory variables (tree characteristics, environmental variables and isolation measures) on the richness of epiphytic bryophytes and lichens and various functional subgroups (based on diaspore size, habitat preference and red list status). Furthermore, we estimated the effect of these variables on the occurrence of two specific bryophyte species (Tayloria rudolphiana, Orthotrichum rogeri) and one lichen species (Lobaria pulmonaria) of major conservation concern. Bryophytes and lichens, as well as their subgroups, were differently and sometimes contrastingly affected by the variables considered: tree diameter at breast height had no significant effect on bryophytes but negatively affected many lichen groups; tree phenological age positively affected red-listed lichens but not red-listed bryophytes; increasing isolation from neighbouring trees negatively affected lichens but not bryophytes. However, the high-priority bryophyte species T. rudolphiana was also negatively affected by increased isolation at small spatial scales. Orthotrichum rogeri was more frequent on young trees and L. pulmonaria was more frequent on trees with thin stems and large crowns. The results indicate that local dispersal is important for lichens, whereas long distance dispersal seems to be more important for colonisation by bryophytes. Furthermore, our study highlights that different conservation measures need to be taken depending on the taxonomic and functional species group or the individual species that is addressed. In practice, for the conservation of a high overall richness in sylvo-pastoral systems, it is crucial to sustain not only old and large trees but rather a wide range of tree sizes and ages. PMID:28742881

Tree die-off in response to global change-type drought: Mortality insights from a decade of plant water potential measurements

USGS Publications Warehouse

Breshears, D.D.; Myers, O.B.; Meyer, Clifton W.; Barnes, F.J.; Zou, C.B.; Allen, Craig D.; McDowell, N.G.; Pockman, W. T.

2009-01-01

Global climate change is projected to produce warmer, longer, and more frequent droughts, referred to here as “global change-type droughts”, which have the potential to trigger widespread tree die-off. However, drought-induced tree mortality cannot be predicted with confidence, because long-term field observations of plant water stress prior to, and culminating in, mortality are rare, precluding the development and testing of mechanisms. Here, we document plant water stress in two widely distributed, co-occurring species, piñon pine (Pinus edulis) and juniper (Juniperus monosperma), over more than a decade, leading up to regional-scale die-off of piñon pine trees in response to global change-related drought. Piñon leaf water potentials remained substantially below their zero carbon assimilation point for at least 10 months prior to dying, in contrast to those of juniper, which rarely dropped below their zero-assimilation point. These data suggest that piñon mortality was driven by protracted water stress, leading to carbon starvation and associated increases in susceptibility to other disturbances (eg bark beetles), a finding that should help to improve predictions of mortality during drought.

Mosquitoes of the Caatinga: 2. Species from periodic sampling of bromeliads and tree holes in a dry Brazilian forest.

PubMed

Marteis, Letícia Silva; Natal, Delsio; Sallum, Maria Anice Mureb; Medeiros-Sousa, Antônio Ralph; Corte, Roseli La

2017-07-01

The Caatinga is a dry tropical forest, located in the Brazilian semiarid region and rich in phytotelmata. This study investigated the culicid fauna of phytotelmata of the caatinga by sampling for 19 consecutive months aquatic immatures from tree holes and bromeliads. A total of 127L of water was taken from the plants, containing 6764 immature culicids of 16 species, of which 11 (69%) are undescribed and respond to 90% of the total abundance of the specimens collected. Epiphytic bromeliads harbor a large number of immature Culicidae, although terrestrial bromeliads are the most abundant and widely distributed in the region. The richness of culicid species was similar between terrestrial and epiphytic bromeliads and lower in habitats represented by tree hole phytotelmata. There was no similarity in the composition of culicid species that developed in bromeliads or tree holes. Temperature and humidity were the environmental parameters most strongly associated with the proportion of positive plants. The Caatinga has a great number of endemic species that remain unknown to science and many additional culicid species may await discovery from there. Copyright © 2017 Elsevier B.V. All rights reserved.

Host trait combinations drive abundance and canopy distribution of atmospheric bromeliad assemblages

PubMed Central

Chaves, Cleber Juliano Neves; Dyonisio, Júlio César; Rossatto, Davi Rodrigo

2016-01-01

Epiphytes are strongly dependent on the conditions created by their host's traits and a certain degree of specificity is expected between them, even if these species are largely abundant in a series of tree hosts of a given environment, as in the case of atmospheric bromeliads. Despite their considerable abundance in these environments, we hypothesize that stochasticity alone cannot explain the presence and abundance of atmospheric bromeliads on host trees, since host traits could have a greater influence on the establishment of these bromeliads. We used secondary and reforested seasonal forests and three distinct silvicultures to test whether species richness, phylogenetic diversity and functional diversity of trees can predict the differential presence, abundance and distribution of atmospheric bromeliads on hosts. We compared the observed parameters of their assemblage with null models and performed successive variance hierarchic partitions of abundance and distribution of the assemblage to detect the influence of multiple traits of the tree hosts. Our results do not indicate direct relationships between the abundance of atmospheric bromeliads and phylogenetic or functional diversity of trees, but instead indicate that bromeliads occurred on fewer tree species than expected by chance. We distinguished functional tree patterns that can improve or reduce the abundance of atmospheric bromeliads, and change their distribution on branches and trunk. While individual tree traits are related to increased abundance, species traits are related to the canopy distribution of atmospheric bromeliad assemblages. A balance among these tree functional patterns drives the atmospheric bromeliad assemblage of the forest patches. PMID:26888951

Distribution and Abundance of Adelges tsugae (Hemiptera: Adelgidae) Within Hemlock Trees

Treesearch

S.V. Joseph; J.L. Hanula; S.K. Braman

2011-01-01

We studied the distribution of hemlock woolly adelgid, Adelges tsugae Annand (Hemiptera: Adelgidae), within hemlock trees for three summer (progrediens) and two winter (sistens) generations in northern Georgia. Eastern hemlock, Tsuga canadensis (L.) Carrie` re, trees were treated with 0, 10, or 25% of 1.5 g of imidacloprid per 2.5 cm of tree diameter at breast height...

Predicting Potential Changes in Suitable Habitat and Distribution by 2100 for Tree Species of the Eastern United States

Treesearch

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

2005-01-01

We predict current distribution and abundance for tree species present in eastern North America, and subsequently estimate potential suitable habitat for those species under a changed climate with 2 x CO2. We used a series of statistical models (i.e., Regression Tree Analysis (RTA), Multivariate Adaptive Regression Splines (MARS), Bagging Trees (...

Tree canopy change and neighborhood stability: A comparative analysis of Washington, D.C. and Baltimore, MD

Treesearch

Wen-Ching Chuang; Christopher G. Boone; Dexter H. Locke; J. Morgan Grove; Ali Whitmer; Geoffrey Buckley; Sainan Zhang

2017-01-01

Trees provide important health, ecosystem, and aesthetic services in urban areas, but they are unevenly distributed. Some neighborhoods have abundant tree canopy and others nearly none. We analyzed how neighborhood characteristics and changes in income over time related to the distribution of urban tree canopy in Washington, D.C. and Baltimore, MD. We used stepwise...

Soil nutrients influence spatial distributions of tropical tree species.

PubMed

John, Robert; Dalling, James W; Harms, Kyle E; Yavitt, Joseph B; Stallard, Robert F; Mirabello, Matthew; Hubbell, Stephen P; Valencia, Renato; Navarrete, Hugo; Vallejo, Martha; Foster, Robin B

2007-01-16

The importance of niche vs. neutral assembly mechanisms in structuring tropical tree communities remains an important unsettled question in community ecology [Bell G (2005) Ecology 86:1757-1770]. There is ample evidence that species distributions are determined by soils and habitat factors at landscape (<10(4) km(2)) and regional scales. At local scales (<1 km(2)), however, habitat factors and species distributions show comparable spatial aggregation, making it difficult to disentangle the importance of niche and dispersal processes. In this article, we test soil resource-based niche assembly at a local scale, using species and soil nutrient distributions obtained at high spatial resolution in three diverse neotropical forest plots in Colombia (La Planada), Ecuador (Yasuni), and Panama (Barro Colorado Island). Using spatial distribution maps of >0.5 million individual trees of 1,400 species and 10 essential plant nutrients, we used Monte Carlo simulations of species distributions to test plant-soil associations against null expectations based on dispersal assembly. We found that the spatial distributions of 36-51% of tree species at these sites show strong associations to soil nutrient distributions. Neutral dispersal assembly cannot account for these plant-soil associations or the observed niche breadths of these species. These results indicate that belowground resource availability plays an important role in the assembly of tropical tree communities at local scales and provide the basis for future investigations on the mechanisms of resource competition among tropical tree species.

A scalable approach for tree segmentation within small-footprint airborne LiDAR data

NASA Astrophysics Data System (ADS)

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

2017-05-01

This paper presents a distributed approach that scales up to segment tree crowns within a LiDAR point cloud representing an arbitrarily large forested area. The approach uses a single-processor tree segmentation algorithm as a building block in order to process the data delivered in the shape of tiles in parallel. The distributed processing is performed in a master-slave manner, in which the master maintains the global map of the tiles and coordinates the slaves that segment tree crowns within and across the boundaries of the tiles. A minimal bias was introduced to the number of detected trees because of trees lying across the tile boundaries, which was quantified and adjusted for. Theoretical and experimental analyses of the runtime of the approach revealed a near linear speedup. The estimated number of trees categorized by crown class and the associated error margins as well as the height distribution of the detected trees aligned well with field estimations, verifying that the distributed approach works correctly. The approach enables providing information of individual tree locations and point cloud segments for a forest-level area in a timely manner, which can be used to create detailed remotely sensed forest inventories. Although the approach was presented for tree segmentation within LiDAR point clouds, the idea can also be generalized to scale up processing other big spatial datasets.

Displayed Trees Do Not Determine Distinguishability Under the Network Multispecies Coalescent

PubMed Central

Zhu, Sha; Degnan, James H.

2017-01-01

Abstract Recent work in estimating species relationships from gene trees has included inferring networks assuming that past hybridization has occurred between species. Probabilistic models using the multispecies coalescent can be used in this framework for likelihood-based inference of both network topologies and parameters, including branch lengths and hybridization parameters. A difficulty for such methods is that it is not always clear whether, or to what extent, networks are identifiable—that is whether there could be two distinct networks that lead to the same distribution of gene trees. For cases in which incomplete lineage sorting occurs in addition to hybridization, we demonstrate a new representation of the species network likelihood that expresses the probability distribution of the gene tree topologies as a linear combination of gene tree distributions given a set of species trees. This representation makes it clear that in some cases in which two distinct networks give the same distribution of gene trees when sampling one allele per species, the two networks can be distinguished theoretically when multiple individuals are sampled per species. This result means that network identifiability is not only a function of the trees displayed by the networks but also depends on allele sampling within species. We additionally give an example in which two networks that display exactly the same trees can be distinguished from their gene trees even when there is only one lineage sampled per species. PMID:27780899

Regeneration of three pine species in a Mediterranean forest: A study to test predictions from species distribution models under changing climates.

PubMed

Tíscar, P A; Candel-Pérez, D; Estrany, J; Balandier, P; Gómez, R; Lucas-Borja, M E

2017-04-15

The study tested the hypothesis that future changes in the composition of tree communities, as predicted by species distribution models, could already be apparent in the current regeneration patterns of three pine species (Pinus pinaster, P. nigra and P. sylvestris)inhabiting the central-eastern mountains of Spain. We carried out both an observational study and a seed-sowing experiment to analyze, along an altitudinal and latitudinal gradient, whether recent recruitment patterns indicate an expansion of P. pinaster forests to the detriment of P. nigra ones in the low-altitude southern sites of these mountains; or whether P. sylvestris is being replaced by P. nigra in the high-altitude sites from the same area. The observational study gathered data from 561 plots of the Spanish National Forest Inventory. The seed-sowing experiment tested the effects of irrigation and stand basal area on seedling emergence and survival. Data were analyzed by means of Generalized Linear Models and Generalized Linear Mixed Models. Regeneration of the three pine species responded similarly to the explicative factors studied, but the density of tree seedlings and saplings exhibited a wide spatial heterogeneity. This result suggested that a mosaic of site- and species-specific responses to climate change might mislead model projections on the future forest occupancy of tree species. Yet, we found no indications of neither an expansion nor a contraction of the near future forest occupancy of the tree species studied. Copyright © 2017 Elsevier B.V. All rights reserved.

Population dynamics in changing environments: the case of an eruptive forest pest species.

PubMed

Kausrud, Kyrre; Okland, Bjørn; Skarpaas, Olav; Grégoire, Jean-Claude; Erbilgin, Nadir; Stenseth, Nils Chr

2012-02-01

In recent decades we have seen rapid and co-occurring changes in landscape structure, species distributions and even climate as consequences of human activity. Such changes affect the dynamics of the interaction between major forest pest species, such as bark beetles (Coleoptera: Curculionidae, Scolytinae), and their host trees. Normally breeding mostly in broken or severely stressed spruce; at high population densities some bark beetle species can colonise and kill healthy trees on scales ranging from single trees in a stand to multi-annual landscape-wide outbreaks. In Eurasia, the largest outbreaks are caused by the spruce bark beetle, Ips typographus (Linnaeus), which is common and shares a wide distribution with its main host, Norway spruce (Picea abies Karst.). A large literature is now available, from which this review aims to synthesize research relevant for the population dynamics of I. typographus and co-occurring species under changing conditions. We find that spruce bark beetle population dynamics tend to be metastable, but that mixed-species and age-heterogeneous forests with good site-matching tend to be less susceptible to large-scale outbreaks. While large accumulations of logs should be removed and/or debarked before the next swarming period, intensive removal of all coarse dead wood may be counterproductive, as it reduces the diversity of predators that in some areas may play a role in keeping I. typographus populations below the outbreak threshold, and sanitary logging frequently causes edge effects and root damage, reducing the resistance of remaining trees. It is very hard to predict the outcome of interspecific interactions due to invading beetle species or I. typographus establishing outside its current range, as they can be of varying sign and strength and may fluctuate depending on environmental factors and population phase. Most research indicates that beetle outbreaks will increase in frequency and magnitude as temperature, wind speed and precipitation variability increases, and that mitigating forestry practices should be adopted as soon as possible considering the time lags involved. © 2011 The Authors. Biological Reviews © 2011 Cambridge Philosophical Society.

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.

Gene tree rooting methods give distributions that mimic the coalescent process.

PubMed

Tian, Yuan; Kubatko, Laura S

2014-01-01

Multi-locus phylogenetic inference is commonly carried out via models that incorporate the coalescent process to model the possibility that incomplete lineage sorting leads to incongruence between gene trees and the species tree. An interesting question that arises in this context is whether data "fit" the coalescent model. Previous work (Rosenfeld et al., 2012) has suggested that rooting of gene trees may account for variation in empirical data that has been previously attributed to the coalescent process. We examine this possibility using simulated data. We show that, in the case of four taxa, the distribution of gene trees observed from rooting estimated gene trees with either the molecular clock or with outgroup rooting can be closely matched by the distribution predicted by the coalescent model with specific choices of species tree branch lengths. We apply commonly-used coalescent-based methods of species tree inference to assess their performance in these situations. Copyright © 2013 Elsevier Inc. All rights reserved.

National Forest Health Monitoring Program Maryland and Massachusetts Street Tree Monitoring Pilot Projects

Treesearch

Buckelew Cumming Anne; Daniel Twardus; William Smith

2006-01-01

Urban forests have many components: park trees, small woodlands, riparian buffers, street trees, and others. While some communities conduct city-wide inventories of street tree populations, there has been no comprehensive, statewide sampling to characterize the structure, health, and function of street tree populations. A statewide Street Tree Monitoring pilot study...

A Performance Comparison of Tree and Ring Topologies in Distributed System

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

Huang, Min

A distributed system is a collection of computers that are connected via a communication network. Distributed systems have become commonplace due to the wide availability of low-cost, high performance computers and network devices. However, the management infrastructure often does not scale well when distributed systems get very large. Some of the considerations in building a distributed system are the choice of the network topology and the method used to construct the distributed system so as to optimize the scalability and reliability of the system, lower the cost of linking nodes together and minimize the message delay in transmission, and simplifymore » system resource management. We have developed a new distributed management system that is able to handle the dynamic increase of system size, detect and recover the unexpected failure of system services, and manage system resources. The topologies used in the system are the tree-structured network and the ring-structured network. This thesis presents the research background, system components, design, implementation, experiment results and the conclusions of our work. The thesis is organized as follows: the research background is presented in chapter 1. Chapter 2 describes the system components, including the different node types and different connection types used in the system. In chapter 3, we describe the message types and message formats in the system. We discuss the system design and implementation in chapter 4. In chapter 5, we present the test environment and results, Finally, we conclude with a summary and describe our future work in chapter 6.« less

Identifying hidden rate changes in the evolution of a binary morphological character: the evolution of plant habit in campanulid angiosperms.

PubMed

Beaulieu, Jeremy M; O'Meara, Brian C; Donoghue, Michael J

2013-09-01

The growth of phylogenetic trees in scope and in size is promising from the standpoint of understanding a wide variety of evolutionary patterns and processes. With trees comprised of larger, older, and globally distributed clades, it is likely that the lability of a binary character will differ significantly among lineages, which could lead to errors in estimating transition rates and the associated inference of ancestral states. Here we develop and implement a new method for identifying different rates of evolution in a binary character along different branches of a phylogeny. We illustrate this approach by exploring the evolution of growth habit in Campanulidae, a flowering plant clade containing some 35,000 species. The distribution of woody versus herbaceous species calls into question the use of traditional models of binary character evolution. The recognition and accommodation of changes in the rate of growth form evolution in different lineages demonstrates, for the first time, a robust picture of growth form evolution across a very large, very old, and very widespread flowering plant clade.

Toxic genes present a unique phylogenetic signature.

PubMed

Avni, Eliran; Snir, Sagi

2017-11-01

Horizontal gene transfer (HGT) is a major part of the evolution of Archaea and Bacteria, to the extent that the validity of the Tree of Life concept for prokaryotes has been seriously questioned. The patterns and routes of HGT remain a subject of intense study and debate. It was discovered that while several genes exhibit rampant HGT across the whole prokaryotic tree of life, others are lethal to certain organisms and therefore cannot be successfully transferred to them. We distinguish between these two classes of genes and show analytically that genes found to be toxic to a specific species (E. coli) also resist HGT in general. Several tools we employ show evidence to support that claim. One of those tools is the quartet plurality distribution (QPD), a mathematical tool that measures tendency to HGT over a large set of genes and species. When aggregated over a collection of genes, it can reveal important properties of this collection. We conclude that evidence of toxicity of certain genes to a wide variety of prokaryotes are revealed using the new tool of quartet plurality distribution. Copyright © 2017 Elsevier Inc. All rights reserved.

Amount and distribution of isozyme variation in various conifer species

Treesearch

M. Thompson Conkle

1980-01-01

Estimation of the relative amount and the geographic distribution of genetically controlled variation is a central topic of tree resource management. Biochemical data from the analysis of forest tree enzyme variants provides a direct and precise measure of allele frequencies of tree genes.

Post-glacial phylogeography and evolution of a wide-ranging highly-exploited keystone forest tree, eastern white pine (Pinus strobus) in North America: single refugium, multiple routes.

PubMed

Zinck, John W R; Rajora, Om P

2016-03-02

Knowledge of the historical distribution and postglacial phylogeography and evolution of a species is important to better understand its current distribution and population structure and potential fate in the future, especially under climate change conditions, and conservation of its genetic resources. We have addressed this issue in a wide-ranging and heavily exploited keystone forest tree species of eastern North America, eastern white pine (Pinus strobus). We examined the range-wide population genetic structure, tested various hypothetical population history and evolutionary scenarios and inferred the location of glacial refugium and post-glacial recolonization routes. Our hypothesis was that eastern white pine survived in a single glacial refugium and expanded through multiple post-glacial recolonization routes. We studied the range-wide genetic diversity and population structure of 33 eastern white pine populations using 12 nuclear and 3 chloroplast microsatellite DNA markers. We used Approximate Bayesian Computation approach to test various evolutionary scenarios. We observed high levels of genetic diversity, and significant genetic differentiation (F ST = 0.104) and population structure among eastern white pine populations across its range. A south to north trend of declining genetic diversity existed, consistent with repeated founder effects during post-glaciation migration northwards. We observed broad consensus from nuclear and chloroplast genetic markers supporting the presence of two main post-glacial recolonization routes that originated from a single southern refugium in the mid-Atlantic plain. One route gave rise to populations at the western margin of the species' range in Minnesota and western Ontario. The second route gave rise to central-eastern populations, which branched into two subgroups: central and eastern. We observed minimal sharing of chloroplast haplotypes between recolonization routes but there was evidence of admixture between the western and west-central populations. Our study reveals a single southern refugium, two recolonization routes and three genetically distinguishable lineages in eastern white pine that we suggest to be treated as separate Evolutionarily Significant Units. Like many wide-ranging North American species, eastern white pine retains the genetic signatures of post-glacial recolonization and evolution, and its contemporary population genetic structure reflects not just the modern distribution and effects of heavy exploitation but also routes northward from its glacial refugium.

Among-tree variability and feedback effects result in different growth responses to climate change at the upper treeline in the Swiss Alps.

PubMed

Jochner, Matthias; Bugmann, Harald; Nötzli, Magdalena; Bigler, Christof

2017-10-01

Upper treeline ecotones are important life form boundaries and particularly sensitive to a warming climate. Changes in growth conditions at these ecotones have wide-ranging implications for the provision of ecosystem services in densely populated mountain regions like the European Alps. We quantify climate effects on short- and long-term tree growth responses, focusing on among-tree variability and potential feedback effects. Although among-tree variability is thought to be substantial, it has not been considered systematically yet in studies on growth-climate relationships. We compiled tree-ring data including almost 600 trees of major treeline species ( Larix decidua , Picea abies , Pinus cembra , and Pinus mugo ) from three climate regions of the Swiss Alps. We further acquired tree size distribution data using unmanned aerial vehicles. To account for among-tree variability, we employed information-theoretic model selections based on linear mixed-effects models (LMMs) with flexible choice of monthly temperature effects on growth. We isolated long-term trends in ring-width indices (RWI) in interaction with elevation. The LMMs revealed substantial amounts of previously unquantified among-tree variability, indicating different strategies of single trees regarding when and to what extent to invest assimilates into growth. Furthermore, the LMMs indicated strongly positive temperature effects on growth during short summer periods across all species, and significant contributions of fall ( L. decidua ) and current year's spring ( L. decidua , P. abies ). In the longer term, all species showed consistently positive RWI trends at highest elevations, but different patterns with decreasing elevation. L. decidua exhibited even negative RWI trends compared to the highest treeline sites, whereas P. abies , P. cembra , and P. mugo showed steeper or flatter trends with decreasing elevation. This does not only reflect effects of ameliorated climate conditions on tree growth over time, but also reveals first signs of long-suspected negative and positive feedback of climate change on stand dynamics at treeline.

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

PubMed

Yao, Yong-Gang

2017-05-18

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

Classification tree and minimum-volume ellipsoid analyses of the distribution of ponderosa pine in the western USA

USGS Publications Warehouse

Norris, Jodi R.; Jackson, Stephen T.; Betancourt, Julio L.

2006-01-01

Aim? Ponderosa pine (Pinus ponderosa Douglas ex Lawson & C. Lawson) is an economically and ecologically important conifer that has a wide geographic range in the western USA, but is mostly absent from the geographic centre of its distribution - the Great Basin and adjoining mountain ranges. Much of its modern range was achieved by migration of geographically distinct Sierra Nevada (P. ponderosa var. ponderosa) and Rocky Mountain (P. ponderosa var. scopulorum) varieties in the last 10,000 years. Previous research has confirmed genetic differences between the two varieties, and measurable genetic exchange occurs where their ranges now overlap in western Montana. A variety of approaches in bioclimatic modelling is required to explore the ecological differences between these varieties and their implications for historical biogeography and impending changes in western landscapes. Location? Western USA. Methods? We used a classification tree analysis and a minimum-volume ellipsoid as models to explain the broad patterns of distribution of ponderosa pine in modern environments using climatic and edaphic variables. Most biogeographical modelling assumes that the target group represents a single, ecologically uniform taxonomic population. Classification tree analysis does not require this assumption because it allows the creation of pathways that predict multiple positive and negative outcomes. Thus, classification tree analysis can be used to test the ecological uniformity of the species. In addition, a multidimensional ellipsoid was constructed to describe the niche of each variety of ponderosa pine, and distances from the niche were calculated and mapped on a 4-km grid for each ecological variable. Results? The resulting classification tree identified three dominant pathways predicting ponderosa pine presence. Two of these three pathways correspond roughly to the distribution of var. ponderosa, and the third pathway generally corresponds to the distribution of var. scopulorum. The classification tree and minimum-volume ellipsoid model show that both varieties have very similar temperature limitations, although var. ponderosa is more limited by the temperature extremes of the continental interior. The precipitation limitations of the two varieties are seasonally different, with var. ponderosa requiring significant winter moisture and var. scopulorum requiring significant summer moisture. Great Basin mountain ranges are too cold at higher elevations to support either variety of ponderosa pine, and at lower elevations are too dry in summer for var. scopulorum and too dry in winter for var. ponderosa. Main conclusions? The classification tree analysis indicates that var. ponderosa is ecologically as well as genetically distinct from var. scopulorum. Ecological differences may maintain genetic separation in spite of a limited zone of introgression between the two varieties in western Montana. Two hypotheses about past and future movements of ponderosa pine emerge from our analyses. The first hypothesis is that, during the last glacial period, colder and/or drier summers truncated most of the range of var. scopulorum in the central Rockies, but had less dramatic effects on the more maritime and winter-wet distribution of var. ponderosa. The second hypothesis is that, all other factors held constant, increasing summer temperatures in the future should produce changes in the distribution of var. scopulorum that are likely to involve range expansions in the central Rockies with the warming of mountain ranges currently too cold but sufficiently wet in summer for var. scopulorum. Finally, our results underscore the growing need to focus on genotypes in biogeographical modelling and ecological forecasting.

Detecting tree-fall gap disturbances in tropical rain forests with airborne lidar

NASA Astrophysics Data System (ADS)

Espirito-Santo, F. D. B.; Saatchi, S.; Keller, M.

2017-12-01

Forest inventory studies in the Amazon indicate a large terrestrial carbon sink. However, field plots may fail to represent forest mortality processes at landscape-scales of tropical forests. Here we characterize the frequency distribution of tree-fall gap disturbances in natural forests of tropical forests using a novel combination of forest inventory and airborne lidar data. We quantify gap size frequency distribution along vertical and horizontal dimensions in ten Neotropical forest canopies distributed across gradients of climate and landscapes using airborne lidar measurements. We assessed all canopy openings related to each class of tree height which yields a three dimensional structure of the distribution of canopy gaps. Gap frequency distributions from lidar CHM data vary markedly with minimum gap size thresholds, but we found that natural forest disturbances (tree-fall gaps) follow a power-law distribution with narrow range of power-law exponents (-1.2 to -1.3). These power-law exponents from gap frequency distributions provide insights into how natural forest disturbances are distributed over tropical forest landscape.

Integrating the effects of forest cover on slope stability in a deterministic landslide susceptibility model (TRIGRS 2.0)

NASA Astrophysics Data System (ADS)

Zieher, T.; Rutzinger, M.; Bremer, M.; Meissl, G.; Geitner, C.

2014-12-01

The potentially stabilizing effects of forest cover in respect of slope stability have been the subject of many studies in the recent past. Hence, the effects of trees are also considered in many deterministic landslide susceptibility models. TRIGRS 2.0 (Transient Rainfall Infiltration and Grid-Based Regional Slope-Stability; USGS) is a dynamic, physically-based model designed to estimate shallow landslide susceptibility in space and time. In the original version the effects of forest cover are not considered. As for further studies in Vorarlberg (Austria) TRIGRS 2.0 is intended to be applied in selected catchments that are densely forested, the effects of trees on slope stability were implemented in the model. Besides hydrological impacts such as interception or transpiration by tree canopies and stems, root cohesion directly influences the stability of slopes especially in case of shallow landslides while the additional weight superimposed by trees is of minor relevance. Detailed data on tree positions and further attributes such as tree height and diameter at breast height were derived throughout the study area (52 km²) from high-resolution airborne laser scanning data. Different scenarios were computed for spruce (Picea abies) in the study area. Root cohesion was estimated area-wide based on published correlations between root reinforcement and distance to tree stems depending on the stem diameter at breast height. In order to account for decreasing root cohesion with depth an exponential distribution was assumed and implemented in the model. Preliminary modelling results show that forest cover can have positive effects on slope stability yet strongly depending on tree age and stand structure. This work has been conducted within C3S-ISLS, which is funded by the Austrian Climate and Energy Fund, 5th ACRP Program.

Keep your feet warm? A cryptic refugium of trees linked to a geothermal spring in an ocean of glaciers.

PubMed

Carcaillet, Christopher; Latil, Jean-Louis; Abou, Sébastien; Ali, Adam; Ghaleb, Bassam; Magnin, Frédéric; Roiron, Paul; Aubert, Serge

2018-06-01

Up to now, the most widely accepted idea of the periglacial environment is that of treeless ecosystems such as the arctic or the alpine tundra, also called the tabula rasa paradigm. However, several palaeoecological studies have recently challenged this idea, that is, treeless environments in periglacial areas where all organisms would have been exterminated near the glacier formed during the Last Glacial Maximum, notably in the Scandinavian mountains. In the Alps, the issue of glacial refugia of trees remains unanswered. Advances in glacier reconstructions show that ice domes did not cover all upper massifs, but glaciers filled valleys. Here, we used fossils of plant and malacofauna from a travertine formation located in a high mountain region to demonstrate that trees (Pinus, Betula) grew with grasses during the Lateglacial-Holocene transition, while the glacier fronts were 200-300 m lower. The geothermal travertine started to accumulate more than 14,500 years ago, but became progressively more meteogene about 11,500 years ago due to a change in groundwater circulation. With trees, land snails (gastropods) associated to woody or open habitats and aquatic mollusc were also present at the onset of the current interglacial, namely the Holocene. The geothermal spring, due to warm water and soil, probably favoured woody glacial ecosystems. This new finding of early tree growth, combined with other scattered proofs of the tree presence before 11,000 years ago in the western Alps, changes our view of the tree distribution in periglacial environments, supporting the notion of tree refugia on nunataks in an ocean of glaciers. Therefore, the tabula rasa paradigm must be revisited because it has important consequences on the global changes, including postglacial plant migrations and biogeochemical cycles. © 2018 John Wiley & Sons Ltd.

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.

Host trait combinations drive abundance and canopy distribution of atmospheric bromeliad assemblages.

PubMed

Chaves, Cleber Juliano Neves; Dyonisio, Júlio César; Rossatto, Davi Rodrigo

2016-01-01

Epiphytes are strongly dependent on the conditions created by their host's traits and a certain degree of specificity is expected between them, even if these species are largely abundant in a series of tree hosts of a given environment, as in the case of atmospheric bromeliads. Despite their considerable abundance in these environments, we hypothesize that stochasticity alone cannot explain the presence and abundance of atmospheric bromeliads on host trees, since host traits could have a greater influence on the establishment of these bromeliads. We used secondary and reforested seasonal forests and three distinct silvicultures to test whether species richness, phylogenetic diversity and functional diversity of trees can predict the differential presence, abundance and distribution of atmospheric bromeliads on hosts. We compared the observed parameters of their assemblage with null models and performed successive variance hierarchic partitions of abundance and distribution of the assemblage to detect the influence of multiple traits of the tree hosts. Our results do not indicate direct relationships between the abundance of atmospheric bromeliads and phylogenetic or functional diversity of trees, but instead indicate that bromeliads occurred on fewer tree species than expected by chance. We distinguished functional tree patterns that can improve or reduce the abundance of atmospheric bromeliads, and change their distribution on branches and trunk. While individual tree traits are related to increased abundance, species traits are related to the canopy distribution of atmospheric bromeliad assemblages. A balance among these tree functional patterns drives the atmospheric bromeliad assemblage of the forest patches. Published by Oxford University Press on behalf of the Annals of Botany Company.

The Near East as a cradle of biodiversity: A phylogeography of banded newts (genus Ommatotriton) reveals extensive inter- and intraspecific genetic differentiation.

PubMed

van Riemsdijk, Isolde; Arntzen, Jan W; Bogaerts, Sergé; Franzen, Michael; Litvinchuk, Spartak N; Olgun, Kurtuluş; Wielstra, Ben

2017-09-01

The banded newt (genus Ommatotriton) is widely distributed in the Near East (Anatolia, Caucasus and the Levant) - an understudied region from the perspective of phylogeography. The genus is polytypic, but the number of species included and the phylogenetic relationships between them are not settled. We sequenced two mitochondrial and two nuclear DNA markers throughout the range of Ommatotriton. For mtDNA we constructed phylogenetic trees, estimated divergence times using fossil calibration, and investigated changes in effective population size with Bayesian skyline plots and mismatch analyses. For nuDNA we constructed phylogenetic trees and haplotype networks. Species trees were constructed for all markers and nuDNA only. Species distribution models were projected on current and Last Glacial Maximum climate layers. We confirm the presence of three Ommatotriton species: O. nesterovi, O. ophryticus and O. vittatus. These species are genetically distinct and their most recent common ancestor was dated at ∼25Ma (Oligocene). No evidence of recent gene flow between species was found. The species show deep intraspecific genetic divergence, represented by geographically structured clades, with crown nodes of species dated ∼8-13Ma (Miocene to Early Quaternary); evidence of long-term in situ evolution and survival in multiple glacial refugia. While a species tree based on nuDNA suggested a sister species relationship between O. vittatus and O. ophryticus, when mtDNA was included, phylogenetic relationships were unresolved, and we refrain from accepting a particular phylogenetic hypothesis at this stage. While species distribution models suggest reduced and fragmented ranges during the Last Glacial Maximum, we found no evidence for strong population bottlenecks. We discuss our results in the light of other phylogeographic studies from the Near East. Our study underlines the important role of the Near East in generating and sustaining biodiversity. Copyright © 2017 Elsevier Inc. All rights reserved.

Soil nutrients influence spatial distributions of tropical tree species

PubMed Central

John, Robert; Dalling, James W.; Harms, Kyle E.; Yavitt, Joseph B.; Stallard, Robert F.; Mirabello, Matthew; Hubbell, Stephen P.; Valencia, Renato; Navarrete, Hugo; Vallejo, Martha; Foster, Robin B.

2007-01-01

The importance of niche vs. neutral assembly mechanisms in structuring tropical tree communities remains an important unsettled question in community ecology [Bell G (2005) Ecology 86:1757–1770]. There is ample evidence that species distributions are determined by soils and habitat factors at landscape (<104 km2) and regional scales. At local scales (<1 km2), however, habitat factors and species distributions show comparable spatial aggregation, making it difficult to disentangle the importance of niche and dispersal processes. In this article, we test soil resource-based niche assembly at a local scale, using species and soil nutrient distributions obtained at high spatial resolution in three diverse neotropical forest plots in Colombia (La Planada), Ecuador (Yasuni), and Panama (Barro Colorado Island). Using spatial distribution maps of >0.5 million individual trees of 1,400 species and 10 essential plant nutrients, we used Monte Carlo simulations of species distributions to test plant–soil associations against null expectations based on dispersal assembly. We found that the spatial distributions of 36–51% of tree species at these sites show strong associations to soil nutrient distributions. Neutral dispersal assembly cannot account for these plant–soil associations or the observed niche breadths of these species. These results indicate that belowground resource availability plays an important role in the assembly of tropical tree communities at local scales and provide the basis for future investigations on the mechanisms of resource competition among tropical tree species. PMID:17215353

Evidence of tree species' range shifts in a complex landscape.

PubMed

Monleon, Vicente J; Lintz, Heather E

2015-01-01

Climate change is expected to change the distribution of species. For long-lived, sessile species such as trees, tracking the warming climate depends on seedling colonization of newly favorable areas. We compare the distribution of seedlings and mature trees for all but the rarest tree species in California, Oregon and Washington, United States of America, a large, environmentally diverse region. Across 46 species, the mean annual temperature of the range of seedlings was 0.120°C colder than that of the range of trees (95% confidence interval from 0.096 to 0.144°C). The extremes of the seedling distributions also shifted towards colder temperature than those of mature trees, but the change was less pronounced. Although the mean elevation and mean latitude of the range of seedlings was higher than and north of those of the range of mature trees, elevational and latitudinal shifts run in opposite directions for the majority of the species, reflecting the lack of a direct biological relationship between species' distributions and those variables. The broad scale, environmental diversity and variety of disturbance regimes and land uses of the study area, the large number and exhaustive sampling of tree species, and the direct causal relationship between the temperature response and a warming climate, provide strong evidence to attribute the observed shifts to climate change.

Tree species exhibit complex patterns of distribution in bottomland hardwood forests

Treesearch

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

2013-01-01

& Context Understanding tree interactions requires an insight into their spatial distribution. & Aims We looked for presence and extent of tree intraspecific spatial point pattern (random, aggregated, or overdispersed) and interspecific spatial point pattern (independent, aggregated, or segregated). & Methods We established twelve 0.64-ha plots in natural...

Managing uneven-aged stands

Treesearch

Jay R. Law; Craig G. Lorimer

1989-01-01

Maintaining uneven-aged stands involves cutting trees from a range of diameter classes in such a way that the residual stand has a balanced, steeply descending diameter distribution curve (fig. 1). The objective is to distribute trees by diameter classes so that over time the stand contains trees of different ages and sizes.

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

Shallow landsliding, root reinforcement, and the spatial distribution of trees in the Oregon Coast Range

USGS Publications Warehouse

Roering, J.J.; Schmidt, K.M.; Stock, J.D.; Dietrich, W.E.; Montgomery, D.R.

2003-01-01

The influence of root reinforcement on shallow landsliding has been well established through mechanistic and empirical studies, yet few studies have examined how local vegetative patterns influence slope stability. Because root networks spread outward from trees, the species, size, and spacing of trees should influence the spatial distribution of root strength. We documented the distribution and characteristics of trees adjacent to 32 shallow landslides that occurred during 1996 in the Oregon Coast Range. Although broadly classified as a conifer-dominated forest, we observed sparse coniferous and abundant hardwood trees near landslide scars in an industrial forest (Mapleton) that experienced widespread burning in the 19th century. In industrial forests that were burned, selectively harvested, and not replanted (Elliott State Forest), swordfern was ubiquitous near landslides, and we observed similar numbers of live conifer and hardwood trees proximal to landslide scarps. We demonstrate that root strength quantified in landslide scarps and soil pits correlates with a geometry-based index of root network contribution derived from mapping the size, species, condition, and spacing of local trees, indicating that root strength can be predicted by mapping the distribution and characteristics of trees on potentially unstable slopes. In our study sites, landslides tend to occur in areas of reduced root strength, suggesting that to make site-specific predictions of landslide occurrence slope stability analyses must account for the diversity and distribution of vegetation in potentially unstable terrain.

Bio-engineering traits of Pinus radiata D.Don

NASA Astrophysics Data System (ADS)

Giadrossich, Filippo; Marden, Michael; Marrosu, Roberto; Schwarz, Massimiliano; Phillips, Chris John; Cohen, Denis; Niedda, Marcello

2017-04-01

Pinus radiata is widely cultivated in New Zealand. Due to steep slopes and intense rainfall, the silviculture of Pinus radiata forests is important to control erosion and slope stability. Bio-engineering traits such as root distribution and root tensile strength are fundamental to understand the effectiveness of Pinus radiata. This information is needed to use the state of the art root reinforcement model (the Root Bundle Model) and the physically-based slope stability model SOSlope. Yet, little is known about root distribution and tensile strength for this specie. We measured soil moisture and carried out 30 field tensile tests on roots of Pinus radiata. We also measured root distribution data from 5 plants, digging arc of circles 0.6 radian around the trees in four opposite directions. We fully excavated the root system of two trees. Using the Root Bundle Model, results of our measurements allow estimation of root reinforcement. With the slope stability model SOSlope, information on the intensity and frequency of harvesting and on the development of weak zones that can be supported by a stand of Pinus radiata in relation to slope stability can be calculated. An added value is that the collected data allow us to make inferences between number and sizes of roots, and growth direction.

An Examination of Diameter Density Prediction with k-NN and Airborne Lidar

DOE PAGES

Strunk, Jacob L.; Gould, Peter J.; Packalen, Petteri; ...

2017-11-16

While lidar-based forest inventory methods have been widely demonstrated, performances of methods to predict tree diameters with airborne lidar (lidar) are not well understood. One cause for this is that the performance metrics typically used in studies for prediction of diameters can be difficult to interpret, and may not support comparative inferences between sampling designs and study areas. To help with this problem we propose two indices and use them to evaluate a variety of lidar and k nearest neighbor (k-NN) strategies for prediction of tree diameter distributions. The indices are based on the coefficient of determination ( R 2),more » and root mean square deviation (RMSD). Both of the indices are highly interpretable, and the RMSD-based index facilitates comparisons with alternative (non-lidar) inventory strategies, and with projects in other regions. K-NN diameter distribution prediction strategies were examined using auxiliary lidar for 190 training plots distribute across the 800 km 2 Savannah River Site in South Carolina, USA. In conclusion, we evaluate the performance of k-NN with respect to distance metrics, number of neighbors, predictor sets, and response sets. K-NN and lidar explained 80% of variability in diameters, and Mahalanobis distance with k = 3 neighbors performed best according to a number of criteria.« less

An Examination of Diameter Density Prediction with k-NN and Airborne Lidar

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

Strunk, Jacob L.; Gould, Peter J.; Packalen, Petteri

While lidar-based forest inventory methods have been widely demonstrated, performances of methods to predict tree diameters with airborne lidar (lidar) are not well understood. One cause for this is that the performance metrics typically used in studies for prediction of diameters can be difficult to interpret, and may not support comparative inferences between sampling designs and study areas. To help with this problem we propose two indices and use them to evaluate a variety of lidar and k nearest neighbor (k-NN) strategies for prediction of tree diameter distributions. The indices are based on the coefficient of determination ( R 2),more » and root mean square deviation (RMSD). Both of the indices are highly interpretable, and the RMSD-based index facilitates comparisons with alternative (non-lidar) inventory strategies, and with projects in other regions. K-NN diameter distribution prediction strategies were examined using auxiliary lidar for 190 training plots distribute across the 800 km 2 Savannah River Site in South Carolina, USA. In conclusion, we evaluate the performance of k-NN with respect to distance metrics, number of neighbors, predictor sets, and response sets. K-NN and lidar explained 80% of variability in diameters, and Mahalanobis distance with k = 3 neighbors performed best according to a number of criteria.« less

Spatial and temporal distribution of trunk-injected imidacloprid in apple tree canopies.

PubMed

Aćimović, Srđan G; VanWoerkom, Anthony H; Reeb, Pablo D; Vandervoort, Christine; Garavaglia, Thomas; Cregg, Bert M; Wise, John C

2014-11-01

Pesticide use in orchards creates drift-driven pesticide losses which contaminate the environment. Trunk injection of pesticides as a target-precise delivery system could greatly reduce pesticide losses. However, pesticide efficiency after trunk injection is associated with the underinvestigated spatial and temporal distribution of the pesticide within the tree crown. This study quantified the spatial and temporal distribution of trunk-injected imidacloprid within apple crowns after trunk injection using one, two, four or eight injection ports per tree. The spatial uniformity of imidacloprid distribution in apple crowns significantly increased with more injection ports. Four ports allowed uniform spatial distribution of imidacloprid in the crown. Uniform and non-uniform spatial distributions were established early and lasted throughout the experiment. The temporal distribution of imidacloprid was significantly non-uniform. Upper and lower crown positions did not significantly differ in compound concentration. Crown concentration patterns indicated that imidacloprid transport in the trunk occurred through radial diffusion and vertical uptake with a spiral pattern. By showing where and when a trunk-injected compound is distributed in the apple tree canopy, this study addresses a key knowledge gap in terms of explaining the efficiency of the compound in the crown. These findings allow the improvement of target-precise pesticide delivery for more sustainable tree-based agriculture. © 2014 Society of Chemical Industry.

Nutritional Correlates of Koala Persistence in a Low-Density Population

PubMed Central

Stalenberg, Eleanor; Wallis, Ian R.; Cunningham, Ross B.; Allen, Chris; Foley, William J.

2014-01-01

It is widely postulated that nutritional factors drive bottom-up, resource-based patterns in herbivore ecology and distribution. There is, however, much controversy over the roles of different plant constituents and how these influence individual herbivores and herbivore populations. The density of koala (Phascolarctos cinereus) populations varies widely and many attribute population trends to variation in the nutritional quality of the eucalypt leaves of their diet, but there is little evidence to support this hypothesis. We used a nested design that involved sampling of trees at two spatial scales to investigate how leaf chemistry influences free-living koalas from a low-density population in south east New South Wales, Australia. Using koala faecal pellets as a proxy for koala visitation to trees, we found an interaction between toxins and nutrients in leaves at a small spatial scale, whereby koalas preferred trees with leaves of higher concentrations of available nitrogen but lower concentrations of sideroxylonals (secondary metabolites found exclusively in eucalypts) compared to neighbouring trees of the same species. We argue that taxonomic and phenotypic diversity is likely to be important when foraging in habitats of low nutritional quality in providing diet choice to tradeoff nutrients and toxins and minimise movement costs. Our findings suggest that immediate nutritional concerns are an important priority of folivores in low-quality habitats and imply that nutritional limitations play an important role in constraining folivore populations. We show that, with a careful experimental design, it is possible to make inferences about populations of herbivores that exist at extremely low densities and thus achieve a better understanding about how plant composition influences herbivore ecology and persistence. PMID:25470599

Sampling the quality of hardwood trees

Treesearch

Adrian M. Gilbert

1959-01-01

Anyone acquainted with the conversion of hardwood trees into wood products knows that timber has a wide range in quality. Some trees will yield better products than others. So, in addition to rate of growth and size, tree values are affected by the quality of products yielded.

Understanding the Scalability of Bayesian Network Inference using Clique Tree Growth Curves

NASA Technical Reports Server (NTRS)

Mengshoel, Ole Jakob

2009-01-01

Bayesian networks (BNs) are used to represent and efficiently compute with multi-variate probability distributions in a wide range of disciplines. One of the main approaches to perform computation in BNs is clique tree clustering and propagation. In this approach, BN computation consists of propagation in a clique tree compiled from a Bayesian network. There is a lack of understanding of how clique tree computation time, and BN computation time in more general, depends on variations in BN size and structure. On the one hand, complexity results tell us that many interesting BN queries are NP-hard or worse to answer, and it is not hard to find application BNs where the clique tree approach in practice cannot be used. On the other hand, it is well-known that tree-structured BNs can be used to answer probabilistic queries in polynomial time. In this article, we develop an approach to characterizing clique tree growth as a function of parameters that can be computed in polynomial time from BNs, specifically: (i) the ratio of the number of a BN's non-root nodes to the number of root nodes, or (ii) the expected number of moral edges in their moral graphs. Our approach is based on combining analytical and experimental results. Analytically, we partition the set of cliques in a clique tree into different sets, and introduce a growth curve for each set. For the special case of bipartite BNs, we consequently have two growth curves, a mixed clique growth curve and a root clique growth curve. In experiments, we systematically increase the degree of the root nodes in bipartite Bayesian networks, and find that root clique growth is well-approximated by Gompertz growth curves. It is believed that this research improves the understanding of the scaling behavior of clique tree clustering, provides a foundation for benchmarking and developing improved BN inference and machine learning algorithms, and presents an aid for analytical trade-off studies of clique tree clustering using growth curves.

Large-scale wind disturbances promote tree diversity in a Central Amazon forest.

PubMed

Marra, Daniel Magnabosco; Chambers, Jeffrey Q; Higuchi, Niro; Trumbore, Susan E; Ribeiro, Gabriel H P M; Dos Santos, Joaquim; Negrón-Juárez, Robinson I; Reu, Björn; Wirth, Christian

2014-01-01

Canopy gaps created by wind-throw events, or blowdowns, create a complex mosaic of forest patches varying in disturbance intensity and recovery in the Central Amazon. Using field and remote sensing data, we investigated the short-term (four-year) effects of large (>2000 m(2)) blowdown gaps created during a single storm event in January 2005 near Manaus, Brazil, to study (i) how forest structure and composition vary with disturbance gradients and (ii) whether tree diversity is promoted by niche differentiation related to wind-throw events at the landscape scale. In the forest area affected by the blowdown, tree mortality ranged from 0 to 70%, and was highest on plateaus and slopes. Less impacted areas in the region affected by the blowdown had overlapping characteristics with a nearby unaffected forest in tree density (583 ± 46 trees ha(-1)) (mean ± 99% Confidence Interval) and basal area (26.7 ± 2.4 m(2) ha(-1)). Highly impacted areas had tree density and basal area as low as 120 trees ha(-1) and 14.9 m(2) ha(-1), respectively. In general, these structural measures correlated negatively with an index of tree mortality intensity derived from satellite imagery. Four years after the blowdown event, differences in size-distribution, fraction of resprouters, floristic composition and species diversity still correlated with disturbance measures such as tree mortality and gap size. Our results suggest that the gradients of wind disturbance intensity encompassed in large blowdown gaps (>2000 m(2)) promote tree diversity. Specialists for particular disturbance intensities existed along the entire gradient. The existence of species or genera taking an intermediate position between undisturbed and gap specialists led to a peak of rarefied richness and diversity at intermediate disturbance levels. A diverse set of species differing widely in requirements and recruitment strategies forms the initial post-disturbance cohort, thus lending a high resilience towards wind disturbances at the community level.

Large-Scale Wind Disturbances Promote Tree Diversity in a Central Amazon Forest

PubMed Central

Marra, Daniel Magnabosco; Chambers, Jeffrey Q.; Higuchi, Niro; Trumbore, Susan E.; Ribeiro, Gabriel H. P. M.; dos Santos, Joaquim; Negrón-Juárez, Robinson I.; Reu, Björn; Wirth, Christian

2014-01-01

Canopy gaps created by wind-throw events, or blowdowns, create a complex mosaic of forest patches varying in disturbance intensity and recovery in the Central Amazon. Using field and remote sensing data, we investigated the short-term (four-year) effects of large (>2000 m2) blowdown gaps created during a single storm event in January 2005 near Manaus, Brazil, to study (i) how forest structure and composition vary with disturbance gradients and (ii) whether tree diversity is promoted by niche differentiation related to wind-throw events at the landscape scale. In the forest area affected by the blowdown, tree mortality ranged from 0 to 70%, and was highest on plateaus and slopes. Less impacted areas in the region affected by the blowdown had overlapping characteristics with a nearby unaffected forest in tree density (583±46 trees ha−1) (mean±99% Confidence Interval) and basal area (26.7±2.4 m2 ha−1). Highly impacted areas had tree density and basal area as low as 120 trees ha−1 and 14.9 m2 ha−1, respectively. In general, these structural measures correlated negatively with an index of tree mortality intensity derived from satellite imagery. Four years after the blowdown event, differences in size-distribution, fraction of resprouters, floristic composition and species diversity still correlated with disturbance measures such as tree mortality and gap size. Our results suggest that the gradients of wind disturbance intensity encompassed in large blowdown gaps (>2000 m2) promote tree diversity. Specialists for particular disturbance intensities existed along the entire gradient. The existence of species or genera taking an intermediate position between undisturbed and gap specialists led to a peak of rarefied richness and diversity at intermediate disturbance levels. A diverse set of species differing widely in requirements and recruitment strategies forms the initial post-disturbance cohort, thus lending a high resilience towards wind disturbances at the community level. PMID:25099118

Large-Scale Wind Disturbances Promote Tree Diversity in a Central Amazon Forest

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

Marra, Daniel Magnabosco; Chambers, Jeffrey Q.; Higuchi, Niro

Canopy gaps created by wind-throw events, or blowdowns, create a complex mosaic of forest patches varying in disturbance intensity and recovery in the Central Amazon. Using field and remote sensing data, we investigated the short-term (four-year) effects of large (>2000 m 2) blowdown gaps created during a single storm event in January 2005 near Manaus, Brazil, to study (i) how forest structure and composition vary with disturbance gradients and (ii) whether tree diversity is promoted by niche differentiation related to wind-throw events at the landscape scale. In the forest area affected by the blowdown, tree mortality ranged from 0 tomore » 70%, and was highest on plateaus and slopes. Less impacted areas in the region affected by the blowdown had overlapping characteristics with a nearby unaffected forest in tree density (583±46 trees ha -1) (mean±99% Confidence Interval) and basal area (26.7±2.4 m 2 ha -1). Highly impacted areas had tree density and basal area as low as 120 trees ha -1 and 14.9 m 2 ha -1, respectively. In general, these structural measures correlated negatively with an index of tree mortality intensity derived from satellite imagery. Four years after the blowdown event, differences in size-distribution, fraction of resprouters, floristic composition and species diversity still correlated with disturbance measures such as tree mortality and gap size. Our results suggest that the gradients of wind disturbance intensity encompassed in large blowdown gaps (>2000 m 2) promote tree diversity. Specialists for particular disturbance intensities existed along the entire gradient. The existence of species or genera taking an intermediate position between undisturbed and gap specialists led to a peak of rarefied richness and diversity at intermediate disturbance levels. A diverse set of species differing widely in requirements and recruitment strategies forms the initial post-disturbance cohort, thus lending a high resilience towards wind disturbances at the community level.« less

Large-Scale Wind Disturbances Promote Tree Diversity in a Central Amazon Forest

DOE PAGES

Marra, Daniel Magnabosco; Chambers, Jeffrey Q.; Higuchi, Niro; ...

2014-08-06

Canopy gaps created by wind-throw events, or blowdowns, create a complex mosaic of forest patches varying in disturbance intensity and recovery in the Central Amazon. Using field and remote sensing data, we investigated the short-term (four-year) effects of large (>2000 m 2) blowdown gaps created during a single storm event in January 2005 near Manaus, Brazil, to study (i) how forest structure and composition vary with disturbance gradients and (ii) whether tree diversity is promoted by niche differentiation related to wind-throw events at the landscape scale. In the forest area affected by the blowdown, tree mortality ranged from 0 tomore » 70%, and was highest on plateaus and slopes. Less impacted areas in the region affected by the blowdown had overlapping characteristics with a nearby unaffected forest in tree density (583±46 trees ha -1) (mean±99% Confidence Interval) and basal area (26.7±2.4 m 2 ha -1). Highly impacted areas had tree density and basal area as low as 120 trees ha -1 and 14.9 m 2 ha -1, respectively. In general, these structural measures correlated negatively with an index of tree mortality intensity derived from satellite imagery. Four years after the blowdown event, differences in size-distribution, fraction of resprouters, floristic composition and species diversity still correlated with disturbance measures such as tree mortality and gap size. Our results suggest that the gradients of wind disturbance intensity encompassed in large blowdown gaps (>2000 m 2) promote tree diversity. Specialists for particular disturbance intensities existed along the entire gradient. The existence of species or genera taking an intermediate position between undisturbed and gap specialists led to a peak of rarefied richness and diversity at intermediate disturbance levels. A diverse set of species differing widely in requirements and recruitment strategies forms the initial post-disturbance cohort, thus lending a high resilience towards wind disturbances at the community level.« less

Initial results of the spatial distribution of rubber trees in Peninsular Malaysia using remotely sensed data for biomass estimate

NASA Astrophysics Data System (ADS)

Shidiq, I. P. A.; Ismail, M. H.; Kamarudin, N.

2014-02-01

The preservation and sustainable management of forest and other land cover ecosystems such as rubber trees will help addressing two major recent issues: climate change and bio-resource energy. The rubber trees are dominantly distributed in the Negeri Sembilan and Kedah on the west coast side of Peninsular Malaysia. This study is aimed to analyse the spatial distribution and biomass of rubber trees in Peninsular Malaysia with special emphasis in Negeri Sembilan State. Geospatial data from remote sensors are used to tackle the time and labour consuming problem due to the large spatial coverage and the need of continuous temporal data. Remote sensing imagery used in this study is a Landsat 5 TM. The image from optical sensor was used to sense the rubber trees and further classified rubber tree by different age.

Modifying Taper-Derived Merchantable Height Estimates to Account for Tree Characteristics

Treesearch

James A. Westfall

2006-01-01

The U.S. Department of Agriculture Forest Service Northeastern Forest Inventory and Analysis program (NE-FIA) is developing regionwide tree-taper equations. Unlike most previous work on modeling tree form, this effort necessarily includes a wide array of tree species. For some species, branching patterns can produce undesirable tree form that reduces the merchantable...

Individual legacy trees influence vertebrate wildlife diversity in commercial forests

Treesearch

M.J. Mazurek; William J. Zielinski

2007-01-01

Old-growth forests provide important structural habitat elements for many species of wildlife. These forests, however, are rare where lands are managed for timber. In commercial forests, large and old trees sometimes exist only as widely-dispersed residual or legacy trees. Legacy trees are old trees that have been spared during harvest or have survived stand-replacing...

The estimation of tree posterior probabilities using conditional clade probability distributions.

PubMed

Larget, Bret

2013-07-01

In this article I introduce the idea of conditional independence of separated subtrees as a principle by which to estimate the posterior probability of trees using conditional clade probability distributions rather than simple sample relative frequencies. I describe an algorithm for these calculations and software which implements these ideas. I show that these alternative calculations are very similar to simple sample relative frequencies for high probability trees but are substantially more accurate for relatively low probability trees. The method allows the posterior probability of unsampled trees to be calculated when these trees contain only clades that are in other sampled trees. Furthermore, the method can be used to estimate the total probability of the set of sampled trees which provides a measure of the thoroughness of a posterior sample.

The distribution of scab in pecan trees in relation to fruit weight

USDA-ARS?s Scientific Manuscript database

Pecan scab, caused by Fusicladium effusum is the most destructive disease of pecan in Georgia and elsewhere in the southeastern US. We describe the distribution of scab and measures of yield in relation to sample height in tall trees. Control trees had significantly more severe disease on fruit lowe...

Reference conditions for old-growth redwood restoration on alluvial flats

Treesearch

Christa M. Dagley; John-Pascal. Berrill

2012-01-01

We quantified structural attributes in three alluvial flat old-growth coast redwood stands. Tree size parameters and occurrences of distinctive features (e.g., burls, goose pens) were similar between stands. Occurrence of distinctive features was greater among larger trees. Tree sizefrequency distributions conformed to a reverse-J diameter distribution. The range of...

NE-TWIGS update: Incorporating tree quality

Treesearch

Daniel A. Yaussy

1993-01-01

A method to distribute tree quality was incorporated into the NE-TWIGS individual-tree growth and yield simulator. The program uses potential tree grade to allow changes in actual tree grade over time. Volume is reported by grade and value is calculated using tree grades. Example screens are shown.

Genome-Wide Analysis of Oleosin Gene Family in 22 Tree Species: An Accelerator for Metabolic Engineering of BioFuel Crops and Agrigenomics Industrial Applications?

PubMed Central

2015-01-01

Abstract Trees contribute to enormous plant oil reserves because many trees contain 50%–80% of oil (triacylglycerols, TAGs) in the fruits and kernels. TAGs accumulate in subcellular structures called oil bodies/droplets, in which TAGs are covered by low-molecular-mass hydrophobic proteins called oleosins (OLEs). The OLEs/TAGs ratio determines the size and shape of intracellular oil bodies. There is a lack of comprehensive sequence analysis and structural information of OLEs among diverse trees. The objectives of this study were to identify OLEs from 22 tree species (e.g., tung tree, tea-oil tree, castor bean), perform genome-wide analysis of OLEs, classify OLEs, identify conserved sequence motifs and amino acid residues, and predict secondary and three-dimensional structures in tree OLEs and OLE subfamilies. Data mining identified 65 OLEs with perfect conservation of the “proline knot” motif (PX5SPX3P) from 19 trees. These OLEs contained >40% hydrophobic amino acid residues. They displayed similar properties and amino acid composition. Genome-wide phylogenetic analysis and multiple sequence alignment demonstrated that these proteins could be classified into five OLE subfamilies. There were distinct patterns of sequence conservation among the OLE subfamilies and within individual tree species. Computational modeling indicated that OLEs were composed of at least three α-helixes connected with short coils without any β-strand and that they exhibited distinct 3D structures and ligand binding sites. These analyses provide fundamental information in the similarity and specificity of diverse OLE isoforms within the same subfamily and among the different species, which should facilitate studying the structure-function relationship and identify critical amino acid residues in OLEs for metabolic engineering of tree TAGs. PMID:26258573

Genome-Wide Analysis of Oleosin Gene Family in 22 Tree Species: An Accelerator for Metabolic Engineering of BioFuel Crops and Agrigenomics Industrial Applications?

PubMed

Cao, Heping

2015-09-01

Trees contribute to enormous plant oil reserves because many trees contain 50%-80% of oil (triacylglycerols, TAGs) in the fruits and kernels. TAGs accumulate in subcellular structures called oil bodies/droplets, in which TAGs are covered by low-molecular-mass hydrophobic proteins called oleosins (OLEs). The OLEs/TAGs ratio determines the size and shape of intracellular oil bodies. There is a lack of comprehensive sequence analysis and structural information of OLEs among diverse trees. The objectives of this study were to identify OLEs from 22 tree species (e.g., tung tree, tea-oil tree, castor bean), perform genome-wide analysis of OLEs, classify OLEs, identify conserved sequence motifs and amino acid residues, and predict secondary and three-dimensional structures in tree OLEs and OLE subfamilies. Data mining identified 65 OLEs with perfect conservation of the "proline knot" motif (PX5SPX3P) from 19 trees. These OLEs contained >40% hydrophobic amino acid residues. They displayed similar properties and amino acid composition. Genome-wide phylogenetic analysis and multiple sequence alignment demonstrated that these proteins could be classified into five OLE subfamilies. There were distinct patterns of sequence conservation among the OLE subfamilies and within individual tree species. Computational modeling indicated that OLEs were composed of at least three α-helixes connected with short coils without any β-strand and that they exhibited distinct 3D structures and ligand binding sites. These analyses provide fundamental information in the similarity and specificity of diverse OLE isoforms within the same subfamily and among the different species, which should facilitate studying the structure-function relationship and identify critical amino acid residues in OLEs for metabolic engineering of tree TAGs.

Observations and Modelling of Alternative Tree Cover States of the Boreal Ecosystem

NASA Astrophysics Data System (ADS)

Abis, B.; Brovkin, V.

2017-12-01

Recently, multimodality of the tree cover distribution of the boreal forests has been detected, revealing the existence of three alternative vegetation modes. Identifying which are the regions with a potential for alternative tree cover states, and assessing which are the main factors underlying their existence, is important to project future change of natural vegetation cover and its effect on climate.Through the use of generalised additive models and phase-space analysis, we study the link between tree cover distribution and eight globally-observed environmental factors, such as rainfall, temperature, and permafrost distribution. Using a classification based on these factors, we show the location of areas with potentially alternative tree cover states under the same environmental conditions in the boreal region. Furthermore, to explain the multimodality found in the data and the asymmetry between North America and Eurasia, we study a conceptual model based on tree species competition, and use it to simulate the sensitivity of tree cover to changes in environmental factors.We find that the link between individual environmental variables and tree cover differs regionally. Nonetheless, environmental conditions uniquely determine the vegetation state among the three dominant modes in ˜95% of the cases. On the other hand, areas with potentially alternative tree cover states encompass ˜1.1 million km2, and correspond to possible transition zones with a reduced resilience to disturbances. Employing our conceptual model, we show that multimodality can be explained through competition between tree species with different adaptations to environmental factors and disturbances. Moreover, the model is able to reproduce the asymmetry in tree species distribution between Eurasia and North America. Finally, we find that changes in permafrost could be associated with bifurcation points of the model, corroborating the importance of permafrost in a changing climate.

GSHR-Tree: a spatial index tree based on dynamic spatial slot and hash table in grid environments

NASA Astrophysics Data System (ADS)

Chen, Zhanlong; Wu, Xin-cai; Wu, Liang

2008-12-01

Computation Grids enable the coordinated sharing of large-scale distributed heterogeneous computing resources that can be used to solve computationally intensive problems in science, engineering, and commerce. Grid spatial applications are made possible by high-speed networks and a new generation of Grid middleware that resides between networks and traditional GIS applications. The integration of the multi-sources and heterogeneous spatial information and the management of the distributed spatial resources and the sharing and cooperative of the spatial data and Grid services are the key problems to resolve in the development of the Grid GIS. The performance of the spatial index mechanism is the key technology of the Grid GIS and spatial database affects the holistic performance of the GIS in Grid Environments. In order to improve the efficiency of parallel processing of a spatial mass data under the distributed parallel computing grid environment, this paper presents a new grid slot hash parallel spatial index GSHR-Tree structure established in the parallel spatial indexing mechanism. Based on the hash table and dynamic spatial slot, this paper has improved the structure of the classical parallel R tree index. The GSHR-Tree index makes full use of the good qualities of R-Tree and hash data structure. This paper has constructed a new parallel spatial index that can meet the needs of parallel grid computing about the magnanimous spatial data in the distributed network. This arithmetic splits space in to multi-slots by multiplying and reverting and maps these slots to sites in distributed and parallel system. Each sites constructs the spatial objects in its spatial slot into an R tree. On the basis of this tree structure, the index data was distributed among multiple nodes in the grid networks by using large node R-tree method. The unbalance during process can be quickly adjusted by means of a dynamical adjusting algorithm. This tree structure has considered the distributed operation, reduplication operation transfer operation of spatial index in the grid environment. The design of GSHR-Tree has ensured the performance of the load balance in the parallel computation. This tree structure is fit for the parallel process of the spatial information in the distributed network environments. Instead of spatial object's recursive comparison where original R tree has been used, the algorithm builds the spatial index by applying binary code operation in which computer runs more efficiently, and extended dynamic hash code for bit comparison. In GSHR-Tree, a new server is assigned to the network whenever a split of a full node is required. We describe a more flexible allocation protocol which copes with a temporary shortage of storage resources. It uses a distributed balanced binary spatial tree that scales with insertions to potentially any number of storage servers through splits of the overloaded ones. The application manipulates the GSHR-Tree structure from a node in the grid environment. The node addresses the tree through its image that the splits can make outdated. This may generate addressing errors, solved by the forwarding among the servers. In this paper, a spatial index data distribution algorithm that limits the number of servers has been proposed. We improve the storage utilization at the cost of additional messages. The structure of GSHR-Tree is believed that the scheme of this grid spatial index should fit the needs of new applications using endlessly larger sets of spatial data. Our proposal constitutes a flexible storage allocation method for a distributed spatial index. The insertion policy can be tuned dynamically to cope with periods of storage shortage. In such cases storage balancing should be favored for better space utilization, at the price of extra message exchanges between servers. This structure makes a compromise in the updating of the duplicated index and the transformation of the spatial index data. Meeting the needs of the grid computing, GSHRTree has a flexible structure in order to satisfy new needs in the future. The GSHR-Tree provides the R-tree capabilities for large spatial datasets stored over interconnected servers. The analysis, including the experiments, confirmed the efficiency of our design choices. The scheme should fit the needs of new applications of spatial data, using endlessly larger datasets. Using the system response time of the parallel processing of spatial scope query algorithm as the performance evaluation factor, According to the result of the simulated the experiments, GSHR-Tree is performed to prove the reasonable design and the high performance of the indexing structure that the paper presented.

Distribution, Pest Status and Fungal Associates of Euwallacea nr. fornicatus in Florida Avocado Groves

PubMed Central

Carrillo, Daniel; Cruz, Luisa F.; Kendra, Paul E.; Narvaez, Teresa I.; Montgomery, Wayne S.; Monterroso, Armando; De Grave, Charlotte; Cooperband, Miriam F.

2016-01-01

Members of a complex of cryptic species, that correspond morphologically to the ambrosia beetle Euwallacea fornicatus (Eichhoff) (Coleoptera: Curculionidae: Scolytinae), were recently found attacking avocado (Persea americana Mill.) in Israel and California. In early 2016, an outbreak of another member of this species complex was detected infesting approximately 1500 avocado trees in an avocado orchard at Homestead, Florida. An area-wide survey was conducted in commercial avocado groves of Miami-Dade County, Florida to determine the distribution and abundance of E. nr. fornicatus, to identify different populations of E. nr. fornicatus and their fungal associates, and to assess the extent of damage to avocado trees. Ewallacea nr. fornicatus were captured in 31 of the 33 sampled sites. A sample of 35 beetles from six different locations was identified as E. nr. fornicatus sp. #2, which is genetically distinct from the species causing damage in California and Israel. Eleven fungal associates were identified: an unknown Fusarium sp., AF-8, AF-6, Graphium euwallaceae, Acremonium sp. Acremonium morum, Acremonium masseei, Elaphocordyceps sp. and three yeast species. The unknown Fusarium isolates were the most abundant and frequently found fungus species associated with adult beetles and lesions surrounding the beetle galleries. In addition to fungal associates, three bacteria species were found associated with adult E. nr. fornicatus. Visual inspections detected significant damage in only two orchards. A large number of beetles were captured in locations with no apparent damage on the avocado trees suggesting that E. nr. fornicatus are associated with other host(s) outside the groves or with dead trees or branches inside the groves. More research is needed to determine the potential threat E. nr. fornicatus and its fungal associates pose to the avocado industry and agricultural and natural ecosystems in Florida. PMID:27754408

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

PubMed

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

2014-02-01

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

Defense pattern of Chinese cork oak across latitudinal gradients: influences of ontogeny, herbivory, climate and soil nutrients

PubMed Central

Wang, Xiao-Fei; Liu, Jian-Feng; Gao, Wen-Qiang; Deng, Yun-Peng; Ni, Yan-Yan; Xiao, Yi-Hua; Kang, Feng-Feng; Wang, Qi; Lei, Jing-Pin; Jiang, Ze-Ping

2016-01-01

Knowledge of latitudinal patterns in plant defense and herbivory is crucial for understanding the mechanisms that govern ecosystem functioning and for predicting their responses to climate change. Using a widely distributed species in East Asia, Quercus variabilis, we aim to reveal defense patterns of trees with respect to ontogeny along latitudinal gradients. Six leaf chemical (total phenolics and total condensed tannin concentrations) and physical (cellulose, hemicellulose, lignin and dry mass concentration) defensive traits as well as leaf herbivory (% leaf area loss) were investigated in natural Chinese cork oak (Q. variabilis) forests across two ontogenetic stages (juvenile and mature trees) along a ~14°-latitudinal gradient. Our results showed that juveniles had higher herbivory values and a higher concentration of leaf chemical defense substances compared with mature trees across the latitudinal gradient. In addition, chemical defense and herbivory in both ontogenetic stages decreased with increasing latitude, which supports the latitudinal herbivory-defense hypothesis and optimal defense theory. The identified trade-offs between chemical and physical defense were primarily determined by environmental variation associated with the latitudinal gradient, with the climatic factors (annual precipitation, minimum temperature of the coldest month) largely contributing to the latitudinal defense pattern in both juvenile and mature oak trees. PMID:27252112

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

PubMed

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

2017-07-17

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

Defense pattern of Chinese cork oak across latitudinal gradients: influences of ontogeny, herbivory, climate and soil nutrients

NASA Astrophysics Data System (ADS)

Wang, Xiao-Fei; Liu, Jian-Feng; Gao, Wen-Qiang; Deng, Yun-Peng; Ni, Yan-Yan; Xiao, Yi-Hua; Kang, Feng-Feng; Wang, Qi; Lei, Jing-Pin; Jiang, Ze-Ping

2016-06-01

Knowledge of latitudinal patterns in plant defense and herbivory is crucial for understanding the mechanisms that govern ecosystem functioning and for predicting their responses to climate change. Using a widely distributed species in East Asia, Quercus variabilis, we aim to reveal defense patterns of trees with respect to ontogeny along latitudinal gradients. Six leaf chemical (total phenolics and total condensed tannin concentrations) and physical (cellulose, hemicellulose, lignin and dry mass concentration) defensive traits as well as leaf herbivory (% leaf area loss) were investigated in natural Chinese cork oak (Q. variabilis) forests across two ontogenetic stages (juvenile and mature trees) along a ~14°-latitudinal gradient. Our results showed that juveniles had higher herbivory values and a higher concentration of leaf chemical defense substances compared with mature trees across the latitudinal gradient. In addition, chemical defense and herbivory in both ontogenetic stages decreased with increasing latitude, which supports the latitudinal herbivory-defense hypothesis and optimal defense theory. The identified trade-offs between chemical and physical defense were primarily determined by environmental variation associated with the latitudinal gradient, with the climatic factors (annual precipitation, minimum temperature of the coldest month) largely contributing to the latitudinal defense pattern in both juvenile and mature oak trees.

Phenology, seed dispersal and difficulties in natural recruitment of the canopy tree Pachira quinata (Malvaceae).

PubMed

Castellanos, Maria Clara; Stevenson, Pablo R

2011-06-01

Life history and recruitment information of tropical trees in natural populations is scarce even for important commercial species. This study focused on a widely exploited Neotropical canopy species, Pachira quinata (Malvaceae), at the southernmost, wettest limit of its natural distribution, in the Colombian Amazonia. We studied phenological patterns, seed production and natural densities; assessed the importance of seed dispersal and density-dependent effects on recruitment, using field experiments. At this seasonal forest P. quinata was overrepresented by large adult trees and had very low recruitment caused by the combination of low fruit production, high seed predation and very high seedling mortality under continuous canopies mostly due to damping off pathogens. There was no evidence of negative distance or density effects on recruitment, but a clear requirement of canopy gaps for seedling survival and growth, where pathogen incidence was drastically reduced. In spite of the strong dependence on light for survival of seedlings, seeds germinated readily in the dark. At the study site, the population of P. quinata appeared to be declining, likely because recruitment depended on the rare combination of large gap formation with the presence of reproductive trees nearby. The recruitment biology of this species makes it very vulnerable to any type of logging in natural populations.

Characterization of reference gene expression in tung tree (Vernicia fordii)

USDA-ARS?s Scientific Manuscript database

Tung oil from tung tree (Vernicia fordii) is widely used as a drying ingredient in paints, varnishes, and other coatings and finishes. Recent research has focused on the understanding of the biosynthesis of oil in tung trees. Many oil biosynthetic genes have been identified in tung tree but little...

Evidence of Tree Species’ Range Shifts in a Complex Landscape

PubMed Central

Monleon, Vicente J.; Lintz, Heather E.

2015-01-01

Climate change is expected to change the distribution of species. For long-lived, sessile species such as trees, tracking the warming climate depends on seedling colonization of newly favorable areas. We compare the distribution of seedlings and mature trees for all but the rarest tree species in California, Oregon and Washington, United States of America, a large, environmentally diverse region. Across 46 species, the mean annual temperature of the range of seedlings was 0.120°C colder than that of the range of trees (95% confidence interval from 0.096 to 0.144°C). The extremes of the seedling distributions also shifted towards colder temperature than those of mature trees, but the change was less pronounced. Although the mean elevation and mean latitude of the range of seedlings was higher than and north of those of the range of mature trees, elevational and latitudinal shifts run in opposite directions for the majority of the species, reflecting the lack of a direct biological relationship between species’ distributions and those variables. The broad scale, environmental diversity and variety of disturbance regimes and land uses of the study area, the large number and exhaustive sampling of tree species, and the direct causal relationship between the temperature response and a warming climate, provide strong evidence to attribute the observed shifts to climate change. PMID:25634090

Molecular phylogeny and diversification of a widespread Neotropical rainforest bird group: The Buff-throated Woodcreeper complex, Xiphorhynchus guttatus/susurrans (Aves: Dendrocolaptidae).

PubMed

Rocha, Tainá C; Sequeira, Fernando; Aleixo, Alexandre; Rêgo, Péricles S; Sampaio, Iracilda; Schneider, Horacio; Vallinoto, Marcelo

2015-04-01

The genus Xiphorhynchus is a species rich avian group widely distributed in Neotropical forests of Central and South America. Although recent molecular studies have improved our understanding of the spatial patterns of genetic diversity in some species of this genus, most are still poorly known, including their taxonomy. Here, we address the historical diversification and phylogenetic relationships of the X. guttatus/susurrans complex, using data from two mitochondrial (cyt b and ND2) and one nuclear (β-fibint7) genes. Phylogenetic relationships were inferred with both gene trees and a Bayesian-based species tree under a coalescent framework (∗BEAST). With exception of the nuclear β-fibint7 gene that produced an unresolved tree, both mtDNA and the species tree showed a similar topology and were congruent in recovering five main clades with high statistical support. These clades, however, are not fully concordant with traditional delimitation of some X. guttatus subspecies, since X. g. polystictus, X. g. guttatus, and X. g. connectens are not supported as distinct clades. Interestingly, these three taxa are more closely related to the mostly trans-Andean X. susurrans than the other southern and western Amazonian subspecies of X. guttatus, which constitutes a paraphyletic species. Timing estimates based on the species tree indicated that diversification in X. guttatus occurred between the end of the Pliocene and early Pleistocene, likely associated with the formation of the modern Amazon River and its main southern tributaries (Xingu, Tocantins, and Madeira), in addition to climate-induced changes in the distribution of rainforest biomes. Our study supports with an enlarged dataset a previous proposal for recognizing at least three species level taxa in the X. guttatus/susurrans complex: X. susurrans, X. guttatus, and X. guttatoides. Copyright © 2015 Elsevier Inc. All rights reserved.

Red Reveals Branch Die-back in Norway Maple Acer platanoides

PubMed Central

Sinkkonen, Aki

2008-01-01

Background and Aims Physiological data suggest that autumn leaf colours of deciduous trees are adaptations to environmental stress. Recently, the evolution of autumn colouration has been linked to tree condition and defence. Most current hypotheses presume that autumn colours vary between tree individuals. This study was designed to test if within-tree variation should be taken into account in experimental and theoretical research on autumn colouration. Methods Distribution of red autumn leaf colours was compared between partially dead and vigorous specimens of Norway maple (Acer platanoides) in a 3-year study. In August, the amount of reddish foliage was estimated in pairs of partially dead and control trees. Within-tree variation in the distribution of reddish leaves was evaluated. Leaf nitrogen and carbon concentrations were analysed. Key Results Reddish leaf colours were more frequent in partially dead trees than in control trees. Reddish leaves were evenly distributed in control trees, while patchiness of red leaf pigments was pronounced in partially dead trees. Large patches of red leaves were found beneath or next to dead tree parts. These patches reoccurred every year. Leaf nitrogen concentration was lower in reddish than in green leaves but the phenomenon seemed similar in both partially dead and control trees. Conclusions The results suggest that red leaf colouration and branch condition are interrelated in Norway maple. Early reddish colours may be used as an indication of leaf nitrogen and carbon levels but not as an indication of tree condition. Studies that concentrate on entire trees may not operate at an optimal level to detect the evolutionary mechanisms behind autumnal leaf colour variation. PMID:18567914

Red reveals branch die-back in Norway maple Acer platanoides.

PubMed

Sinkkonen, Aki

2008-09-01

Physiological data suggest that autumn leaf colours of deciduous trees are adaptations to environmental stress. Recently, the evolution of autumn colouration has been linked to tree condition and defence. Most current hypotheses presume that autumn colours vary between tree individuals. This study was designed to test if within-tree variation should be taken into account in experimental and theoretical research on autumn colouration. Distribution of red autumn leaf colours was compared between partially dead and vigorous specimens of Norway maple (Acer platanoides) in a 3-year study. In August, the amount of reddish foliage was estimated in pairs of partially dead and control trees. Within-tree variation in the distribution of reddish leaves was evaluated. Leaf nitrogen and carbon concentrations were analysed. Reddish leaf colours were more frequent in partially dead trees than in control trees. Reddish leaves were evenly distributed in control trees, while patchiness of red leaf pigments was pronounced in partially dead trees. Large patches of red leaves were found beneath or next to dead tree parts. These patches reoccurred every year. Leaf nitrogen concentration was lower in reddish than in green leaves but the phenomenon seemed similar in both partially dead and control trees. The results suggest that red leaf colouration and branch condition are interrelated in Norway maple. Early reddish colours may be used as an indication of leaf nitrogen and carbon levels but not as an indication of tree condition. Studies that concentrate on entire trees may not operate at an optimal level to detect the evolutionary mechanisms behind autumnal leaf colour variation.

Tree cover at fine and coarse spatial grains interacts with shade tolerance to shape plant species distributions across the Alps

PubMed Central

Nieto-Lugilde, Diego; Lenoir, Jonathan; Abdulhak, Sylvain; Aeschimann, David; Dullinger, Stefan; Gégout, Jean-Claude; Guisan, Antoine; Pauli, Harald; Renaud, Julien; Theurillat, Jean-Paul; Thuiller, Wilfried; Van Es, Jérémie; Vittoz, Pascal; Willner, Wolfgang; Wohlgemuth, Thomas; Zimmermann, Niklaus E.; Svenning, Jens-Christian

2015-01-01

The role of competition for light among plants has long been recognised at local scales, but its importance for plant species distributions at larger spatial scales has generally been ignored. Tree cover modifies the local abiotic conditions below the canopy, notably by reducing light availability, and thus, also the performance of species that are not adapted to low-light conditions. However, this local effect may propagate to coarser spatial grains, by affecting colonisation probabilities and local extinction risks of herbs and shrubs. To assess the effect of tree cover at both the plot- and landscape-grain sizes (approximately 10-m and 1-km), we fit Generalised Linear Models (GLMs) for the plot-level distributions of 960 species of herbs and shrubs using 6,935 vegetation plots across the European Alps. We ran four models with different combinations of variables (climate, soil and tree cover) at both spatial grains for each species. We used partial regressions to evaluate the independent effects of plot- and landscape-grain tree cover on plot-level plant communities. Finally, the effects on species-specific elevational range limits were assessed by simulating a removal experiment comparing the species distributions under high and low tree cover. Accounting for tree cover improved the model performance, with the probability of the presence of shade-tolerant species increasing with increasing tree cover, whereas shade-intolerant species showed the opposite pattern. The tree cover effect occurred consistently at both the plot and landscape spatial grains, albeit most strongly at the former. Importantly, tree cover at the two grain sizes had partially independent effects on plot-level plant communities. With high tree cover, shade-intolerant species exhibited narrower elevational ranges than with low tree cover whereas shade-tolerant species showed wider elevational ranges at both limits. These findings suggest that forecasts of climate-related range shifts for herb and shrub species may be modified by tree cover dynamics. PMID:26290621

Varying selection differential throughout the climatic range of Norway spruce in Central Europe.

PubMed

Kapeller, Stefan; Dieckmann, Ulf; Schueler, Silvio

2017-01-01

Predicting species distribution changes in global warming requires an understanding of how climatic constraints shape the genetic variation of adaptive traits and force local adaptations. To understand the genetic capacity of Norway spruce populations in Central Europe, we analyzed the variation in tree heights at the juvenile stage in common garden experiments established from the species' warm-dry to cold-moist distribution limits. We report the following findings: First, 47% of the total tree height variation at trial sites is attributable to the tree populations irrespective of site climate. Second, tree height variation within populations is higher at cold-moist trial sites than at warm-dry sites and higher within populations originating from cold-moist habitats than from warm-dry habitats. Third, for tree ages of 7-15 years, the variation within populations increases at cold-moist trial sites, whereas it remains constant at warm-dry sites. Fourth, tree height distributions are right-skewed at cold-moist trial sites, whereas they are nonskewed, but platykurtic at warm-dry sites. Our results suggest that in cold environments, climatic conditions impose stronger selection and probably restrict the distribution of spruce, whereas at the warm distribution limit, the species' realized niche might rather be controlled by external drivers, for example, forest insects.

Quantifying root lateral distribution and turnover using pine trees with a distinct stable carbon isotope signature

Treesearch

Kurt H. Johnsen; Chris A. Maier; Lance W. Kress

2005-01-01

In order to help assess spatial competition for below-ground resources, we quantified the effects of fertilization on root biomass quantity and lateral root distribution of midrotation Pinus taeda trees. Open-top chambers exposed trees to ambient or ambient plus 200 µmol mol-1 atmospheric CO2...

Stand dynamics of mixed red alder-conifer forests of southeast Alaska.

Treesearch

Robert L. Deal; Paul E. Hennon; Ewa H. Orlikowska; David V. D' Amore

2004-01-01

Stand structure and dynamics were evaluated in mixed red alder (Alnus rubra Bong.) - conifer forests of southeast Alaska. We assessed stand development, tree density, total basal area, diameter distribution of live and dead trees, height distribution of live trees, and mean diameter of all and largest conifers in 40-year-old red alder - conifer...

The abundance and diversity of legume-nodulating rhizobia in 28-year-old plantations of tropical, subtropical, and exotic tree species: a case study from the Forest Reserve of Bandia, Senegal.

PubMed

Sene, Godar; Thiao, Mansour; Samba-Mbaye, Ramatoulaye; Khasa, Damase; Kane, Aboubacry; Mbaye, Mame Samba; Beaulieu, Marie-Ève; Manga, Anicet; Sylla, Samba Ndao

2013-01-01

Several fast-growing and multipurpose tree species have been widely used in West Africa to both reverse the tendency of land degradation and restore soil productivity. Although beneficial effects have been reported on soil stabilization, there still remains a lack of information about their impact on soil microorganisms. Our investigation has been carried out in exotic and native tree plantations of 28 years and aimed to survey and compare the abundance and genetic diversity of natural legume-nodulating rhizobia (LNR). The study of LNR is supported by the phylogenetic analysis which clustered the isolates into three genera: Bradyrhizobium, Mesorhizobium, and Sinorhizobium. The results showed close positive correlations between the sizes of LNR populations estimated both in the dry and rainy seasons and the presence of legume tree hosts. There were significant increases in Rhizobium spp. population densities in response to planting with Acacia spp., and high genetic diversities and richness of genotypes were fittest in these tree plantations. This suggests that enrichment of soil Rhizobium spp. populations is host specific. The results indicated also that species of genera Mesorhizobium and Sinorhizobium were lacking in plantations of non-host species. By contrast, there was a widespread distribution of Bradyrhizobium spp. strains across the tree plantations, with no evident specialization in regard to plantation type. Finally, the study provides information about the LNR communities associated with a range of old tree plantations and some aspects of their relationships to soil factors, which may facilitate the management of man-made forest systems that target ecosystem rehabilitation and preservation of soil biota.

Climatic Signals in Tree Rings of Heritiera fomes Buch.-Ham. in the Sundarbans, Bangladesh

PubMed Central

Chowdhury, Md. Qumruzzaman; De Ridder, Maaike; Beeckman, Hans

2016-01-01

Mangroves occur along the coastlines throughout the tropics and sub-tropics, supporting a wide variety of resources and services. In order to understand the responses of future climate change on this ecosystem, we need to know how mangrove species have responded to climate changes in the recent past. This study aims at exploring the climatic influences on the radial growth of Heritiera fomes from a local to global scale. A total of 40 stem discs were collected at breast height position from two different zones with contrasting salinity in the Sundarbans, Bangladesh. All specimens showed distinct tree rings and most of the trees (70%) could be visually and statistically crossdated. Successful crossdating enabled the development of two zone-specific chronologies. The mean radial increment was significantly higher at low salinity (eastern) zone compared to higher salinity (western) zone. The two zone-specific chronologies synchronized significantly, allowing for the construction of a regional chronology. The annual and monsoon precipitation mainly influence the tree growth of H. fomes. The growth response to local precipitation is similar in both zones except June and November in the western zone, while the significant influence is lacking. The large-scale climatic drivers such as sea surface temperature (SST) of equatorial Pacific and Indian Ocean as well as the El Niño-Southern Oscillation (ENSO) revealed no teleconnection with tree growth. The tree rings of this species are thus an indicator for monsoon precipitation variations in Bangladesh. The wider distribution of this species from the South to South East Asian coast presents an outstanding opportunity for developing a large-scale tree-ring network of mangroves. PMID:26927229

Managing Your Seasonal Allergies

MedlinePlus

... your lawn. If you mow, wear a mask. Tree Pollen Trees produce pollen earliest, as soon as January in ... distributed miles away. Fewer than 100 kinds of trees cause allergies. The most common tree allergy is ...

Topological patterns in street networks of self-organized urban settlements

NASA Astrophysics Data System (ADS)

Buhl, J.; Gautrais, J.; Reeves, N.; Solé, R. V.; Valverde, S.; Kuntz, P.; Theraulaz, G.

2006-02-01

Many urban settlements result from a spatially distributed, decentralized building process. Here we analyze the topological patterns of organization of a large collection of such settlements using the approach of complex networks. The global efficiency (based on the inverse of shortest-path lengths), robustness to disconnections and cost (in terms of length) of these graphs is studied and their possible origins analyzed. A wide range of patterns is found, from tree-like settlements (highly vulnerable to random failures) to meshed urban patterns. The latter are shown to be more robust and efficient.

[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.

Snow distribution and heat flow in the taiga

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

Sturm, M.

1992-05-01

The trees of the taiga intercept falling snow and cause it to become distributed in an uneven fashion. Around aspen and birch, cone-shaped accumulations form. Beneath large spruce trees, the snow cover is depleted, forming a bowl-shaped depression called a tree well. Small spruce trees become covered with snow, creating cavities that funnel cold air to the snow/ground interface. The depletion of snow under large spruce trees results in greater heat loss from the ground. A finite difference model suggests that heat flow from tree wells can be more than twice that of undisturbed snow. In forested watersheds, this increasemore » can be a significant percentage of the total winter energy exchange.« less

Ectomycorrhizal fungal communities of native and non-native Pinus and Quercus species in a common garden of 35-year-old trees.

PubMed

Trocha, Lidia K; Kałucka, Izabela; Stasińska, Małgorzata; Nowak, Witold; Dabert, Mirosława; Leski, Tomasz; Rudawska, Maria; Oleksyn, Jacek

2012-02-01

Non-native tree species have been widely planted or have become naturalized in most forested landscapes. It is not clear if native trees species collectively differ in ectomycorrhizal fungal (EMF) diversity and communities from that of non-native tree species. Alternatively, EMF species community similarity may be more determined by host plant phylogeny than by whether the plant is native or non-native. We examined these unknowns by comparing two genera, native and non-native Quercus robur and Quercus rubra and native and non-native Pinus sylvestris and Pinus nigra in a 35-year-old common garden in Poland. Using molecular and morphological approaches, we identified EMF species from ectomycorrhizal root tips and sporocarps collected in the monoculture tree plots. A total of 69 EMF species were found, with 38 species collected only as sporocarps, 18 only as ectomycorrhizas, and 13 both as ectomycorrhizas and sporocarps. The EMF species observed were all native and commonly associated with a Holarctic range in distribution. We found that native Q. robur had ca. 120% higher total EMF species richness than the non-native Q. rubra, while native P. sylvestris had ca. 25% lower total EMF species richness than non-native P. nigra. Thus, across genera, there was no evidence that native species have higher EMF species diversity than exotic species. In addition, we found a higher similarity in EMF communities between the two Pinus species than between the two Quercus species. These results support the naturalization of non-native trees by means of mutualistic associations with cosmopolitan and novel fungi.

Spatial Structure of Evolutionary Models of Dialects in Contact

PubMed Central

Murawaki, Yugo

2015-01-01

Phylogenetic models, originally developed to demonstrate evolutionary biology, have been applied to a wide range of cultural data including natural language lexicons, manuscripts, folktales, material cultures, and religions. A fundamental question regarding the application of phylogenetic inference is whether trees are an appropriate approximation of cultural evolutionary history. Their validity in cultural applications has been scrutinized, particularly with respect to the lexicons of dialects in contact. Phylogenetic models organize evolutionary data into a series of branching events through time. However, branching events are typically not included in dialectological studies to interpret the distributions of lexical terms. Instead, dialectologists have offered spatial interpretations to represent lexical data. For example, new lexical items that emerge in a politico-cultural center are likely to spread to peripheries, but not vice versa. To explore the question of the tree model’s validity, we present a simple simulation model in which dialects form a spatial network and share lexical items through contact rather than through common ancestors. We input several network topologies to the model to generate synthetic data. We then analyze the synthesized data using conventional phylogenetic techniques. We found that a group of dialects can be considered tree-like even if it has not evolved in a temporally tree-like manner but has a temporally invariant, spatially tree-like structure. In addition, the simulation experiments appear to reproduce unnatural results observed in reconstructed trees for real data. These results motivate further investigation into the spatial structure of the evolutionary history of dialect lexicons as well as other cultural characteristics. PMID:26221958

Traits and trade-offs in whole-tree hydraulic architecture along the vertical axis of Eucalyptus grandis.

PubMed

Pfautsch, Sebastian; Aspinwall, Michael J; Drake, John E; Chacon-Doria, Larissa; Langelaan, Rob J A; Tissue, David T; Tjoelker, Mark G; Lens, Frederic

2018-01-25

Sapwood traits like vessel diameter and intervessel pit characteristics play key roles in maintaining hydraulic integrity of trees. Surprisingly little is known about how sapwood traits covary with tree height and how such trait-based variation could affect the efficiency of water transport in tall trees. This study presents a detailed analysis of structural and functional traits along the vertical axes of tall Eucalyptus grandis trees. To assess a wide range of anatomical and physiological traits, light and electron microscopy was used, as well as field measurements of tree architecture, water use, stem water potential and leaf area distribution. Strong apical dominance of water transport resulted in increased volumetric water supply per unit leaf area with tree height. This was realized by continued narrowing (from 250 to 20 µm) and an exponential increase in frequency (from 600 to 13 000 cm-2) of vessels towards the apex. The widest vessels were detected at least 4 m above the stem base, where they were associated with the thickest intervessel pit membranes. In addition, this study established the lower limit of pit membrane thickness in tall E. grandis at ~375 nm. This minimum thickness was maintained over a large distance in the upper stem, where vessel diameters continued to narrow. The analyses of xylem ultrastructure revealed complex, synchronized trait covariation and trade-offs with increasing height in E. grandis. Anatomical traits related to xylem vessels and those related to architecture of pit membranes were found to increase efficiency and apical dominance of water transport. This study underlines the importance of studying tree hydraulic functioning at organismal scale. Results presented here will improve understanding height-dependent structure-function patterns in tall trees. © The Author(s) 2018. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

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

PubMed

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

2012-01-01

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

Mapping species distributions: a comparison of skilled naturalist and lay citizen science recording.

PubMed

van der Wal, René; Anderson, Helen; Robinson, Annie; Sharma, Nirwan; Mellish, Chris; Roberts, Stuart; Darvill, Ben; Siddharthan, Advaith

2015-11-01

To assess the ability of traditional biological recording schemes and lay citizen science approaches to gather data on species distributions and changes therein, we examined bumblebee records from the UK's national repository (National Biodiversity Network) and from BeeWatch. The two recording approaches revealed similar relative abundances of bumblebee species but different geographical distributions. For the widespread common carder (Bombus pascuorum), traditional recording scheme data were patchy, both spatially and temporally, reflecting active record centre rather than species distribution. Lay citizen science records displayed more extensive geographic coverage, reflecting human population density, thus offering better opportunities to account for recording effort. For the rapidly spreading tree bumblebee (Bombus hypnorum), both recording approaches revealed similar distributions due to a dedicated mapping project which overcame the patchy nature of naturalist records. We recommend, where possible, complementing skilled naturalist recording with lay citizen science programmes to obtain a nation-wide capability, and stress the need for timely uploading of data to the national repository.

CliniWeb: managing clinical information on the World Wide Web.

PubMed

Hersh, W R; Brown, K E; Donohoe, L C; Campbell, E M; Horacek, A E

1996-01-01

The World Wide Web is a powerful new way to deliver on-line clinical information, but several problems limit its value to health care professionals: content is highly distributed and difficult to find, clinical information is not separated from non-clinical information, and the current Web technology is unable to support some advanced retrieval capabilities. A system called CliniWeb has been developed to address these problems. CliniWeb is an index to clinical information on the World Wide Web, providing a browsing and searching interface to clinical content at the level of the health care student or provider. Its database contains a list of clinical information resources on the Web that are indexed by terms from the Medical Subject Headings disease tree and retrieved with the assistance of SAPHIRE. Limitations of the processes used to build the database are discussed, together with directions for future research.

Development and characterization of thirteen microsatellite loci in Clark's nutcracker (Nucifraga columbiana)

USGS Publications Warehouse

Oyler-McCance, Sara J.; Fike, Jennifer A.; Castoe, Todd A.; Tomback, Diana F.; Wunder, Michael B.; Schaming, Taza D.

2013-01-01

Clark’s nutcrackers are important seed dispersers for two widely-distributed western North American conifers, whitebark pine and limber pine, which are declining due to outbreaks of mountain pine beetle and white pine blister rust. Because nutcracker seed dispersal services are key to maintaining viable populations of these imperiled pines, knowledge of movement patterns of Clark’s nutcrackers helps managers understand local extinction risks for these trees. To investigate population structure within Clark’s nutcracker, we developed primers for and characterized 13 polymorphic microsatellite loci. In a screen of 22 individuals from one population, levels of variability ranged from 6 to 15 alleles. No loci were found to be linked, although 4 loci revealed significant departures from Hardy–Weinberg equilibrium and evidence of null alleles. These microsatellite loci will enable population genetic analyses of Clark’s nutcrackers, which could provide insights into the spatial relationships between nutcrackers and the trees they help disperse.

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.

Trees of Yap: a field guide

Treesearch

Marjorie V. Cushing Falanruw

2015-01-01

Descriptions, drawings, and photographs are presented for trees found on the Yap Islands in the Federated States of Micronesia. Included are all recorded native trees and most introduced trees as well as new records of native and introduced trees. Additional information is provided on tree distribution, status, vernacular names in Micronesia, and English names when...

Tree cover bimodality in savannas and forests emerging from the switching between two fire dynamics.

PubMed

De Michele, Carlo; Accatino, Francesco

2014-01-01

Moist savannas and tropical forests share the same climatic conditions and occur side by side. Experimental evidences show that the tree cover of these ecosystems exhibits a bimodal frequency distribution. This is considered as a proof of savanna-forest bistability, predicted by dynamic vegetation models based on non-linear differential equations. Here, we propose a change of perspective about the bimodality of tree cover distribution. We show, using a simple matrix model of tree dynamics, how the bimodality of tree cover can emerge from the switching between two linear dynamics of trees, one in presence and one in absence of fire, with a feedback between fire and trees. As consequence, we find that the transitions between moist savannas and tropical forests, if sharp, are not necessarily catastrophic.

Why are there more arboreal ant species in primary than in secondary tropical forests?

PubMed

Klimes, Petr; Idigel, Cliffson; Rimandai, Maling; Fayle, Tom M; Janda, Milan; Weiblen, George D; Novotny, Vojtech

2012-09-01

1. Species diversity of arboreal arthropods tends to increase during rainforest succession so that primary forest communities comprise more species than those from secondary vegetation, but it is not well understood why. Primary forests differ from secondary forests in a wide array of factors whose relative impacts on arthropod diversity have not yet been quantified. 2. We assessed the effects of succession-related determinants on a keystone ecological group, arboreal ants, by conducting a complete census of 1332 ant nests from all trees with diameter at breast height ≥ 5 cm occurring within two (unreplicated) 0·32-ha plots, one in primary and one in secondary lowland forest in New Guinea. Specifically, we used a novel rarefaction-based approach to match number, size distribution and taxonomic structure of trees in primary forest communities to those in secondary forest and compared the resulting numbers of ant species. 3. In total, we recorded 80 nesting ant species from 389 trees in primary forest but only 42 species from 295 trees in secondary forest. The two habitats did not differ in the mean number of ant species per tree or in the relationship between ant diversity and tree size. However, the between-tree similarity of ant communities was higher in secondary forest than in primary forest, as was the between-tree nest site similarity, suggesting that secondary trees were more uniform in providing nesting microhabitats. 4. Using our rarefaction method, the difference in ant species richness between two forest types was partitioned according to the effects of higher tree density (22·6%), larger tree size (15·5%) and higher taxonomic diversity of trees (14·3%) in primary than in secondary forest. The remaining difference (47·6%) was because of higher beta diversity of ant communities between primary forest trees. In contrast, difference in nest density was explained solely by difference in tree density. 5. Our study shows that reduction in plant taxonomic diversity in secondary forests is not the main driver of the reduction in canopy ant species richness. We suggest that the majority of arboreal species losses in secondary tropical forests are attributable to simpler vegetation structure, combined with lower turnover of nesting microhabitats between trees. © 2012 The Authors. Journal of Animal Ecology © 2012 British Ecological Society.

Recursive algorithms for phylogenetic tree counting.

PubMed

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

2013-10-28

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

Tree Age Distributions Reveal Large-Scale Disturbance-Recovery Cycles in Three Tropical Forests.

PubMed

Vlam, Mart; van der Sleen, Peter; Groenendijk, Peter; Zuidema, Pieter A

2016-01-01

Over the past few decades there has been a growing realization that a large share of apparently 'virgin' or 'old-growth' tropical forests carries a legacy of past natural or anthropogenic disturbances that have a substantial effect on present-day forest composition, structure and dynamics. Yet, direct evidence of such disturbances is scarce and comparisons of disturbance dynamics across regions even more so. Here we present a tree-ring based reconstruction of disturbance histories from three tropical forest sites in Bolivia, Cameroon, and Thailand. We studied temporal patterns in tree regeneration of shade-intolerant tree species, because establishment of these trees is indicative for canopy disturbance. In three large areas (140-300 ha), stem disks and increment cores were collected for a total of 1154 trees (>5 cm diameter) from 12 tree species to estimate the age of every tree. Using these age estimates we produced population age distributions, which were analyzed for evidence of past disturbance. Our approach allowed us to reconstruct patterns of tree establishment over a period of around 250 years. In Bolivia, we found continuous regeneration rates of three species and a peaked age distribution of a long-lived pioneer species. In both Cameroon and Thailand we found irregular age distributions, indicating strongly reduced regeneration rates over a period of 10-60 years. Past fires, windthrow events or anthropogenic disturbances all provide plausible explanations for the reported variation in tree age across the three sites. Our results support the recent idea that the long-term dynamics of tropical forests are impacted by large-scale disturbance-recovery cycles, similar to those driving temperate forest dynamics.

Tree Age Distributions Reveal Large-Scale Disturbance-Recovery Cycles in Three Tropical Forests

PubMed Central

Vlam, Mart; van der Sleen, Peter; Groenendijk, Peter; Zuidema, Pieter A.

2017-01-01

Over the past few decades there has been a growing realization that a large share of apparently ‘virgin’ or ‘old-growth’ tropical forests carries a legacy of past natural or anthropogenic disturbances that have a substantial effect on present-day forest composition, structure and dynamics. Yet, direct evidence of such disturbances is scarce and comparisons of disturbance dynamics across regions even more so. Here we present a tree-ring based reconstruction of disturbance histories from three tropical forest sites in Bolivia, Cameroon, and Thailand. We studied temporal patterns in tree regeneration of shade-intolerant tree species, because establishment of these trees is indicative for canopy disturbance. In three large areas (140–300 ha), stem disks and increment cores were collected for a total of 1154 trees (>5 cm diameter) from 12 tree species to estimate the age of every tree. Using these age estimates we produced population age distributions, which were analyzed for evidence of past disturbance. Our approach allowed us to reconstruct patterns of tree establishment over a period of around 250 years. In Bolivia, we found continuous regeneration rates of three species and a peaked age distribution of a long-lived pioneer species. In both Cameroon and Thailand we found irregular age distributions, indicating strongly reduced regeneration rates over a period of 10–60 years. Past fires, windthrow events or anthropogenic disturbances all provide plausible explanations for the reported variation in tree age across the three sites. Our results support the recent idea that the long-term dynamics of tropical forests are impacted by large-scale disturbance-recovery cycles, similar to those driving temperate forest dynamics. PMID:28105034

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).

Butt-log grade distributions for five Appalachian hardwood species

Treesearch

John R. Myers; Gary W. Miller; Harry V., Jr. Wiant; Joseph E. Barnard; Joseph E. Barnard

1986-01-01

Tree quality is an important factor in determining the market value of hardwood timber stands, but many forest inventories do not include estimates of tree quality. Butt-log grade distributions were developed for northern red oak, black oak, white oak, chestnut oak, and yellow-poplar using USDA Forest Service log grades on more than 4,700 trees in West Virginia. Butt-...

Estimating individual tree mid- and understory rank-size distributions from airborne laser scanning in semi-arid forests

Treesearch

Tyson L. Swetnam; Donald A. Falk; Ann M. Lynch; Stephen R. Yool

2014-01-01

Limitations inherent to airborne laser scanning (ALS) technology and the complex sorting and packing relationships of forests complicate accurate remote sensing of mid- and understory trees, especially in denser forest stands. Self-similarities in rank-sized individual tree distributions (ITD), e.g. bole diameter or height, are a well-understood property of natural,...

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

Treesearch

Kenneth L. Cole; Kirsten Ironside; Jon Eischeid; Gregg Garfin; Phillip B. Duffy; Chris Toney

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...

An indicator of tree migration in forests of the eastern United States

Treesearch

C.W. Woodall; C.M. Oswalt; J.A. Westfall; C.H. Perry; M.D. Nelson; A.O. Finley

2009-01-01

Changes in tree species distributions are a potential impact of climate change on forest ecosystems. The examination of tree species shifts in forests of the eastern United States largely has been limited to simulation activities due to a lack of consistent, long-term forest inventory datasets. The goal of this study was to compare current geographic distributions of...

Why choose Random Forest to predict rare species distribution with few samples in large undersampled areas? Three Asian crane species models provide supporting evidence.

PubMed

Mi, Chunrong; Huettmann, Falk; Guo, Yumin; Han, Xuesong; Wen, Lijia

2017-01-01

Species distribution models (SDMs) have become an essential tool in ecology, biogeography, evolution and, more recently, in conservation biology. How to generalize species distributions in large undersampled areas, especially with few samples, is a fundamental issue of SDMs. In order to explore this issue, we used the best available presence records for the Hooded Crane ( Grus monacha , n  = 33), White-naped Crane ( Grus vipio , n  = 40), and Black-necked Crane ( Grus nigricollis , n  = 75) in China as three case studies, employing four powerful and commonly used machine learning algorithms to map the breeding distributions of the three species: TreeNet (Stochastic Gradient Boosting, Boosted Regression Tree Model), Random Forest, CART (Classification and Regression Tree) and Maxent (Maximum Entropy Models). In addition, we developed an ensemble forecast by averaging predicted probability of the above four models results. Commonly used model performance metrics (Area under ROC (AUC) and true skill statistic (TSS)) were employed to evaluate model accuracy. The latest satellite tracking data and compiled literature data were used as two independent testing datasets to confront model predictions. We found Random Forest demonstrated the best performance for the most assessment method, provided a better model fit to the testing data, and achieved better species range maps for each crane species in undersampled areas. Random Forest has been generally available for more than 20 years and has been known to perform extremely well in ecological predictions. However, while increasingly on the rise, its potential is still widely underused in conservation, (spatial) ecological applications and for inference. Our results show that it informs ecological and biogeographical theories as well as being suitable for conservation applications, specifically when the study area is undersampled. This method helps to save model-selection time and effort, and allows robust and rapid assessments and decisions for efficient conservation.

Why choose Random Forest to predict rare species distribution with few samples in large undersampled areas? Three Asian crane species models provide supporting evidence

PubMed Central

Mi, Chunrong; Huettmann, Falk; Han, Xuesong; Wen, Lijia

2017-01-01

Species distribution models (SDMs) have become an essential tool in ecology, biogeography, evolution and, more recently, in conservation biology. How to generalize species distributions in large undersampled areas, especially with few samples, is a fundamental issue of SDMs. In order to explore this issue, we used the best available presence records for the Hooded Crane (Grus monacha, n = 33), White-naped Crane (Grus vipio, n = 40), and Black-necked Crane (Grus nigricollis, n = 75) in China as three case studies, employing four powerful and commonly used machine learning algorithms to map the breeding distributions of the three species: TreeNet (Stochastic Gradient Boosting, Boosted Regression Tree Model), Random Forest, CART (Classification and Regression Tree) and Maxent (Maximum Entropy Models). In addition, we developed an ensemble forecast by averaging predicted probability of the above four models results. Commonly used model performance metrics (Area under ROC (AUC) and true skill statistic (TSS)) were employed to evaluate model accuracy. The latest satellite tracking data and compiled literature data were used as two independent testing datasets to confront model predictions. We found Random Forest demonstrated the best performance for the most assessment method, provided a better model fit to the testing data, and achieved better species range maps for each crane species in undersampled areas. Random Forest has been generally available for more than 20 years and has been known to perform extremely well in ecological predictions. However, while increasingly on the rise, its potential is still widely underused in conservation, (spatial) ecological applications and for inference. Our results show that it informs ecological and biogeographical theories as well as being suitable for conservation applications, specifically when the study area is undersampled. This method helps to save model-selection time and effort, and allows robust and rapid assessments and decisions for efficient conservation. PMID:28097060

a Comparitive Study Using Geometric and Vertical Profile Features Derived from Airborne LIDAR for Classifying Tree Genera

NASA Astrophysics Data System (ADS)

Ko, C.; Sohn, G.; Remmel, T. K.

2012-07-01

We present a comparative study between two different approaches for tree genera classification using descriptors derived from tree geometry and those derived from the vertical profile analysis of LiDAR point data. The different methods provide two perspectives for processing LiDAR point clouds for tree genera identification. The geometric perspective analyzes individual tree crowns in relation to valuable information related to characteristics of clusters and line segments derived within crowns and overall tree shapes to highlight the spatial distribution of LiDAR points within the crown. Conversely, analyzing vertical profiles retrieves information about the point distributions with respect to height percentiles; this perspective emphasizes of the importance that point distributions at specific heights express, accommodating for the decreased point density with respect to depth of canopy penetration by LiDAR pulses. The targeted species include white birch, maple, oak, poplar, white pine and jack pine at a study site northeast of Sault Ste. Marie, Ontario, Canada.

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

Tree species distribution in temperate forests is more influenced by soil than by climate.

PubMed

Walthert, Lorenz; Meier, Eliane Seraina

2017-11-01

Knowledge of the ecological requirements determining tree species distributions is a precondition for sustainable forest management. At present, the abiotic requirements and the relative importance of the different abiotic factors are still unclear for many temperate tree species. We therefore investigated the relative importance of climatic and edaphic factors for the abundance of 12 temperate tree species along environmental gradients. Our investigations are based on data from 1,075 forest stands across Switzerland including the cold-induced tree line of all studied species and the drought-induced range boundaries of several species. Four climatic and four edaphic predictors represented the important growth factors temperature, water supply, nutrient availability, and soil aeration. The climatic predictors were derived from the meteorological network of MeteoSwiss, and the edaphic predictors were available from soil profiles. Species cover abundances were recorded in field surveys. The explanatory power of the predictors was assessed by variation partitioning analyses with generalized linear models. For six of the 12 species, edaphic predictors were more important than climatic predictors in shaping species distribution. Over all species, abundances depended mainly on nutrient availability, followed by temperature, water supply, and soil aeration. The often co-occurring species responded similar to these growth factors. Drought turned out to be a determinant of the lower range boundary for some species. We conclude that over all 12 studied tree species, soil properties were more important than climate variables in shaping tree species distribution. The inclusion of appropriate soil variables in species distribution models allowed to better explain species' ecological niches. Moreover, our study revealed that the ecological requirements of tree species assessed in local field studies and in experiments are valid at larger scales across Switzerland.

Larger trees suffer most during drought in forests worldwide

USGS Publications Warehouse

Bennett, Amy C.; McDowell, Nathan G.; Allen, Craig D.; Anderson-Teixeira, Kristina J.

2015-01-01

The frequency of severe droughts is increasing in many regions around the world as a result of climate change. Droughts alter the structure and function of forests. Site- and region-specific studies suggest that large trees, which play keystone roles in forests and can be disproportionately important to ecosystem carbon storage and hydrology, exhibit greater sensitivity to drought than small trees. Here, we synthesize data on tree growth and mortality collected during 40 drought events in forests worldwide to see whether this size-dependent sensitivity to drought holds more widely. We find that droughts consistently had a more detrimental impact on the growth and mortality rates of larger trees. Moreover, drought-related mortality increased with tree size in 65% of the droughts examined, especially when community-wide mortality was high or when bark beetles were present. The more pronounced drought sensitivity of larger trees could be underpinned by greater inherent vulnerability to hydraulic stress, the higher radiation and evaporative demand experienced by exposed crowns, and the tendency for bark beetles to preferentially attack larger trees. We suggest that future droughts will have a more detrimental impact on the growth and mortality of larger trees, potentially exacerbating feedbacks to climate change.

The role of disappeared disturbances in driving the North American prairie-forest boundary

NASA Astrophysics Data System (ADS)

Heilman, K.; McLachlan, J. S.; Staver, A. C.

2016-12-01

Globally, transitions from savanna to forest are often characterized by abrupt changes in tree density that cannot be fully explained by climate and edaphic factors. In the tropics, fire-vegetation feedbacks drive a bimodal distribution in tree cover that leads to alternative forest and savanna stable states within the same climate space. In temperate North America, the pre-European settlement prairie-forest transition has also been hypothesized to be influenced by widespread fires (anthropogenic or natural). However, large scale evidence for fire disturbance feedbacks on tree density in the temperate zone is currently lacking. We investigate both the pre-European and modern tree density along the North American prairie-forest boundary. We hypothesized that the pre-European distribution of tree density was distinctly bimodal due to intact vegetation-disturbance feedbacks along the prairie-forest boundary before settlement, but that fragmentation and fire suppression has produced a modern prairie-forest boundary that is less abrupt and less bimodal. We estimated tree density from aggregated Public Land Survey (PLS) data collected before the time of European agricultural settlement in Minnesota, Wisconsin, Michigan, Indiana, and Illinois and compared PLS density distributions to tree density estimated from modern USFS Forest Inventory Analysis (FIA) data. PLS tree density follows a bimodal distribution that abruptly shifts from savanna to forest at the boundary. Only 15% of the variance in pre-settlement tree density is explained by historical Mean Annual Precipitation (MAP), suggesting that the bimodality may be due to internal feedbacks in the vegetation-disturbance system, rather than to the past underlying environmental gradient. On the modern landscape, MAP explains 6% of FIA tree density variance, and tree density is not bimodal. Regions that had low tree density savannas in the PLS era have significantly increased in tree density, suggesting that the disappearance of disturbances that accompanied agricultural settlement resulted in closed forests where savannas were once an alternative stable state (p < 0.01). Additionally, the once high tree density forests in the PLS have significantly declined in density, suggesting that logging has contributed to land cover change in North America.

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

PubMed Central

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

2013-01-01

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

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

PubMed Central

2012-01-01

Background The increased use of multi-locus data sets for phylogenetic reconstruction has increased the need to determine whether a set of gene trees significantly deviate from the phylogenetic patterns of other genes. Such unusual gene trees may have been influenced by other evolutionary processes such as selection, gene duplication, or horizontal gene transfer. Results Motivated by this problem we propose a nonparametric goodness-of-fit test for two empirical distributions of gene trees, and we developed the software GeneOut to estimate a p-value for the test. Our approach maps trees into a multi-dimensional vector space and then applies support vector machines (SVMs) to measure the separation between two sets of pre-defined trees. We use a permutation test to assess the significance of the SVM separation. To demonstrate the performance of GeneOut, we applied it to the comparison of gene trees simulated within different species trees across a range of species tree depths. Applied directly to sets of simulated gene trees with large sample sizes, GeneOut was able to detect very small differences between two set of gene trees generated under different species trees. Our statistical test can also include tree reconstruction into its test framework through a variety of phylogenetic optimality criteria. When applied to DNA sequence data simulated from different sets of gene trees, results in the form of receiver operating characteristic (ROC) curves indicated that GeneOut performed well in the detection of differences between sets of trees with different distributions in a multi-dimensional space. Furthermore, it controlled false positive and false negative rates very well, indicating a high degree of accuracy. Conclusions The non-parametric nature of our statistical test provides fast and efficient analyses, and makes it an applicable test for any scenario where evolutionary or other factors can lead to trees with different multi-dimensional distributions. The software GeneOut is freely available under the GNU public license. PMID:22909268

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.

Interplay between geometry and flow distribution in an airway tree.

PubMed

Mauroy, B; Filoche, M; Andrade, J S; Sapoval, B

2003-04-11

Uniform flow distribution in a symmetric volume can be realized through a symmetric branched tree. It is shown here, however, by 3D numerical simulation of the Navier-Stokes equations, that the flow partitioning can be highly sensitive to deviations from exact symmetry if inertial effects are present. The flow asymmetry is quantified and found to depend on the Reynolds number. Moreover, for a given Reynolds number, we show that the flow distribution depends on the aspect ratio of the branching elements as well as their angular arrangement. Our results indicate that physiological variability should be severely restricted in order to ensure adequate fluid distribution through a tree.

Understanding tree growth in response to moisture variability: Linking 32 years of satellite based soil moisture observations with tree rings

NASA Astrophysics Data System (ADS)

Albrecht, Franziska; Dorigo, Wouter; Gruber, Alexander; Wagner, Wolfgang; Kainz, Wolfgang

2014-05-01

Climate change induced drought variability impacts global forest ecosystems and forest carbon cycle dynamics. Physiological drought stress might even become an issue in regions generally not considered water-limited. The water balance at the soil surface is essential for forest growth. Soil moisture is a key driver linking precipitation and tree development. Tree ring based analyses are a potential approach to study the driving role of hydrological parameters for tree growth. However, at present two major research gaps are apparent: i) soil moisture records are hardly considered and ii) only a few studies are linking tree ring chronologies and satellite observations. Here we used tree ring chronologies obtained from the International Tree ring Data Bank (ITRDB) and remotely sensed soil moisture observations (ECV_SM) to analyze the moisture-tree growth relationship. The ECV_SM dataset, which is being distributed through ESA's Climate Change Initiative for soil moisture covers the period 1979 to 2010 at a spatial resolution of 0.25°. First analyses were performed for Mongolia, a country characterized by a continental arid climate. We extracted 13 tree ring chronologies suitable for our analysis from the ITRDB. Using monthly satellite based soil moisture observations we confirmed previous studies on the seasonality of soil moisture in Mongolia. Further, we investigated the relationship between tree growth (as reflected by tree ring width index) and remotely sensed soil moisture records by applying correlation analysis. In terms of correlation coefficient a strong response of tree growth to soil moisture conditions of current April to August was observed, confirming a strong linkage between tree growth and soil water storage. The highest correlation was found for current April (R=0.44), indicating that sufficient water supply is vital for trees at the beginning of the growing season. To verify these results, we related the chronologies to reanalysis precipitation and temperature datasets. Precipitation was important during both the current and previous growth season. Temperature showed the strongest correlation for previous (R=0.12) and current October (R=0.21). Hence, our results demonstrated that water supply is most likely limiting tree growth during the growing season, while temperature is determining its length. We are confident that long-term satellite based soil moisture observations can bridge spatial and temporal limitations that are inherent to in situ measurements, which are traditionally used for tree ring research. Our preliminary results are a foundation for further studies linking remotely sensed datasets and tree ring chronologies, an approach that has not been widely investigated among the scientific community.

Technical guide to crop tree release in hardwood forests

Treesearch

Gary W. Miller; Jeffrey W. Stringer; David C. Mercker

2007-01-01

Crop tree release (CTR) is a widely applicable silvicultural technique used to enhance the performance of individual trees. It offers flexibility in that it can be applied on small or large properties, and with certain modifications, it can be applied as a precommercial or commercial operation. By favoring the development of selected crop trees within a hardwood stand...

Modeled distributions of 12 tree species in New York

Treesearch

Rachel I. Riemann; Barry T. Wilson; Andrew J. Lister; Oren Cook; Sierra Crane-Murdoch

2014-01-01

These maps depict the distribution of 12 tree species across the state of New York. The maps show where these trees do not occur (gray), occasionally occur (pale green), are a minor component (medium green), are a major component (dark green), or are the dominant species (black) in the forest, as determined by that species' total basal area. Basal area is the area...

Tree mortality estimates and species distribution probabilities in southeastern United States forests

Treesearch

Martin A. Spetich; Zhaofei Fan; Zhen Sui; Michael Crosby; Hong S. He; Stephen R. Shifley; Theodor D. Leininger; W. Keith Moser

2017-01-01

Stresses to trees under a changing climate can lead to changes in forest tree survival, mortality and distribution.  For instance, a study examining the effects of human-induced climate change on forest biodiversity by Hansen and others (2001) predicted a 32% reduction in loblolly–shortleaf pine habitat across the eastern United States.  However, they also...

Predicting volume of distribution with decision tree-based regression methods using predicted tissue:plasma partition coefficients.

PubMed

Freitas, Alex A; Limbu, Kriti; Ghafourian, Taravat

2015-01-01

Volume of distribution is an important pharmacokinetic property that indicates the extent of a drug's distribution in the body tissues. This paper addresses the problem of how to estimate the apparent volume of distribution at steady state (Vss) of chemical compounds in the human body using decision tree-based regression methods from the area of data mining (or machine learning). Hence, the pros and cons of several different types of decision tree-based regression methods have been discussed. The regression methods predict Vss using, as predictive features, both the compounds' molecular descriptors and the compounds' tissue:plasma partition coefficients (Kt:p) - often used in physiologically-based pharmacokinetics. Therefore, this work has assessed whether the data mining-based prediction of Vss can be made more accurate by using as input not only the compounds' molecular descriptors but also (a subset of) their predicted Kt:p values. Comparison of the models that used only molecular descriptors, in particular, the Bagging decision tree (mean fold error of 2.33), with those employing predicted Kt:p values in addition to the molecular descriptors, such as the Bagging decision tree using adipose Kt:p (mean fold error of 2.29), indicated that the use of predicted Kt:p values as descriptors may be beneficial for accurate prediction of Vss using decision trees if prior feature selection is applied. Decision tree based models presented in this work have an accuracy that is reasonable and similar to the accuracy of reported Vss inter-species extrapolations in the literature. The estimation of Vss for new compounds in drug discovery will benefit from methods that are able to integrate large and varied sources of data and flexible non-linear data mining methods such as decision trees, which can produce interpretable models. Graphical AbstractDecision trees for the prediction of tissue partition coefficient and volume of distribution of drugs.

Rangewide determinants of population performance in Prunus lusitanica: Lessons for the contemporary conservation of a Tertiary relict tree

NASA Astrophysics Data System (ADS)

Pardo, Adara; Cáceres, Yonatan; Pulido, Fernando

2018-01-01

Relict species are an extremely important part of biodiversity and as such studies on the factors that allow their current persistence are required. The aim of this study was to assess the determinants of the distribution and range-wide population performance of the Tertiary relict tree Prunus lusitanica L. This threatened species is confined to Iberia, Northern Morocco and Macaronesia with a fragmented and scattered distribution. Using ecological niche modelling, we calculated the level of range filling across the range and tested its relationship with human impact. We then assessed the relative importance of climatic suitability as obtained through niche modelling, topographic factors and contemporary human impact on range-wide population performance. Results showed that the species occupies only 2.4% of the overall area predicted to be climatically suitable for its presence and the level of range filling varied across regions. A weak negative relationship among range filling and human impact was found. Overall climatic suitability was the strongest predictor of population performance. However, it showed high variability across regions: the effect was positive in Iberia whereas negative but not significant in Macaronesia and Morocco. Human impact showed a significant negative effect and finally topographic factors such as altitude had a minor negative effect. Our results highlight that both climate and human impact play a major role in the current limited range filling and performance of the species. Management plans to minimize anthropogenic disturbances together with reforestation measures are urgently needed in order to conserve this unique species.

137Cs distribution among annual rings of different tree species contaminated after the Chernobyl accident.

PubMed

Soukhova, N V; Fesenko, S V; Klein, D; Spiridonov, S I; Sanzharova, N I; Badot, P M

2003-01-01

The distributions of 137Cs among annual rings of Pinus sylvestris and Betula pendula at four experimental sites located in the most contaminated areas in the Russian territory after the Chernobyl accident in 1986 were studied. Trees of different ages were sampled from four forest sites with different tree compositions and soil properties. The data analysis shows that 137Cs is very mobile in wood and the 1986 rings do not show the highest contamination. The difference between pine and birch in the pattern of radial 137Cs distribution can be satisfactorily explained by the difference in radial ray composition. 137Cs radial distribution in the wood can be described as the sum of two exponential functions for both species. The function parameters are height, age and species dependent. The distribution of 137Cs in birch wood reveals much more pronounced dependence on site characteristics and/or the age of trees than pines. The data obtained can be used to assess 137Cs content in wood.

The reanalysis of biogeography of the Asian tree frog, Rhacophorus (Anura: Rhacophoridae): geographic shifts and climatic change influenced the dispersal process and diversification

PubMed Central

Wang, Hui; Wu, Jun; Kang, Xing; Qian, Lifu; Chen, Jinyun; Rao, Dingqi; Jiang, Jianping

2017-01-01

Rapid uplifts of the Tibetan Plateau and climate change in Asia are thought to have profoundly modulated the diversification of most of the species distributed throughout Asia. The ranoid tree frog genus Rhacophorus, the largest genus in the Rhacophoridae, is widely distributed in Asia and especially speciose in the areas south and east of the Tibetan Plateau. Here, we infer phylogenetic relationships among species and estimate divergence times, asking whether the spatiotemporal characteristics of diversification within Rhacophorus were related to rapid uplifts of the Tibetan Plateau and concomitant climate change. Phylogenetic analysis recovered distinct lineage structures in Rhacophorus, which indicated a clear distribution pattern from Southeast Asia toward East Asia and India. Molecular dating suggests that the first split within the genus date back to the Middle Oligocene (approx. 30 Ma). The Rhacophorus lineage through time (LTT) showed that there were periods of increased speciation rate: 14–12 Ma and 10–4 Ma. In addition, ancestral area reconstructions supported Southeast Asia as the ancestral area of Rhacophorus. According to the results of molecular dating, ancestral area reconstructions and LTT we think the geographic shifts, the staged rapid rises of the Tibetan Plateau with parallel climatic changes and reinforcement of the Asian monsoons (15 Ma, 8 Ma and 4–3 Ma), possibly prompted a burst of diversification in Rhacophorus. PMID:29177111

Using classification tree analysis to predict oak wilt distribution in Minnesota and Texas

Treesearch

Marla c. Downing; Vernon L. Thomas; Jennifer Juzwik; David N. Appel; Robin M. Reich; Kim Camilli

2008-01-01

We developed a methodology and compared results for predicting the potential distribution of Ceratocystis fagacearum (causal agent of oak wilt), in both Anoka County, MN, and Fort Hood, TX. The Potential Distribution of Oak Wilt (PDOW) utilizes a binary classification tree statistical technique that incorporates: geographical information systems (GIS...

Tree Data (TD)

Treesearch

Robert E. Keane

2006-01-01

The Tree Data (TD) methods are used to sample individual live and dead trees on a fixed-area plot to estimate tree density, size, and age class distributions before and after fire in order to assess tree survival and mortality rates. This method can also be used to sample individual shrubs if they are over 4.5 ft tall. When trees are larger than the user-specified...

Changes in fine-root production, phenology and spatial distribution in response to N application in irrigated sweet cherry trees.

PubMed

Artacho, Pamela; Bonomelli, Claudia

2016-05-01

Factors regulating fine-root growth are poorly understood, particularly in fruit tree species. In this context, the effects of N addition on the temporal and spatial distribution of fine-root growth and on the fine-root turnover were assessed in irrigated sweet cherry trees. The influence of other exogenous and endogenous factors was also examined. The rhizotron technique was used to measure the length-based fine-root growth in trees fertilized at two N rates (0 and 60 kg ha(-1)), and the above-ground growth, leaf net assimilation, and air and soil variables were simultaneously monitored. N fertilization exerted a basal effect throughout the season, changing the magnitude, temporal patterns and spatial distribution of fine-root production and mortality. Specifically, N addition enhanced the total fine-root production by increasing rates and extending the production period. On average, N-fertilized trees had a length-based production that was 110-180% higher than in control trees, depending on growing season. Mortality was proportional to production, but turnover rates were inconsistently affected. Root production and mortality was homogeneously distributed in the soil profile of N-fertilized trees while control trees had 70-80% of the total fine-root production and mortality concentrated below 50 cm depth. Root mortality rates were associated with soil temperature and water content. In contrast, root production rates were primarily under endogenous control, specifically through source-sink relationships, which in turn were affected by N supply through changes in leaf photosynthetic level. Therefore, exogenous and endogenous factors interacted to control the fine-root dynamics of irrigated sweet cherry trees. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Changes in fine-root production, phenology and spatial distribution in response to N application in irrigated sweet cherry trees

PubMed Central

Artacho, Pamela; Bonomelli, Claudia

2016-01-01

Factors regulating fine-root growth are poorly understood, particularly in fruit tree species. In this context, the effects of N addition on the temporal and spatial distribution of fine-root growth and on the fine-root turnover were assessed in irrigated sweet cherry trees. The influence of other exogenous and endogenous factors was also examined. The rhizotron technique was used to measure the length-based fine-root growth in trees fertilized at two N rates (0 and 60 kg ha−1), and the above-ground growth, leaf net assimilation, and air and soil variables were simultaneously monitored. N fertilization exerted a basal effect throughout the season, changing the magnitude, temporal patterns and spatial distribution of fine-root production and mortality. Specifically, N addition enhanced the total fine-root production by increasing rates and extending the production period. On average, N-fertilized trees had a length-based production that was 110–180% higher than in control trees, depending on growing season. Mortality was proportional to production, but turnover rates were inconsistently affected. Root production and mortality was homogeneously distributed in the soil profile of N-fertilized trees while control trees had 70–80% of the total fine-root production and mortality concentrated below 50 cm depth. Root mortality rates were associated with soil temperature and water content. In contrast, root production rates were primarily under endogenous control, specifically through source–sink relationships, which in turn were affected by N supply through changes in leaf photosynthetic level. Therefore, exogenous and endogenous factors interacted to control the fine-root dynamics of irrigated sweet cherry trees. PMID:26888890

Revisiting the two-layer hypothesis: coexistence of alternative functional rooting strategies in savannas.

PubMed

Holdo, Ricardo M

2013-01-01

The two-layer hypothesis of tree-grass coexistence posits that trees and grasses differ in rooting depth, with grasses exploiting soil moisture in shallow layers while trees have exclusive access to deep water. The lack of clear differences in maximum rooting depth between these two functional groups, however, has caused this model to fall out of favor. The alternative model, the demographic bottleneck hypothesis, suggests that trees and grasses occupy overlapping rooting niches, and that stochastic events such as fires and droughts result in episodic tree mortality at various life stages, thus preventing trees from otherwise displacing grasses, at least in mesic savannas. Two potential problems with this view are: 1) we lack data on functional rooting profiles in trees and grasses, and these profiles are not necessarily reflected by differences in maximum or physical rooting depth, and 2) subtle, difficult-to-detect differences in rooting profiles between the two functional groups may be sufficient to result in coexistence in many situations. To tackle this question, I coupled a plant uptake model with a soil moisture dynamics model to explore the environmental conditions under which functional rooting profiles with equal rooting depth but different depth distributions (i.e., shapes) can coexist when competing for water. I show that, as long as rainfall inputs are stochastic, coexistence based on rooting differences is viable under a wide range of conditions, even when these differences are subtle. The results also indicate that coexistence mechanisms based on rooting niche differentiation are more viable under some climatic and edaphic conditions than others. This suggests that the two-layer model is both viable and stochastic in nature, and that a full understanding of tree-grass coexistence and dynamics may require incorporating fine-scale rooting differences between these functional groups and realistic stochastic climate drivers into future models.

Revisiting the Two-Layer Hypothesis: Coexistence of Alternative Functional Rooting Strategies in Savannas

PubMed Central

Holdo, Ricardo M.

2013-01-01

The two-layer hypothesis of tree-grass coexistence posits that trees and grasses differ in rooting depth, with grasses exploiting soil moisture in shallow layers while trees have exclusive access to deep water. The lack of clear differences in maximum rooting depth between these two functional groups, however, has caused this model to fall out of favor. The alternative model, the demographic bottleneck hypothesis, suggests that trees and grasses occupy overlapping rooting niches, and that stochastic events such as fires and droughts result in episodic tree mortality at various life stages, thus preventing trees from otherwise displacing grasses, at least in mesic savannas. Two potential problems with this view are: 1) we lack data on functional rooting profiles in trees and grasses, and these profiles are not necessarily reflected by differences in maximum or physical rooting depth, and 2) subtle, difficult-to-detect differences in rooting profiles between the two functional groups may be sufficient to result in coexistence in many situations. To tackle this question, I coupled a plant uptake model with a soil moisture dynamics model to explore the environmental conditions under which functional rooting profiles with equal rooting depth but different depth distributions (i.e., shapes) can coexist when competing for water. I show that, as long as rainfall inputs are stochastic, coexistence based on rooting differences is viable under a wide range of conditions, even when these differences are subtle. The results also indicate that coexistence mechanisms based on rooting niche differentiation are more viable under some climatic and edaphic conditions than others. This suggests that the two-layer model is both viable and stochastic in nature, and that a full understanding of tree-grass coexistence and dynamics may require incorporating fine-scale rooting differences between these functional groups and realistic stochastic climate drivers into future models. PMID:23950900

Succession after stand replacing disturbances by fire, wind throw, and insects in the dark Taiga of Central Siberia.

PubMed

Schulze, E-D; Wirth, C; Mollicone, D; Ziegler, W

2005-11-01

The dark taiga of Siberia is a boreal vegetation dominated by Picea obovata, Abies sibirica, and Pinus sibirica during the late succession. This paper investigates the population and age structure of 18 stands representing different stages after fire, wind throw, and insect damage. To our knowledge, this is the first time that the forest dynamics of the Siberian dark taiga is described quantitatively in terms of succession, and age after disturbance, stand density, and basal area. The basis for the curve-linear age/diameter relation of trees is being analyzed. (1) After a stand-replacing fire Betula dominates (4,000 trees) for about 70 years. Although tree density of Betula decreases rapidly, basal area (BA) reached >30 m2/ha after 40 years. (2) After fire, Abies, Picea, and Pinus establish at the same time as Betula, but grow slower, continue to gain height and eventually replace Betula. Abies has the highest seedling number (about 1,000 trees/ha) and the highest mortality. Picea establishes with 100-400 trees/ha, it has less mortality, but reached the highest age (>350 years, DBH 51 cm). Picea is the most important indicator for successional age after disturbance. Pinus sibirica is an accompanying species. The widely distributed "mixed boreal forest" is a stage about 120 years after fire reaching a BA of >40 m2/ha. (3) Wind throw and insect damage occur in old conifer stands. Betula does not establish. Abies initially dominates (2,000-6,000 trees/ha), but Picea becomes dominant after 150-200 years since Abies is shorter lived. (4) Without disturbance the forest develops into a pure coniferous canopy (BA 40-50 m2/ha) with a self-regenerating density of 1,000 coniferous canopy trees/ha. There is no collapse of old-growth stands. The dark taiga may serve as an example in which a limited set to tree species may gain dominance under certain disturbance conditions without ever getting monotypic.

Changes in composition, structure and aboveground biomass over seventy-six years (1930-2006) in the Black Rock Forest, Hudson Highlands, southeastern New York State.

PubMed

Schuster, W S F; Griffin, K L; Roth, H; Turnbull, M H; Whitehead, D; Tissue, D T

2008-04-01

We sought to quantify changes in tree species composition, forest structure and aboveground forest biomass (AGB) over 76 years (1930-2006) in the deciduous Black Rock Forest in southeastern New York, USA. We used data from periodic forest inventories, published floras and a set of eight long-term plots, along with species-specific allometric equations to estimate AGB and carbon content. Between the early 1930s and 2000, three species were extirpated from the forest (American elm (Ulmus americana L.), paper birch (Betula papyrifera Marsh.) and black spruce (Picea mariana (nigra) (Mill.) BSP)) and seven species invaded the forest (non-natives tree-of-heaven (Ailanthus altissima (Mill.) Swingle) and white poplar (Populus alba L.) and native, generally southerly distributed, southern catalpa (Catalpa bignonioides Walt.), cockspur hawthorn (Crataegus crus-galli L.), red mulberry (Morus rubra L.), eastern cottonwood (Populus deltoides Bartr.) and slippery elm (Ulmus rubra Muhl.)). Forest canopy was dominated by red oak and chestnut oak, but the understory tree community changed substantially from mixed oak-maple to red maple-black birch. Density decreased from an average of 1500 to 735 trees ha(-1), whereas basal area doubled from less than 15 m(2) ha(-1) to almost 30 m(2) ha(-1) by 2000. Forest-wide mean AGB from inventory data increased from about 71 Mg ha(-1) in 1930 to about 145 Mg ha(-1) in 1985, and mean AGB on the long-term plots increased from 75 Mg ha(-1) in 1936 to 218 Mg ha(-1) in 1998. Over 76 years, red oak (Quercus rubra L.) canopy trees stored carbon at about twice the rate of similar-sized canopy trees of other species. However, there has been a significant loss of live tree biomass as a result of canopy tree mortality since 1999. Important constraints on long-term biomass increment have included insect outbreaks and droughts.

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...

Multi-model comparison on the effects of climate change on tree species in the eastern U.S.: results from an enhanced niche model and process-based ecosystem and landscape models

Treesearch

Louis R. Iverson; Frank R. Thompson; Stephen Matthews; Matthew Peters; Anantha Prasad; William D. Dijak; Jacob Fraser; Wen J. Wang; Brice Hanberry; Hong He; Maria Janowiak; Patricia Butler; Leslie Brandt; Chris Swanston

2016-01-01

Context. Species distribution models (SDM) establish statistical relationships between the current distribution of species and key attributes whereas process-based models simulate ecosystem and tree species dynamics based on representations of physical and biological processes. TreeAtlas, which uses DISTRIB SDM, and Linkages and LANDIS PRO, process...

Distribution and abundance of red tree voles in Oregon based on occurrence in pellets of northern spotted owls.

Treesearch

Eric D. Forsman; Robert G. Anthony; Cynthia J. Zabel

2004-01-01

Red tree voles are one of the least understood small mammals in the Pacific Northwest, because they live in the forest canopy and are difficult to sample using conventional trapping methods. We examined the distribution and relative abundance of tree voles in different regions of Oregon based on their occurrence in diets of northern spotted owls. We identified the...

Acoustic tomography for decay detection in black cherry trees

Treesearch

Xiping Wang; Jan Wiedenbeck; Shanqing Liang

2009-01-01

This study investigated the potential of using acoustic tomography for detecting internal decay in high-value hardwood trees in the forest. Twelve black cherry (Prunus serotina) trees that had a wide range of physical characteristics were tested in a stand of second-growth hardwoods in Kane, PA, using a PiCUS Sonic Tomograph tool. The trees were felled after the field...

A Multipurpose Tree for Puerto Rico

Treesearch

Martin Chudnoff; C. B. Briscoe

1965-01-01

Cadam (Anthocaephalus cadamba Miq.) grows very rapidly on a wide variety of sited in Puerto Rico. Tree form is excellent, seed is produced in abundance every year by mature trees, planting is easy and cheap, and relatively little care is required after planting. No important attacks of insects of disease have occurred on trees grown in Puerto Rico for 35 years. The...

Field Tests of Pine Oil as a Repellent for Southern Pine Bark Beetles

Treesearch

J.C. Nod; F.L. Hastings; A.S. Jones

1990-01-01

An experimental mixture of terpene hydrocarbons derived from wood pulping, BBR-2, sprayed on the lower 6 m of widely separated southern pine trees did not protect nearby trees from southern pine beetle attacks. Whether treated trees were protected from southern pine beetle was inconclusive. The pine oil mixture did not repellpsfrom treated trees or nearby untreated...

Genetic differentiation in spite of high gene flow in the dominant rainforest tree of southeastern Australia, Nothofagus cunninghamii.

PubMed

Duncan, C J; Worth, J R P; Jordan, G J; Jones, R C; Vaillancourt, R E

2016-01-01

Nothofagus cunninghamii is a long-lived, wind-pollinated tree species that dominates the cool temperate rainforests of southeastern Australia. The species' distribution is more or less continuous in western Tasmania but is fragmented elsewhere. However, it is unknown whether this fragmentation has affected the species' genetic architecture. Thus, we examined N. cunninghamii using 12 nuclear microsatellites and 633 individuals from 18 populations spanning the species' natural range. Typical of wind-pollinated trees, there was low range-wide genetic structure (FST=0.04) consistent with significant gene flow across most of the species' range. However, gene flow was not high enough to overcome the effects of drift across some disjunctions. Victorian populations (separated from Tasmania by the 240 km wide Bass Strait) formed a genetic group distinct from Tasmanian populations, had lower diversity (mean allelic richness (Ar)=5.4 in Victoria versus 6.9 in Tasmania) and were significantly more differentiated from one another than those in Tasmania (FST=0.045 in Victoria versus 0.012 in Tasmania). Evidence for bottlenecking was found in small populations that were at least 20 km from other populations. Interestingly, we found little divergence in microsatellite markers between the extremes of genetically based morphological and physiological altitudinal clines suggesting adaptive differentiation is strongly driven by selection because it is likely to be occurring in the presence of gene flow. Even though the cool temperate rainforests of Australia are highly relictual, the species is relatively robust to population fragmentation due to high levels of genetic diversity and gene flow, especially in Tasmania.

Spatial Distribution and Site-Specific Spraying of Main Sucking Pests of Elm Trees.

PubMed

Karimzadeh, R; Iranipour, S

2017-06-01

Elm trees are important landscape trees and sucking insects weaken the elm trees and produce large amounts of honeydew. The main objectives of this study were to identify main honeydew-producing pests of elm trees and do site-specific spraying against these pests. To map the spatial distribution of the sucking pests in the large scale, the study area was divided into 40 × 40 m grids and one tree was chosen randomly from each grid (a total of 55 trees). These trees were sampled twice a year in 2011 and 2012. Each sample was a 30-cm branch terminal. Eight samples were taken from each tree in four cardinal directions and two canopy levels. The number of sucking insects and leaves of each sample were counted and recorded. Spatial analysis of the data was carried out using geostatistics. Kriging was used for producing prediction maps. Insecticide application was restricted to the regions with populations higher than threshold. To identify within-tree distribution of the honeydew-producing pests, six and four elm trees were chosen in 2011 and 2012 respectively, and sampled weekly. These trees were sampled as described previously. European elm scale (EES), Gossyparia spuria (Modeer) and two species of aphids were the dominant honeydew-producing pests. The results revealed that the effects of direction, canopy level and their interactions on insect populations were not statistically significant (P < 0.05). Site-specific spraying decreased the amount of insecticides used by ca. 20%, while satisfactory control of the sucking pests and honeydew excretion was obtained. Considering the environmental and economic benefits of site-specific spraying, it is worth doing more complementary works in this area.

Lognormal Approximations of Fault Tree Uncertainty Distributions.

PubMed

El-Shanawany, Ashraf Ben; Ardron, Keith H; Walker, Simon P

2018-01-26

Fault trees are used in reliability modeling to create logical models of fault combinations that can lead to undesirable events. The output of a fault tree analysis (the top event probability) is expressed in terms of the failure probabilities of basic events that are input to the model. Typically, the basic event probabilities are not known exactly, but are modeled as probability distributions: therefore, the top event probability is also represented as an uncertainty distribution. Monte Carlo methods are generally used for evaluating the uncertainty distribution, but such calculations are computationally intensive and do not readily reveal the dominant contributors to the uncertainty. In this article, a closed-form approximation for the fault tree top event uncertainty distribution is developed, which is applicable when the uncertainties in the basic events of the model are lognormally distributed. The results of the approximate method are compared with results from two sampling-based methods: namely, the Monte Carlo method and the Wilks method based on order statistics. It is shown that the closed-form expression can provide a reasonable approximation to results obtained by Monte Carlo sampling, without incurring the computational expense. The Wilks method is found to be a useful means of providing an upper bound for the percentiles of the uncertainty distribution while being computationally inexpensive compared with full Monte Carlo sampling. The lognormal approximation method and Wilks's method appear attractive, practical alternatives for the evaluation of uncertainty in the output of fault trees and similar multilinear models. © 2018 Society for Risk Analysis.

Tree-ring δ18O in African mahogany (Entandrophragma utile) records regional precipitation and can be used for climate reconstructions

NASA Astrophysics Data System (ADS)

van der Sleen, Peter; Groenendijk, Peter; Zuidema, Pieter A.

2015-04-01

The availability of instrumental climate data in West and Central Africa is very restricted, both in space and time. This limits the understanding of the regional climate system and the monitoring of climate change and causes a need for proxies that allow the reconstruction of paleoclimatic variability. Here we show that oxygen isotope values (δ18O) in tree rings of Entandrophragma utile from North-western Cameroon correlate to precipitation on a regional to sub-continental scale (1930-2009). All found correlations were negative, following the proposed recording of the 'amount effect' by trees in the tropics. The capacity of E. utile to record the variability of regional precipitation is also confirmed by the significant correlation of tree-ring δ18O with river discharge data (1944-1983), outgoing longwave radiation (a proxy for cloud cover; 1974-2011) and sea surface salinity in the Gulf of Guinea (1950-2011). Furthermore, the high values in the δ18O chronology from 1970 onwards coincide with the Sahel drought period. Given that E. utile presents clear annual growth rings, has a wide-spread distribution in tropical Africa and is long lived (> 250 years), we argue that the analysis of oxygen isotopes in growth rings of this species is a promising tool for the study of paleoclimatic variability during the last centuries in West and Central Africa.

A Robust Semi-Parametric Test for Detecting Trait-Dependent Diversification.

PubMed

Rabosky, Daniel L; Huang, Huateng

2016-03-01

Rates of species diversification vary widely across the tree of life and there is considerable interest in identifying organismal traits that correlate with rates of speciation and extinction. However, it has been challenging to develop methodological frameworks for testing hypotheses about trait-dependent diversification that are robust to phylogenetic pseudoreplication and to directionally biased rates of character change. We describe a semi-parametric test for trait-dependent diversification that explicitly requires replicated associations between character states and diversification rates to detect effects. To use the method, diversification rates are reconstructed across a phylogenetic tree with no consideration of character states. A test statistic is then computed to measure the association between species-level traits and the corresponding diversification rate estimates at the tips of the tree. The empirical value of the test statistic is compared to a null distribution that is generated by structured permutations of evolutionary rates across the phylogeny. The test is applicable to binary discrete characters as well as continuous-valued traits and can accommodate extremely sparse sampling of character states at the tips of the tree. We apply the test to several empirical data sets and demonstrate that the method has acceptable Type I error rates. © The Author(s) 2015. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Cosmic phylogeny: reconstructing the chemical history of the solar neighbourhood with an evolutionary tree

NASA Astrophysics Data System (ADS)

Jofré, Paula; Das, Payel; Bertranpetit, Jaume; Foley, Robert

2017-05-01

Using 17 chemical elements as a proxy for stellar DNA, we present a full phylogenetic study of stars in the solar neighbourhood. This entails applying a clustering technique that is widely used in molecular biology to construct an evolutionary tree from which three branches emerge. These are interpreted as stellar populations that separate in age and kinematics and can be thus attributed to the thin disc, the thick disc and an intermediate population of probable distinct origin. We further find six lone stars of intermediate age that could not be assigned to any population with enough statistical significance. Combining the ages of the stars with their position on the tree, we are able to quantify the mean rate of chemical enrichment of each of the populations, and thus show in a purely empirical way that the star formation rate in the thick disc is much higher than that in the thin disc. We are also able to estimate the relative contribution of dynamical processes such as radial migration and disc heating to the distribution of chemical elements in the solar neighbourhood. Our method offers an alternative approach to chemical tagging methods with the advantage of visualizing the behaviour of chemical elements in evolutionary trees. This offers a new way to search for 'common ancestors' that can reveal the origin of solar neighbourhood stars.

Sympatric distribution of three human Taenia tapeworms collected between 1935 and 2005 in Korea.

PubMed

Jeon, Hyeong-Kyu; Kim, Kyu-Heon; Chai, Jong-Yil; Yang, Hyun-Jong; Rim, Han-Jong; Eom, Keeseon S

2008-12-01

Taeniasis has been known as one of the prevalent parasitic infections in Korea. Until recently, Taenia saginata had long been considered a dominant, and widely distributed species but epidemiological profiles of human Taenia species in Korea still remain unclear. In order to better understand distribution patterns of human Taenia tapeworms in Korea, partial nucleotide sequences of mitochondrial cox1 and ITS2 (internal transcribed spacer 2) were determined, along with morphological examinations, on 68 Taenia specimens obtained from university museum collections deposited since 1935. Genomic DNA was extracted from formalin-preserved specimens. Phylogenetic relationships among the genotypes (cox1 haplotype) detected in this study were inferred using the neighbor-joining method as a tree building method. Morphological and genetic analyses identified 3 specimens as T. solium, 51 specimens as T. asiatica, and 14 specimens as T. saginata. Our results indicate that all 3 Taenia tapeworms are sympatrically distributed in Korea with T. asiatica dominating over T. saginata and T. solium.

Sympatric Distribution of Three Human Taenia Tapeworms Collected between 1935 and 2005 in Korea

PubMed Central

Jeon, Hyeong-Kyu; Kim, Kyu-Heon; Chai, Jong-Yil; Yang, Hyun-Jong; Rim, Han-Jong

2008-01-01

Taeniasis has been known as one of the prevalent parasitic infections in Korea. Until recently, Taenia saginata had long been considered a dominant, and widely distributed species but epidemiological profiles of human Taenia species in Korea still remain unclear. In order to better understand distribution patterns of human Taenia tapeworms in Korea, partial nucleotide sequences of mitochondrial cox1 and ITS2 (internal transcribed spacer 2) were determined, along with morphological examinations, on 68 Taenia specimens obtained from university museum collections deposited since 1935. Genomic DNA was extracted from formalin-preserved specimens. Phylogenetic relationships among the genotypes (cox1 haplotype) detected in this study were inferred using the neighbor-joining method as a tree building method. Morphological and genetic analyses identified 3 specimens as T. solium, 51 specimens as T. asiatica, and 14 specimens as T. saginata. Our results indicate that all 3 Taenia tapeworms are sympatrically distributed in Korea with T. asiatica dominating over T. saginata and T. solium. PMID:19127329

Effects of dispersal, shrubs, and density-dependent morality on seed and seedling distributions in temperate forests

Treesearch

Janneke Hille Ris Lambers; James S. Clark

2003-01-01

Processes limiting recruitment of trees may have large impacts on forest dynamics. In this paper, we determined the effects of dispersal, shrubs (Rhododendron maximum), and density-dependent mortality on seed and seedling distributions of Southern Appalachian trees. We quantified the spatial distribution of seed rain, seed bank densities, first-year...

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...

The temporal distribution and carbon storage of large oak wood in streams and floodplain deposits

Treesearch

Richard P. Guyette; Daniel C. Dey; Michael C. Stambaugh

2008-01-01

We used tree-ring dating and 14C dating to document the temporal distribution and carbon storage of oak (Quercus spp.) wood in trees recruited and buried by streams and floodplains in northern Missouri, USA. Frequency distributions indicated that oak wood has been accumulating in Midwest streams continually since at least the...

Development of a distributed air pollutant dry deposition modeling framework

Treesearch

Satoshi Hirabayashi; Charles N. Kroll; David J. Nowak

2012-01-01

A distributed air pollutant dry deposition modeling systemwas developed with a geographic information system (GIS) to enhance the functionality of i-Tree Eco (i-Tree, 2011). With the developed system, temperature, leaf area index (LAI) and air pollutant concentration in a spatially distributed form can be estimated, and based on these and other input variables, dry...

The role of submerged trees in the early development of fishes in a Neotropical reservoir.

PubMed

Gogola, T M; Daga, P S; Gubiani, É A; da Silva, P L R; Sanches, P V

2016-07-01

It was hypothesized that the structural heterogeneity provided by submerged trees positively favours the spatial distribution of fish abundance at early stages of development in an area under the influence of a Neotropical reservoir in the Paraná River basin. The distribution at early stages of development of the most abundant species was evaluated. To remove any possible confounding effect related to local environmental variables, changes in these were also evaluated. Sampling was carried out at sites with and without submerged trees. Among all individuals sampled, 96·1% were classified as larvae and 3·9% as juveniles. The area without submerged trees showed higher total abundance, but there were spatial differences in the distribution of early stage fishes. From the moment the larvae are able to swim actively, they search for sites with a complex structure. The results show that reaches with submerged trees play an important role in the early development of fishes in reservoirs, and, hence, the preservation of those trees is essential to maintain biodiversity in reservoirs. © 2016 The Fisheries Society of the British Isles.

Tree mortality rates and tree population projections in Baltimore, Maryland, USA

Treesearch

David J. Nowak; Miki Kuroda; Daniel E. Crane

2004-01-01

Based on re-measurements (1999 and 2001) of randomly-distributed permanent plots within the city boundaries of Baltimore, Maryland, trees are estimated to have an annual mortality rate of 6.6% with an overall annual net change in the number of live trees of -4.2%. Tree mortality rates were significantly different based on tree size, condition, species, and Land use....

Modeling the distribution of white spruce (Picea glauca) for Alaska with high accuracy: an open access role-model for predicting tree species in last remaining wilderness areas

Treesearch

Bettina Ohse; Falk Huettmann; Stefanie M. Ickert-Bond; Glenn P. Juday

2009-01-01

Most wilderness areas still lack accurate distribution information on tree species. We met this need with a predictive GIS modeling approach, using freely available digital data and computer programs to efficiently obtain high-quality species distribution maps. Here we present a digital map with the predicted distribution of white spruce (Picea glauca...

Student Interpretations of Phylogenetic Trees in an Introductory Biology Course

ERIC Educational Resources Information Center

Dees, Jonathan; Momsen, Jennifer L.; Niemi, Jarad; Montplaisir, Lisa

2014-01-01

Phylogenetic trees are widely used visual representations in the biological sciences and the most important visual representations in evolutionary biology. Therefore, phylogenetic trees have also become an important component of biology education. We sought to characterize reasoning used by introductory biology students in interpreting taxa…

77 FR 42694 - Helena National Forest, Montana, Telegraph Vegetation Project

Federal Register 2010, 2011, 2012, 2013, 2014

2012-07-20

... slashing generally small diameter trees followed by prescribed burning within the Jericho Mountain... dead and dying trees, promoting desirable regeneration, reducing fuels and the risk of wildfire, and... for Action Wide-scale tree mortality has occurred throughout the project area due to the mountain pine...

DNApod: DNA polymorphism annotation database from next-generation sequence read archives.

PubMed

Mochizuki, Takako; Tanizawa, Yasuhiro; Fujisawa, Takatomo; Ohta, Tazro; Nikoh, Naruo; Shimizu, Tokurou; Toyoda, Atsushi; Fujiyama, Asao; Kurata, Nori; Nagasaki, Hideki; Kaminuma, Eli; Nakamura, Yasukazu

2017-01-01

With the rapid advances in next-generation sequencing (NGS), datasets for DNA polymorphisms among various species and strains have been produced, stored, and distributed. However, reliability varies among these datasets because the experimental and analytical conditions used differ among assays. Furthermore, such datasets have been frequently distributed from the websites of individual sequencing projects. It is desirable to integrate DNA polymorphism data into one database featuring uniform quality control that is distributed from a single platform at a single place. DNA polymorphism annotation database (DNApod; http://tga.nig.ac.jp/dnapod/) is an integrated database that stores genome-wide DNA polymorphism datasets acquired under uniform analytical conditions, and this includes uniformity in the quality of the raw data, the reference genome version, and evaluation algorithms. DNApod genotypic data are re-analyzed whole-genome shotgun datasets extracted from sequence read archives, and DNApod distributes genome-wide DNA polymorphism datasets and known-gene annotations for each DNA polymorphism. This new database was developed for storing genome-wide DNA polymorphism datasets of plants, with crops being the first priority. Here, we describe our analyzed data for 679, 404, and 66 strains of rice, maize, and sorghum, respectively. The analytical methods are available as a DNApod workflow in an NGS annotation system of the DNA Data Bank of Japan and a virtual machine image. Furthermore, DNApod provides tables of links of identifiers between DNApod genotypic data and public phenotypic data. To advance the sharing of organism knowledge, DNApod offers basic and ubiquitous functions for multiple alignment and phylogenetic tree construction by using orthologous gene information.

DNApod: DNA polymorphism annotation database from next-generation sequence read archives

PubMed Central

Mochizuki, Takako; Tanizawa, Yasuhiro; Fujisawa, Takatomo; Ohta, Tazro; Nikoh, Naruo; Shimizu, Tokurou; Toyoda, Atsushi; Fujiyama, Asao; Kurata, Nori; Nagasaki, Hideki; Kaminuma, Eli; Nakamura, Yasukazu

2017-01-01

With the rapid advances in next-generation sequencing (NGS), datasets for DNA polymorphisms among various species and strains have been produced, stored, and distributed. However, reliability varies among these datasets because the experimental and analytical conditions used differ among assays. Furthermore, such datasets have been frequently distributed from the websites of individual sequencing projects. It is desirable to integrate DNA polymorphism data into one database featuring uniform quality control that is distributed from a single platform at a single place. DNA polymorphism annotation database (DNApod; http://tga.nig.ac.jp/dnapod/) is an integrated database that stores genome-wide DNA polymorphism datasets acquired under uniform analytical conditions, and this includes uniformity in the quality of the raw data, the reference genome version, and evaluation algorithms. DNApod genotypic data are re-analyzed whole-genome shotgun datasets extracted from sequence read archives, and DNApod distributes genome-wide DNA polymorphism datasets and known-gene annotations for each DNA polymorphism. This new database was developed for storing genome-wide DNA polymorphism datasets of plants, with crops being the first priority. Here, we describe our analyzed data for 679, 404, and 66 strains of rice, maize, and sorghum, respectively. The analytical methods are available as a DNApod workflow in an NGS annotation system of the DNA Data Bank of Japan and a virtual machine image. Furthermore, DNApod provides tables of links of identifiers between DNApod genotypic data and public phenotypic data. To advance the sharing of organism knowledge, DNApod offers basic and ubiquitous functions for multiple alignment and phylogenetic tree construction by using orthologous gene information. PMID:28234924

Fifty-year development of Douglas-fir stands planted at various spacings.

Treesearch

Donald L. Reukema

1979-01-01

A 51-yr record of observations in stands planted at six spacings, ranging from 4 to 12 ft, illustrates clearly the beneficial effects of wide initial spacing and the detrimental effects of carrying too many trees relative to the size to which they will be grown. Not only are trees larger, but yields per acre are greater at wide spacings.

Impacts of Population Structure and Analytical Models in Genome-Wide Association Studies of Complex Traits in Forest Trees: A Case Study in Eucalyptus globulus

PubMed Central

Garcia, Martín N.; Acuña, Cintia; Borralho, Nuno M. G.; Grattapaglia, Dario; Marcucci Poltri, Susana N.

2013-01-01

The promise of association genetics to identify genes or genomic regions controlling complex traits has generated a flurry of interest. Such phenotype-genotype associations could be useful to accelerate tree breeding cycles, increase precision and selection intensity for late expressing, low heritability traits. However, the prospects of association genetics in highly heterozygous undomesticated forest trees can be severely impacted by the presence of cryptic population and pedigree structure. To investigate how to better account for this, we compared the GLM and five combinations of the Unified Mixed Model (UMM) on data of a low-density genome-wide association study for growth and wood property traits carried out in a Eucalyptus globulus population (n = 303) with 7,680 Diversity Array Technology (DArT) markers. Model comparisons were based on the degree of deviation from the uniform distribution and estimates of the mean square differences between the observed and expected p-values of all significant marker-trait associations detected. Our analysis revealed the presence of population and family structure. There was not a single best model for all traits. Striking differences in detection power and accuracy were observed among the different models especially when population structure was not accounted for. The UMM method was the best and produced superior results when compared to GLM for all traits. Following stringent correction for false discoveries, 18 marker-trait associations were detected, 16 for tree diameter growth and two for lignin monomer composition (S∶G ratio), a key wood property trait. The two DArT markers associated with S∶G ratio on chromosome 10, physically map within 1 Mbp of the ferulate 5-hydroxylase (F5H) gene, providing a putative independent validation of this marker-trait association. This study details the merit of collectively integrate population structure and relatedness in association analyses in undomesticated, highly heterozygous forest trees, and provides additional insights into the nature of complex quantitative traits in Eucalyptus. PMID:24282578

A review on Balanites aegyptiaca Del (desert date): phytochemical constituents, traditional uses, and pharmacological activity

PubMed Central

Chothani, Daya L.; Vaghasiya, H. U.

2011-01-01

Balanites aegyptiaca Del. (Zygophyllaceae), known as ‘desert date,’ is spiny shrub or tree up to l0 m tall, widely distributed in dry land areas of Africa and South Asia. It is traditionally used in treatment of various ailments i.e. jaundice, intestinal worm infection, wounds, malaria, syphilis, epilepsy, dysentery, constipation, diarrhea, hemorrhoid, stomach aches, asthma, and fever. It contains protein, lipid, carbohydrate, alkaloid, saponin, flavonoid, and organic acid. Present review summarizes the traditional claims, phytochemistry, and pharmacology of B. aegyptiaca Del reported in scientific literature. PMID:22096319

Generalized Processing Tree Models: Jointly Modeling Discrete and Continuous Variables.

PubMed

Heck, Daniel W; Erdfelder, Edgar; Kieslich, Pascal J

2018-05-24

Multinomial processing tree models assume that discrete cognitive states determine observed response frequencies. Generalized processing tree (GPT) models extend this conceptual framework to continuous variables such as response times, process-tracing measures, or neurophysiological variables. GPT models assume finite-mixture distributions, with weights determined by a processing tree structure, and continuous components modeled by parameterized distributions such as Gaussians with separate or shared parameters across states. We discuss identifiability, parameter estimation, model testing, a modeling syntax, and the improved precision of GPT estimates. Finally, a GPT version of the feature comparison model of semantic categorization is applied to computer-mouse trajectories.

36 CFR 230.3 - National program administration.

Code of Federal Regulations, 2011 CFR

2011-07-01

... implementation of such policy and procedure over the life of the Program. (b) The Chief shall annually distribute... State foresters. (c) Tree planting, tree maintenance, and tree improvement are national priorities for...

36 CFR 230.3 - National program administration.

Code of Federal Regulations, 2010 CFR

2010-07-01

... implementation of such policy and procedure over the life of the Program. (b) The Chief shall annually distribute... State foresters. (c) Tree planting, tree maintenance, and tree improvement are national priorities for...

Tree growth and management in Ugandan agroforestry systems: effects of root pruning on tree growth and crop yield.

PubMed

Wajja-Musukwe, Tellie-Nelson; Wilson, Julia; Sprent, Janet I; Ong, Chin K; Deans, J Douglas; Okorio, John

2008-02-01

Tree root pruning is a potential tool for managing belowground competition when trees and crops are grown together in agroforestry systems. We investigated the effects of tree root pruning on shoot growth and root distribution of Alnus acuminata (H.B. & K.), Casuarina equisetifolia L., Grevillea robusta A. Cunn. ex R. Br., Maesopsis eminii Engl. and Markhamia lutea (Benth.) K. Schum. and on yield of adjacent crops in sub-humid Uganda. The trees were 3 years old at the commencement of the study, and most species were competing strongly with crops. Tree roots were pruned 41 months after planting by cutting and back-filling a trench to a depth of 0.3 m, at a distance of 0.3 m from the trees, on one side of the tree row. The trench was reopened and roots recut at 50 and 62 months after planting. We assessed the effects on tree growth and root distribution over a 3 year period, and crop yield after the third root pruning at 62 months. Overall, root pruning had only a slight effect on aboveground tree growth: height growth was unaffected and diameter growth was reduced by only 4%. A substantial amount of root regrowth was observed by 11 months after pruning. Tree species varied in the number and distribution of roots, and C. equisetifolia and M. lutea had considerably more roots per unit of trunk volume than the other species, especially in the surface soil layers. Casuarina equisetifolia and M. eminii were the tree species most competitive with crops and G. robusta and M. lutea the least competitive. Crop yield data provided strong evidence of the redistribution of root activity following root pruning, with competition increasing on the unpruned side of tree rows. Thus, one-sided root pruning will be useful in only a few circumstances.

A scaling law derived from optimal dendritic wiring

PubMed Central

Cuntz, Hermann; Mathy, Alexandre; Häusser, Michael

2012-01-01

The wide diversity of dendritic trees is one of the most striking features of neural circuits. Here we develop a general quantitative theory relating the total length of dendritic wiring to the number of branch points and synapses. We show that optimal wiring predicts a 2/3 power law between these measures. We demonstrate that the theory is consistent with data from a wide variety of neurons across many different species and helps define the computational compartments in dendritic trees. Our results imply fundamentally distinct design principles for dendritic arbors compared with vascular, bronchial, and botanical trees. PMID:22715290

Environmental stress and whole-tree physiology

Treesearch

Peter L. Jr. Lorio

1993-01-01

Interactions among bark beetles, pathogens, and conifers constitute a triangle. Another triangle of interactions exist among the invading organism (bark beetles and pathogens), the trees, and the environment. How important, variable or constant, simple or complex, is the role of trees in these triangles? Understanding the wide range of interactions that take place...

Structural Equation Model Trees

ERIC Educational Resources Information Center

Brandmaier, Andreas M.; von Oertzen, Timo; McArdle, John J.; Lindenberger, Ulman

2013-01-01

In the behavioral and social sciences, structural equation models (SEMs) have become widely accepted as a modeling tool for the relation between latent and observed variables. SEMs can be seen as a unification of several multivariate analysis techniques. SEM Trees combine the strengths of SEMs and the decision tree paradigm by building tree…

Slow release fertilizers in bareroot nurseries

Treesearch

J. G. Iyer; J. Dobrahner; B. Lowery; J. Vandettey

2002-01-01

Maintaining sufficient soil fertility in tree nurseries for good tree growth can be implemented by annually performing soil analyses and following a fertility maintenance program. Percentage recovery by trees of fertilizer applied indicates efficiency of fertilizer use. There is a wide variation in the recovery among the various fertilizer elements. Our research has...

Considerations for evaluating controlled exposure studies of tree seedlings.

Treesearch

E. Charles Peterson; A. Robert Mickler

1994-01-01

Tree seedling exposure studies, covering a wide range of experimental conditions in pollutant treatments, species, facilities, and exposure regimes, have been conducted during the past several years to determine acute effects and relative sensitivity of tree species in response to simulated acid precipitation and gaseous pollutants. Because of tile difficulties...

Dependency Tree Annotation Software

DTIC Science & Technology

2015-11-01

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

Three-dimensional feature extraction and geometric mappings for improved parameter estimation in forested terrain using airborne LiDAR data

NASA Astrophysics Data System (ADS)

Lee, Heezin

Scanning laser ranging technology is well suited for measuring point-to-point distances because of its ability to generate small beam divergences. As a result, many of the laser pulses emitted from airborne light detection and ranging (LiDAR) systems are able to reach the ground underneath tree canopies through small (10 cm scale) gaps in the foliage. Using high pulse rate lasers and fast optical scanners, airborne LiDAR systems can provide both high spatial resolution and canopy penetration, and these data have become more widely available in recent years for use in environmental and forestry applications. The small-footprint, discrete-return Airborne Laser Swath Mapping (ALSM) system at the University of Florida (UF) is used to directly measure ground surface elevations and the three-dimensional (3D) distribution of the vegetative material above the soil surface. Field of view geometric mappings are explored to find optical gaps inside forests. First, a method is developed to detect walking trails in natural forests that are obscured from above by the canopy. Several features are derived from the ALSM data and used to constrain the search space and infer the location of trails. Second, a robust and simple procedure for estimating intercepted photosynthetically active radiation (IPAR), which is an important measure of forest timber productivity and of daylight visibility in forested terrain, is presented. Simple scope functions that isolate the relevant LiDAR reflections between observer locations and the sun are defined and shown to give good agreement between the LiDAR-derived estimates and values of IPAR measured in situ. A conical scope function with an angular divergence from the centerline of +/-7° provided the best agreement with the in situ measurements. This scope function yielded remarkably consistent IPAR estimates for different pine species and growing conditions. The developed idea could be extended, through potential future work, to characterize the spatial distribution of attenuation of GPS (L-band) microwave signals and of detectability from the sky for military personnel operating in forested terrain. Measuring individual trees can provide valuable information about forests, and airborne LiDAR sensors have been recently used to identify individual trees and measure structural tree parameters. Past results, however, have been mixed because of reliance on interpolated (image) versions of the LiDAR measurements and search methods that do not adapt to variations in canopies. In this work, an adaptive clustering method is developed using 3D airborne LiDAR data acquired over two distinctly different managed pine forests in North-Central Florida, USA. A critical issue in isolating individual trees is determining the appropriate size of the moving window (search radius) when locating seed points. The proposed approach works directly on the 3D "cloud" of LiDAR points and adapts to irregular canopy sizes. The region growing step yields collectively exhaustive sets in an initial segmentation of tree canopies. An agglomerative clustering step is then used to merge clusters that represent parts of whole canopies using the locally varying height distribution. The overall tree detection accuracy achieved is 95.1% with no significant bias. The tree detection enables subsequent estimation of tree height and vertical crown length to an accuracy of better than 0.8 m and 1.5 m, respectively. Lastly, a compact representation of the different geometric characteristics of the segmented LiDAR points is introduced using spin images as a new tool that can potentially help tree detection in complex natural forests.

User’s guide to the collection and analysis of tree cores to assess the distribution of subsurface volatile organic compounds

USGS Publications Warehouse

Vroblesky, Don A.

2008-01-01

Analysis of the volatile organic compound content of tree cores is an inexpensive, rapid, simple approach to examining the distribution of subsurface volatile organic compound contaminants. The method has been shown to detect several volatile petroleum hydrocarbons and chlorinated aliphatic compounds associated with vapor intrusion and ground-water contamination. Tree cores, which are approximately 3 inches long, are obtained by using an increment borer. The cores are placed in vials and sealed. After a period of equilibration, the cores can be analyzed by headspace analysis gas chromatography. Because the roots are exposed to volatile organic compound contamination in the unsaturated zone or shallow ground water, the volatile organic compound concentrations in the tree cores are an indication of the presence of subsurface volatile organic compound contamination. Thus, tree coring can be used to detect and map subsurface volatile organic compound contamination. For comparison of tree-core data at a particular site, it is important to maintain consistent methods for all aspects of tree-core collection, handling, and analysis. Factors affecting the volatile organic compound concentrations in tree cores include the type of volatile organic compound, the tree species, the rooting depth, ground-water chemistry, the depth to the contaminated horizon, concentration differences around the trunk related to variations in the distribution of subsurface volatile organic compounds, concentration differences with depth of coring related to volatilization loss through the bark and possibly other unknown factors, dilution by rain, seasonal influences, sorption, vapor-exchange rates, and within-tree volatile organic compound degradation.

Toward the modeling of mucus draining from the human lung: role of the geometry of the airway tree

NASA Astrophysics Data System (ADS)

Mauroy, Benjamin; Fausser, Christian; Pelca, Dominique; Merckx, Jacques; Flaud, Patrice

2011-10-01

Mucociliary clearance and cough are the two main natural mucus draining methods in the bronchial tree. If they are affected by a pathology, they can become insufficient or even ineffective, then therapeutic draining of mucus plays a critical role to keep mucus levels in the lungs acceptable. The manipulations of physical therapists are known to be very efficient clinically but they are mostly empirical since the biophysical mechanisms involved in these manipulations have never been studied. We develop in this work a model of mucus clearance in idealized rigid human bronchial trees and focus our study on the interaction between (1) tree geometry, (2) mucus physical properties and (3) amplitude of flow rate in the tree. The mucus is considered as a Bingham fluid (gel-like) which is moved upward in the tree thanks to its viscous interaction with air flow. Our studies point out the important roles played both by the geometry and by the physical properties of mucus (yield stress and viscosity). More particularly, the yield stress has to be overcome to make mucus flow. Air flow rate and yield stress determine the maximal possible mucus thickness in each branch of the tree at equilibrium. This forms a specific distribution of mucus in the tree whose characteristics are strongly related to the multi-scaled structure of the tree. The behavior of any mucus distribution is then dependent on this distribution. Finally, our results indicate that increasing air flow rates ought to be more efficient to drain mucus out of the bronchial tree while minimizing patient discomfort.

Indirect effects of ecosystem engineering combine with consumer behaviour to determine the spatial distribution of herbivory.

PubMed

Griffen, Blaine D; Riley, Megan E; Cannizzo, Zachary J; Feller, Ilka C

2017-10-01

Ecosystem engineers alter environments by creating, modifying or destroying habitats. The indirect impacts of ecosystem engineering on trophic interactions should depend on the combination of the spatial distribution of engineered structures and the foraging behaviour of consumers that use these structures as refuges. In this study, we assessed the indirect effects of ecosystem engineering by a wood-boring beetle in a neotropical mangrove forest system. We identified herbivory patterns in a dwarf mangrove forest on the archipelago of Twin Cays, Belize. Past wood-boring activity impacted more than one-third of trees through the creation of tree holes that are now used, presumably as predation or thermal refuge, by the herbivorous mangrove tree crab Aratus pisonii. The presence of these refuges had a significant impact on plant-animal interactions; herbivory was more than fivefold higher on trees influenced by tree holes relative to those that were completely isolated from these refuges. Additionally, herbivory decreased exponentially with increasing distance from tree holes. We use individual-based simulation modelling to demonstrate that the creation of these herbivory patterns depends on a combination of the use of engineered tree holes for refuge by tree crabs, and the use of two behaviour patterns in this species-site fidelity to a "home tree," and more frequent foraging near their home tree. We demonstrate that understanding the spatial distribution of herbivory in this system depends on combining both the use of ecosystem engineering structures with individual behavioural patterns of herbivores. © 2017 The Authors. Journal of Animal Ecology © 2017 British Ecological Society.

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

NASA Astrophysics Data System (ADS)

Schueler, Silvio; Lackner, Magdalena; Chakraborty, Debojyoti

2017-04-01

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

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

PubMed

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

2010-05-01

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

A Comparison of Two Tree Construction Methods for Obtaining Proximity Measures among Words. Number 47.

ERIC Educational Resources Information Center

Rapoport, Amnon

The prediction that two different methods of constructing linear, tree graphs will yield the same formal structure of semantic space and measurement of word proximity was tested by comparing the distribution of node degree, the distribution of the number of pairs of nodes connected y times, and the distribution of adjective degree in trees…

Spatial distribution and succession of epiphytes on Tsuga heterophylla (western hemlock) in an old-growth Douglas-fir forest

Treesearch

Betsy Lyons; Nalini M. Nadkarni; Malcolm P. North

2000-01-01

We examined the distribution and abundance of nonvascular epiphytes on western hemlock trees in an oldgrowth coniferous forest focusing on patterns of epiphyte distribution at different spatial scales, epiphyte abundance amongst trees differing in size, and crown structures associated with epiphyte abundance. Total epiphyte cover was greatest in four canopy...

Factors influencing non-native tree species distribution in urban landscapes

Treesearch

Wayne C. Zipperer

2010-01-01

Non-native species are presumed to be pervasive across the urban landscape. Yet, we actually know very little about their actual distribution. For this study, vegetation plot data from Syracuse, NY and Baltimore, MD were used to examine non-native tree species distribution in urban landscapes. Data were collected from remnant and emergent forest patches on upland sites...

Equations for estimating loblolly pine branch and foliage weight and surface area distributions

Treesearch

V. Clark Baldwin; Kelly D. Peterson; Harold E. Burkhatt; Ralph L. Amateis; Phillip M. Dougherty

1996-01-01

Equations to predict foliage weight and surface area, and their vertical and horizontal distributions, within the crowns of unthinned loblolly pine (Pinus tueduL.) trees are presented. A right-truncated Weibull function was used for describing vertical foliage distributions. This function ensures that all of the foliage located between the tree tip and the foliage base...

Atlas of current and potential future distributions of common trees of the eastern United States

Treesearch

Louis R. Iverson; Anantha M. Prasad; Betsy J. Hale; Elaine Kennedy Sutherland

1999-01-01

This atlas documents the current and possible future distribution of 80 common tree species in the Eastern United States and gives detailed information on environmental characteristics defining these distributions. Also included are outlines of life history characteristics and summary statistics for these species. Much of the data are derived from Forest Inventory and...

Proceedings of the Chornobyl phytoremediation and biomass energy conversion workshop (in English;Russian)

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

Hartley, J.; Tokarevsky, V.

1998-06-01

Many concepts, systems, technical approaches, technologies, ideas, agreements, and disagreements were vigorously discussed during the course of the 2-day workshop. The workshop was successful in generating intensive discussions on the merits of the proposed concept that includes removal of radionuclides by plants and trees (phytoremediation) to clean up soil in the Chornobyl Exclusion Zone (CEZ), use of the resultant biomass (plants and trees) to generate electrical power, and incorporation of ash in concrete casks to be used as storage containers in a licensed repository for low-level waste. Twelve years after the Chornobyl Nuclear Power Plant (ChNPP) Unit 4 accident, whichmore » occurred on April 26, 1986, the primary 4radioactive contamination of concern is from radioactive cesium ({sup 137}Cs) and strontium ({sup 90}Sr). The {sup 137}Cs and {sup 90}Sr were widely distributed throughout the CEZ. The attendees from Ukraine, Russia, Belarus, Denmark and the US provided information, discussed and debated the following issues considerably: distribution and characteristics of radionuclides in CEZ; efficacy of using trees and plants to extract radioactive cesium (Cs) and strontium (Sr) from contaminated soil; selection of energy conversion systems and technologies; necessary infrastructure for biomass harvesting, handling, transportation, and energy conversion; radioactive ash and emission management; occupational health and safety concerns for the personnel involved in this work; and economics. The attendees concluded that the overall concept has technical and possibly economic merits. However, many issues (technical, economic, risk) remain to be resolved before a viable commercial-scale implementation could take place.« less

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

Convergence of tree water use within an arid-zone woodland.

PubMed

O'Grady, A P; Cook, P G; Eamus, D; Duguid, A; Wischusen, J D H; Fass, T; Worldege, D

2009-07-01

We examined spatial and temporal patterns of tree water use and aspects of hydraulic architecture in four common tree species of central Australia--Corymbia opaca, Eucalyptus victrix, E. camaldulensis and Acacia aneura--to better understand processes that constrain water use in these environments. These four widely distributed species occupy contrasting niches within arid environments including woodlands, floodplains and riparian environments. Measurements of tree water use and leaf water potential were made at two sites with contrasting water table depths during a period of high soil water availability following summer rainfall and during a period of low soil water availability following 7 months of very little rainfall during 2007. There were significant differences in specific leaf area (SLA), sapwood area to leaf area ratios and sapwood density between species. Sapwood to leaf area ratio increased in all species from April to November indicating a decline in leaf area per unit sapwood area. Despite very little rainfall in the intervening period three species, C. opaca, E. victrix and E. camaldulensis maintained high leaf water potentials and tree water use during both periods. In contrast, leaf water potential and water use in the A. aneura were significantly reduced in November compared to April. Despite contrasting morphology and water use strategies, we observed considerable convergence in water use among the four species. Wood density in particular was strongly related to SLA, sapwood area to leaf area ratios and soil to leaf conductance, with all four species converging on a common relationship. Identifying convergence in hydraulic traits can potentially provide powerful tools for scaling physiological processes in natural ecosystems.

Concentrations and distributions of polybrominated diphenyl ethers and novel brominated flame retardants in tree bark and human hair from Yunnan Province, China.

PubMed

Yuan, Haodong; Jin, Jun; Bai, Yao; Li, Qiuxu; Wang, Ying; Hu, Jicheng

2016-07-01

The concentrations and distributions of polybrominated diphenyl ethers (PBDEs) and novel brominated flame retardants (NBFRs) in tree bark and hair samples from the same area in Yunnan Province, China, were determined. The total PBDE and NBFR concentrations in the tree bark samples were 3.8 ng/g lipid weight to 91 ng/g lipid weight and 0.23 ng/g lipid weight to 5.0 ng/g lipid weight, respectively. The total PBDE and NBFR concentrations in the hair samples were 2.1 ng/g dry weight to 14 ng/g dry weight and 0.083 ng/g dry weight to 0.29 ng/g dry weight, respectively. Decabromodiphenyl ether had similar distributions in the tree bark and hair samples, but other PBDE congeners and NBFRs had different distributions in the tree bark and hair samples. External exposure was found to be mainly responsible for the total PBDE and pentabromotoluene concentrations in hair, but both external and internal exposure were responsible for the pentabromophenyl and hexabromobenzene concentrations in hair. Copyright © 2016 Elsevier Ltd. All rights reserved.

Atlas of United States Trees, Volume 2: Alaska Trees and Common Shrubs.

ERIC Educational Resources Information Center

Viereck, Leslie A.; Little, Elbert L., Jr.

This volume is the second in a series of atlases describing the natural distribution or range of native tree species in the United States. The 82 species maps include 32 of trees in Alaska, 6 of shrubs rarely reaching tree size, and 44 more of common shrubs. More than 20 additional maps summarize environmental factors and furnish general…

Early indicators of change: divergent climate envelopes between tree life stages imply range shifts in the western United States

USGS Publications Warehouse

Bell, David M.; Bradford, John B.; Lauenroth, William K.

2014-01-01

Our results indicated that climate-induced contractions and shifts in seedling distribution in response to recent change are already under way and are particularly severe in montane tree species. While adult trees may persist for hundreds of years without significant regeneration, tree species ranges will eventually contract where tree regeneration fails.

Environmental distribution of Cryptococcus neoformans and C. gattii around the Mediterranean basin.

PubMed

Cogliati, Massimo; D'Amicis, Roberta; Zani, Alberto; Montagna, Maria Teresa; Caggiano, Giuseppina; De Giglio, Osvalda; Balbino, Stella; De Donno, Antonella; Serio, Francesca; Susever, Serdar; Ergin, Cagri; Velegraki, Aristea; Ellabib, Mohamed S; Nardoni, Simona; Macci, Cristina; Oliveri, Salvatore; Trovato, Laura; Dipineto, Ludovico; Rickerts, Volker; McCormick-Smith, Ilka; Akcaglar, Sevim; Tore, Okan; Mlinaric-Missoni, Emilija; Bertout, Sebastien; Mallié, Michele; Martins, Maria da Luz; Vencà, Ana C F; Vieira, Maria L; Sampaio, Ana C; Pereira, Cheila; Criseo, Giuseppe; Romeo, Orazio; Ranque, Stéphane; Al-Yasiri, Mohammed H Y; Kaya, Meltem; Cerikcioglu, Nilgun; Marchese, Anna; Vezzulli, Luigi; Ilkit, Macit; Desnos-Ollivier, Marie; Pasquale, Vincenzo; Korem, Maya; Polacheck, Itzhack; Scopa, Antonio; Meyer, Wieland; Ferreira-Paim, Kennio; Hagen, Ferry; Theelen, Bart; Boekhout, Teun; Lockhart, Shawn R; Tintelnot, Kathrin; Tortorano, Anna Maria; Dromer, Françoise; Varma, Ashok; Kwon-Chung, Kyung J; Inácio, Joäo; Alonso, Beatriz; Colom, Maria F

2016-06-01

In order to elucidate the distribution of Cryptococcus neoformans and C. gattii in the Mediterranean basin, an extensive environmental survey was carried out during 2012-2015. A total of 302 sites located in 12 countries were sampled, 6436 samples from 3765 trees were collected and 5% of trees were found to be colonized by cryptococcal yeasts. Cryptococcus neoformans was isolated from 177 trees and C. gattii from 13. Cryptococcus neoformans colonized 27% of Ceratonia, 10% of Olea, Platanus and Prunus trees and a lower percentage of other tree genera. The 13 C. gattii isolates were collected from five Eucalyptus, four Ceratonia, two Pinus and two Olea trees. Cryptococcus neoformans was distributed all around the Mediterranean basin, whereas C. gattii was isolated in Greece, Southern Italy and Spain, in agreement with previous findings from both clinical and environmental sources. Among C. neoformans isolates, VNI was the prevalent molecular type but VNII, VNIV and VNIII hybrid strains were also isolated. With the exception of a single VGIV isolate, all C. gattii isolates were VGI. The results confirmed the presence of both Cryptococcus species in the Mediterranean environment, and showed that both carob and olive trees represent an important niche for these yeasts. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Ailanthus, tree-of-heaven update, a northeast regional biological control project

Treesearch

Scott M. Salom; Loke T. Kok; Nathan Herrick; Tom McAvoy; Donald Davis; Mark Schall; Matt Kasson; Du Yu-Zhou; Ji Hailong; He Xiao; Richard Reardon

2009-01-01

The tree-of-heaven (TOH), Ailanthus altissima (Mill.) Swingle (Sapindales: Simaroubaceae), is an invasive weed tree distributed throughout most of the continental United States. It is a hardy pioneer species that...

Origin and diversification of Hibiscus glaber, species endemic to the oceanic Bonin Islands, revealed by chloroplast DNA polymorphism.

PubMed

Takayama, Koji; Ohi-Toma, Tetsuo; Kudoh, Hiroshi; Kato, Hidetoshi

2005-04-01

Abstract Two woody Hibiscus species co-occur in the Bonin Islands of the northwestern Pacific Ocean: Hibiscus glaber Matsum. is endemic to the islands, and its putative ancestral species, Hibiscus tiliaceus L., is widely distributed in coastal areas of the tropics and subtropics. To infer isolating mechanisms that led to speciation of H. glaber and the processes that resulted in co-occurrence of the two closely related species on the Bonin Islands, we conducted molecular phylogenetic analyses on chloroplast DNA (cpDNA) sequences. Materials collected from a wide area of the Pacific and Indian Oceans were used, and two closely related species, Hibiscus hamabo Siebold Zucc. and Hibiscus macrophyllus Roxb., were also included in the analyses. The constructed tree suggested that H. glaber has been derived from H. tiliaceus, and that most of the modern Bonin populations of H. tiliaceus did not share most recent ancestry with H. glaber. Geographic isolation appears to be the most important mechanism in the speciation of H. glaber. The co-occurrence of the two species can be attributed to multiple migrations of different lineages into the islands. While a wide and overlapping geographical distribution of haplotypes was found in H. tiliaceus, localized geographical distribution of haplotypes was detected in H. glaber. It is hypothesized that a shift to inland habitats may have affected the mode of seed dispersal from ocean currents to gravity and hence resulted in geographical structuring of H. glaber haplotypes.

Difficulties with estimating city-wide urban forest cover change from national, remotely-sensed tree canopy maps

Treesearch

Jeffrey T. Walton

2008-01-01

Two datasets of percent urban tree canopy cover were compared. The first dataset was based on a 1991 AVHRR forest density map. The second was the US Geological Survey's National Land Cover Database (NLCD) 2001 sub-pixel tree canopy. A comparison of these two tree canopy layers was conducted in 36 census designated places of western New York State. Reference data...

Relationship between Tree Value, Diameter, and Age in High-Quality Sugar Maple (Acer saccharum) on the Menominee Reservation, Wisconsin

Treesearch

Daniel C. Dey; John Dwyer; Jan Wiedenbeck

2017-01-01

Guidelines for managing sugar maple-dominated forests by the single-tree selection method are well established and widely adopted. The forests of the Menominee Tribe in Wisconsin provide an opportunity to validate current guidelines by testing tree value and size/age relationships in forests that have substantially older and larger high-quality trees than can be found...

Changes in the distribution of radiocesium in the wood of Japanese cedar trees from 2011 to 2013.

PubMed

Ogawa, Hideki; Hirano, Yurika; Igei, Shigemitsu; Yokota, Kahori; Arai, Shio; Ito, Hirohisa; Kumata, Atsushi; Yoshida, Hirohisa

2016-09-01

The changes in the distribution of (137)Cs in the wood of Japanese cedar (Cryptomeria japonica) trunks within three years after the Fukushima Dai-ichi Nuclear Power Plant (FDNP) accident in 2011 were investigated. Thirteen trees were felled to collect samples at 6 forests in 2 regions of the Fukushima prefecture. The radial distribution of (137)Cs in the wood was measured at different heights. Profiles of (137)Cs distribution in the wood changed considerably from 2011 to 2013, and the process of (137)Cs distribution change in the wood was clarified. From 2011 to 2012, the active transportation from sapwood to heartwood and the radial diffusion in heartwood proceeded quickly, and the radial (137)Cs distribution differed according to the vertical positon of trees. From 2012 to 2013, the vertical diffusion of (137)Cs from the treetop to the ground, probably caused by the gradient of (137)Cs concentration in the trunk, was observed. Eventually, the radial (137)Cs distributions were nearly identical at any vertical positions in 2013. Our results suggested that the active transportation from sapwood to heartwood and the vertical and radial diffusion in heartwood proceeded according to the vertical position of the tree and (137)Cs distribution in the wood approached the equilibrium state within three years after the accident. Copyright © 2016 Elsevier Ltd. All rights reserved.

A Well-Resolved Phylogeny of the Trees of Puerto Rico Based on DNA Barcode Sequence Data

PubMed Central

Muscarella, Robert; Uriarte, María; Erickson, David L.; Swenson, Nathan G.; Zimmerman, Jess K.; Kress, W. John

2014-01-01

Background The use of phylogenetic information in community ecology and conservation has grown in recent years. Two key issues for community phylogenetics studies, however, are (i) low terminal phylogenetic resolution and (ii) arbitrarily defined species pools. Methodology/principal findings We used three DNA barcodes (plastid DNA regions rbcL, matK, and trnH-psbA) to infer a phylogeny for 527 native and naturalized trees of Puerto Rico, representing the vast majority of the entire tree flora of the island (89%). We used a maximum likelihood (ML) approach with and without a constraint tree that enforced monophyly of recognized plant orders. Based on 50% consensus trees, the ML analyses improved phylogenetic resolution relative to a comparable phylogeny generated with Phylomatic (proportion of internal nodes resolved: constrained ML = 74%, unconstrained ML = 68%, Phylomatic = 52%). We quantified the phylogenetic composition of 15 protected forests in Puerto Rico using the constrained ML and Phylomatic phylogenies. We found some evidence that tree communities in areas of high water stress were relatively phylogenetically clustered. Reducing the scale at which the species pool was defined (from island to soil types) changed some of our results depending on which phylogeny (ML vs. Phylomatic) was used. Overall, the increased terminal resolution provided by the ML phylogeny revealed additional patterns that were not observed with a less-resolved phylogeny. Conclusions/significance With the DNA barcode phylogeny presented here (based on an island-wide species pool), we show that a more fully resolved phylogeny increases power to detect nonrandom patterns of community composition in several Puerto Rican tree communities. Especially if combined with additional information on species functional traits and geographic distributions, this phylogeny will (i) facilitate stronger inferences about the role of historical processes in governing the assembly and composition of Puerto Rican forests, (ii) provide insight into Caribbean biogeography, and (iii) aid in incorporating evolutionary history into conservation planning. PMID:25386879

A well-resolved phylogeny of the trees of Puerto Rico based on DNA barcode sequence data.

PubMed

Muscarella, Robert; Uriarte, María; Erickson, David L; Swenson, Nathan G; Zimmerman, Jess K; Kress, W John

2014-01-01

The use of phylogenetic information in community ecology and conservation has grown in recent years. Two key issues for community phylogenetics studies, however, are (i) low terminal phylogenetic resolution and (ii) arbitrarily defined species pools. We used three DNA barcodes (plastid DNA regions rbcL, matK, and trnH-psbA) to infer a phylogeny for 527 native and naturalized trees of Puerto Rico, representing the vast majority of the entire tree flora of the island (89%). We used a maximum likelihood (ML) approach with and without a constraint tree that enforced monophyly of recognized plant orders. Based on 50% consensus trees, the ML analyses improved phylogenetic resolution relative to a comparable phylogeny generated with Phylomatic (proportion of internal nodes resolved: constrained ML = 74%, unconstrained ML = 68%, Phylomatic = 52%). We quantified the phylogenetic composition of 15 protected forests in Puerto Rico using the constrained ML and Phylomatic phylogenies. We found some evidence that tree communities in areas of high water stress were relatively phylogenetically clustered. Reducing the scale at which the species pool was defined (from island to soil types) changed some of our results depending on which phylogeny (ML vs. Phylomatic) was used. Overall, the increased terminal resolution provided by the ML phylogeny revealed additional patterns that were not observed with a less-resolved phylogeny. With the DNA barcode phylogeny presented here (based on an island-wide species pool), we show that a more fully resolved phylogeny increases power to detect nonrandom patterns of community composition in several Puerto Rican tree communities. Especially if combined with additional information on species functional traits and geographic distributions, this phylogeny will (i) facilitate stronger inferences about the role of historical processes in governing the assembly and composition of Puerto Rican forests, (ii) provide insight into Caribbean biogeography, and (iii) aid in incorporating evolutionary history into conservation planning.

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...

The complete chloroplast genome sequence of tung tree (Vernicia fordii): Organization and phylogenetic relationships with other angiosperms

USDA-ARS?s Scientific Manuscript database

Tung tree (Vernicia fordii) is an economically important plant widely cultivated for industrial oil production in China. To better understand the molecular basis of tung tree chloroplasts, we sequenced and characterized the complete chloroplast genome. The chloroplast genome was 161,524 bp in length...

A Pollen Primer | NIH MedlinePlus the Magazine

MedlinePlus

... air filters (HEPA) or an electrostatic air filter. Tree Pollen Trees produce pollen earliest, as soon as January in ... distributed miles away. Fewer than 100 kinds of trees cause allergies. Some common ones are catalpa, elm, ...

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

A common thermal niche among geographically diverse populations of the widely distributed tree species Eucalyptus tereticornis: No evidence for adaptation to climate-of-origin.

PubMed

Drake, John E; Vårhammar, Angelica; Kumarathunge, Dushan; Medlyn, Belinda E; Pfautsch, Sebastian; Reich, Peter B; Tissue, David T; Ghannoum, Oula; Tjoelker, Mark G

2017-12-01

Impacts of climate warming depend on the degree to which plants are constrained by adaptation to their climate-of-origin or exhibit broad climatic suitability. We grew cool-origin, central and warm-origin provenances of Eucalyptus tereticornis in an array of common temperature environments from 18 to 35.5°C to determine if this widely distributed tree species consists of geographically contrasting provenances with differentiated and narrow thermal niches, or if provenances share a common thermal niche. The temperature responses of photosynthesis, respiration, and growth were equivalent across the three provenances, reflecting a common thermal niche despite a 2,200 km geographic distance and 13°C difference in mean annual temperature at seed origin. The temperature dependence of growth was primarily mediated by changes in leaf area per unit plant mass, photosynthesis, and whole-plant respiration. Thermal acclimation of leaf, stem, and root respiration moderated the increase in respiration with temperature, but acclimation was constrained at high temperatures. We conclude that this species consists of provenances that are not differentiated in their thermal responses, thus rejecting our hypothesis of adaptation to climate-of-origin and suggesting a shared thermal niche. In addition, growth declines with warming above the temperature optima were driven by reductions in whole-plant leaf area and increased respiratory carbon losses. The impacts of climate warming will nonetheless vary across the geographic range of this and other such species, depending primarily on each provenance's climate position on the temperature response curves for photosynthesis, respiration, and growth. © 2017 John Wiley & Sons Ltd.

Complex longitudinal diversification across South China and Vietnam in Stejneger's pit viper, Viridovipera stejnegeri (Schmidt, 1925) (Reptilia: Serpentes: Viperidae).

PubMed

Guo, Peng; Liu, Qin; Zhu, Fei; Zhong, Guang H; Chen, Xin; Myers, Edward A; Che, Jing; Zhang, Liang; Ziegler, Thomas; Nguyen, Truong Q; Burbrink, Frank T

2016-06-01

Viridovipera stejnegeri is one of the most common pit vipers in Asia, with a wide distribution in southern China and Vietnam. We investigated historical demography and explored how the environment and climatic factors have shaped genetic diversity and the evolutionary history of this venomous snake. A total of 171 samples from 47 localities were sequenced and analysed for two mitochondrial gene fragments and three nuclear genes. Gene trees reveal the existence of two well-supported clades (Southwest China and Southeast China) with seven distinct and strongly supported, geographically structured subclades within V. stejnegeri. Estimation of divergence time and ancestral area suggests that V. stejnegeri originated at ~6.0 Ma in the late Miocene on the Yunnan-Guizhou Plateau. The estimated date of origin and divergence of the island populations of Taiwan and Hainan closely matches the geological origin of the both islands. The mtDNA gene tree reveals the presence of west-east diversification in V. stejnegeri populations. Complex orogenesis and heterogeneous habitats, as well as climate-mediated habitat differentiation including glacial cycles, all have influenced population structure and the distribution of this taxon. The validity of V. stejnegeri chenbihuii is questionable, and this subspecies most probably represents an invalid taxon. © 2016 John Wiley & Sons Ltd.

Combining binary decision tree and geostatistical methods to estimate snow distribution in a mountain watershed

USGS Publications Warehouse

Balk, Benjamin; Elder, Kelly

2000-01-01

We model the spatial distribution of snow across a mountain basin using an approach that combines binary decision tree and geostatistical techniques. In April 1997 and 1998, intensive snow surveys were conducted in the 6.9‐km2 Loch Vale watershed (LVWS), Rocky Mountain National Park, Colorado. Binary decision trees were used to model the large‐scale variations in snow depth, while the small‐scale variations were modeled through kriging interpolation methods. Binary decision trees related depth to the physically based independent variables of net solar radiation, elevation, slope, and vegetation cover type. These decision tree models explained 54–65% of the observed variance in the depth measurements. The tree‐based modeled depths were then subtracted from the measured depths, and the resulting residuals were spatially distributed across LVWS through kriging techniques. The kriged estimates of the residuals were added to the tree‐based modeled depths to produce a combined depth model. The combined depth estimates explained 60–85% of the variance in the measured depths. Snow densities were mapped across LVWS using regression analysis. Snow‐covered area was determined from high‐resolution aerial photographs. Combining the modeled depths and densities with a snow cover map produced estimates of the spatial distribution of snow water equivalence (SWE). This modeling approach offers improvement over previous methods of estimating SWE distribution in mountain basins.

Evolutionary history of a vanishing radiation: isolation-dependent persistence and diversification in Pacific Island partulid tree snails.

PubMed

Lee, Taehwan; Li, Jingchun; Churchill, Celia K C; Foighil, Diarmaid Ó

2014-09-24

Partulid tree snails are endemic to Pacific high islands and have experienced extraordinary rates of extinction in recent decades. Although they collectively range across a 10,000 km swath of Oceania, half of the family's total species diversity is endemic to a single Eastern Pacific hot spot archipelago (the Society Islands) and all three partulid genera display highly distinctive distributions. Our goal was to investigate broad scale (range wide) and fine scale (within-Society Islands) molecular phylogenetic relationships of the two widespread genera, Partula and Samoana. What can such data tell us regarding the genesis of such divergent generic distribution patterns, and nominal species diversity levels across Oceania? Museum, captive (zoo) and contemporary field specimens enabled us to genotype 54 of the ~120 recognized species, including many extinct or extirpated taxa, from 14 archipelagoes. The genera Partula and Samoana are products of very distinct diversification processes. Originating at the western edge of the familial range, the derived genus Samoana is a relatively recent arrival in the far eastern archipelagoes (Society, Austral, Marquesas) where it exhibits a stepping-stone phylogenetic pattern and has proven adept at both intra-and inter- archipelago colonization. The pronounced east-west geographic disjunction exhibited by the genus Partula stems from a much older long-distance dispersal event and its high taxonomic diversity in the Society Islands is a product of a long history of within-archipelago diversification. The central importance of isolation for partulid lineage persistence and diversification is evident in time-calibrated phylogenetic trees that show that remote archipelagoes least impacted by continental biotas bear the oldest clades and/or the most speciose radiations. In contemporary Oceania, that isolation is being progressively undermined and these tree snails are now directly exposed to introduced continental predators throughout the family's range. Persistence of partulids in the wild will require proactive exclusion of alien predators in at least some designated refuge islands.

A New Tool for Exploring Climate Change Induced Range Shifts of Conifer Species in China

PubMed Central

Kou, Xiaojun; Li, Qin; Beierkuhnlein, Carl; Zhao, Yiheng; Liu, Shirong

2014-01-01

It is inevitable that tree species will undergo considerable range shifts in response to anthropogenic induced climate change, even in the near future. Species Distribution Models (SDMs) are valuable tools in exploring general temporal trends and spatial patterns of potential range shifts. Understanding projections to future climate for tree species will facilitate policy making in forestry. Comparative studies for a large number of tree species require the availability of suitable and standardized indices. A crucial limitation when deriving such indices is the threshold problem in defining ranges, which has made interspecies comparison problematic until now. Here we propose a set of threshold-free indices, which measure range explosion (I), overlapping (O), and range center movement in three dimensions (Dx, Dy, Dz), based on fuzzy set theory (Fuzzy Set based Potential Range Shift Index, F-PRS Index). A graphical tool (PRS_Chart) was developed to visualize these indices. This technique was then applied to 46 Pinaceae species that are widely distributed and partly common in China. The spatial patterns of the modeling results were then statistically tested for significance. Results showed that range overlap was generally low; no trends in range size changes and longitudinal movements could be found, but northward and poleward movement trends were highly significant. Although range shifts seemed to exhibit huge interspecies variation, they were very consistent for certain climate change scenarios. Comparing the IPCC scenarios, we found that scenario A1B would lead to a larger extent of range shifts (less overlapping and more latitudinal movement) than the A2 and the B1 scenarios. It is expected that the newly developed standardized indices and the respective graphical tool will facilitate studies on PRS's for other tree species groups that are important in forestry as well, and thus support climate adaptive forest management. PMID:25268604

A new tool for exploring climate change induced range shifts of conifer species in China.

PubMed

Kou, Xiaojun; Li, Qin; Beierkuhnlein, Carl; Zhao, Yiheng; Liu, Shirong

2014-01-01

It is inevitable that tree species will undergo considerable range shifts in response to anthropogenic induced climate change, even in the near future. Species Distribution Models (SDMs) are valuable tools in exploring general temporal trends and spatial patterns of potential range shifts. Understanding projections to future climate for tree species will facilitate policy making in forestry. Comparative studies for a large number of tree species require the availability of suitable and standardized indices. A crucial limitation when deriving such indices is the threshold problem in defining ranges, which has made interspecies comparison problematic until now. Here we propose a set of threshold-free indices, which measure range explosion (I), overlapping (O), and range center movement in three dimensions (Dx, Dy, Dz), based on fuzzy set theory (Fuzzy Set based Potential Range Shift Index, F-PRS Index). A graphical tool (PRS_Chart) was developed to visualize these indices. This technique was then applied to 46 Pinaceae species that are widely distributed and partly common in China. The spatial patterns of the modeling results were then statistically tested for significance. Results showed that range overlap was generally low; no trends in range size changes and longitudinal movements could be found, but northward and poleward movement trends were highly significant. Although range shifts seemed to exhibit huge interspecies variation, they were very consistent for certain climate change scenarios. Comparing the IPCC scenarios, we found that scenario A1B would lead to a larger extent of range shifts (less overlapping and more latitudinal movement) than the A2 and the B1 scenarios. It is expected that the newly developed standardized indices and the respective graphical tool will facilitate studies on PRS's for other tree species groups that are important in forestry as well, and thus support climate adaptive forest management.

Metagenomic Signatures of Bacterial Adaptation to Life in the Phyllosphere of a Salt-Secreting Desert Tree.

PubMed

Finkel, Omri M; Delmont, Tom O; Post, Anton F; Belkin, Shimshon

2016-05-01

The leaves of Tamarix aphylla, a globally distributed, salt-secreting desert tree, are dotted with alkaline droplets of high salinity. To successfully inhabit these organic carbon-rich droplets, bacteria need to be adapted to multiple stress factors, including high salinity, high alkalinity, high UV radiation, and periodic desiccation. To identify genes that are important for survival in this harsh habitat, microbial community DNA was extracted from the leaf surfaces of 10 Tamarix aphylla trees along a 350-km longitudinal gradient. Shotgun metagenomic sequencing, contig assembly, and binning yielded 17 genome bins, six of which were >80% complete. These genomic bins, representing three phyla (Proteobacteria,Bacteroidetes, and Firmicutes), were closely related to halophilic and alkaliphilic taxa isolated from aquatic and soil environments. Comparison of these genomic bins to the genomes of their closest relatives revealed functional traits characteristic of bacterial populations inhabiting the Tamarix phyllosphere, independent of their taxonomic affiliation. These functions, most notably light-sensing genes, are postulated to represent important adaptations toward colonization of this habitat. Plant leaves are an extensive and diverse microbial habitat, forming the main interface between solar energy and the terrestrial biosphere. There are hundreds of thousands of plant species in the world, exhibiting a wide range of morphologies, leaf surface chemistries, and ecological ranges. In order to understand the core adaptations of microorganisms to this habitat, it is important to diversify the type of leaves that are studied. This study provides an analysis of the genomic content of the most abundant bacterial inhabitants of the globally distributed, salt-secreting desert tree Tamarix aphylla Draft genomes of these bacteria were assembled, using the culture-independent technique of assembly and binning of metagenomic data. Analysis of the genomes reveals traits that are important for survival in this habitat, most notably, light-sensing and light utilization genes. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Tree species traits influence soil physical, chemical, and biological properties in high elevation forests.

PubMed

Ayres, Edward; Steltzer, Heidi; Berg, Sarah; Wallenstein, Matthew D; Simmons, Breana L; Wall, Diana H

2009-06-18

Previous studies have shown that plants often have species-specific effects on soil properties. In high elevation forests in the Southern Rocky Mountains, North America, areas that are dominated by a single tree species are often adjacent to areas dominated by another tree species. Here, we assessed soil properties beneath adjacent stands of trembling aspen, lodgepole pine, and Engelmann spruce, which are dominant tree species in this region and are distributed widely in North America. We hypothesized that soil properties would differ among stands dominated by different tree species and expected that aspen stands would have higher soil temperatures due to their open structure, which, combined with higher quality litter, would result in increased soil respiration rates, nitrogen availability, and microbial biomass, and differences in soil faunal community composition. We assessed soil physical, chemical, and biological properties at four sites where stands of aspen, pine, and spruce occurred in close proximity to one-another in the San Juan Mountains, Colorado. Leaf litter quality differed among the tree species, with the highest nitrogen (N) concentration and lowest lignin:N in aspen litter. Nitrogen concentration was similar in pine and spruce litter, but lignin:N was highest in pine litter. Soil temperature and moisture were highest in aspen stands, which, in combination with higher litter quality, probably contributed to faster soil respiration rates from stands of aspen. Soil carbon and N content, ammonium concentration, and microbial biomass did not differ among tree species, but nitrate concentration was highest in aspen soil and lowest in spruce soil. In addition, soil fungal, bacterial, and nematode community composition and rotifer, collembolan, and mesostigmatid mite abundance differed among the tree species, while the total abundance of nematodes, tardigrades, oribatid mites, and prostigmatid mites did not. Although some soil characteristics were unaffected by tree species identity, our results clearly demonstrate that these dominant tree species are associated with soils that differ in several physical, chemical, and biotic properties. Ongoing environmental changes in this region, e.g. changes in fire regime, frequency of insect outbreaks, changes in precipitation patterns and snowpack, and land-use change, may alter the relative abundance of these tree species over coming decades, which in turn will likely alter the soils.

Local adaptation at the range peripheries of Sitka spruce.

PubMed

Mimura, M; Aitken, S N

2010-02-01

High-dispersal rates in heterogeneous environments and historical rapid range expansion can hamper local adaptation; however, we often see clinal variation in high-dispersal tree species. To understand the mechanisms of the species' distribution, we investigated local adaptation and adaptive plasticity in a range-wide context in Sitka spruce, a wind-pollinated tree species that has recently expanded its range after glaciations. Phenotypic traits were observed using growth chamber experiments that mimicked temperature and photoperiodic regimes from the limits of the species realized niche. Bud phenology exhibited parallel reaction norms among populations; however, putatively adaptive plasticity and strong divergent selection were seen in bud burst and bud set timing respectively. Natural selection appears to have favoured genotypes that maximize growth rate during available frost-free periods in each environment. We conclude that Sitka spruce has developed local adaptation and adaptive plasticity throughout its range in response to current climatic conditions despite generally high pollen flow and recent range expansion.

Performance of a cavity-method-based algorithm for the prize-collecting Steiner tree problem on graphs

NASA Astrophysics Data System (ADS)

Biazzo, Indaco; Braunstein, Alfredo; Zecchina, Riccardo

2012-08-01

We study the behavior of an algorithm derived from the cavity method for the prize-collecting steiner tree (PCST) problem on graphs. The algorithm is based on the zero temperature limit of the cavity equations and as such is formally simple (a fixed point equation resolved by iteration) and distributed (parallelizable). We provide a detailed comparison with state-of-the-art algorithms on a wide range of existing benchmarks, networks, and random graphs. Specifically, we consider an enhanced derivative of the Goemans-Williamson heuristics and the dhea solver, a branch and cut integer linear programming based approach. The comparison shows that the cavity algorithm outperforms the two algorithms in most large instances both in running time and quality of the solution. Finally we prove a few optimality properties of the solutions provided by our algorithm, including optimality under the two postprocessing procedures defined in the Goemans-Williamson derivative and global optimality in some limit cases.

Chemoprevention of Colorectal Cancer by Artocarpin, a Dietary Phytochemical from Artocarpus heterophyllus.

PubMed

Sun, Guochuan; Zheng, Zongping; Lee, Mee-Hyun; Xu, Yijuan; Kang, Soouk; Dong, Zigang; Wang, Mingfu; Gu, Zhennan; Li, Haitao; Chen, Wei

2017-05-03

Artocarpus heterophyllus is an evergreen tree distributed in tropical regions, and its fruit (jackfruit) is well-known as the world's largest tree-borne fruit. Although A. heterophyllus has been widely used in folk medicines against inflammation, its potential in cancer chemoprevention remains unclear. Herein we identified artocarpin from A. heterophyllus as a promising colorectal cancer chemopreventive agent by targeting Akt kinase. Phenotypically, artocarpin exhibited selective cytotoxicity against human colon cancer cells. Artocarpin impaired the anchorage-independent growth capability, suppressed colon cancer cell growth, and induced a G1 phase cell cycle arrest which was followed by apoptotic as well as autophagic cell death. Mechanistic studies revealed that artocarpin directly targeted Akt 1 and 2 kinase activity evidenced by in vitro kinase assay, ex vivo binding assay as well as Akt downstream cellular signal transduction. Importantly, oral administration of artocarpin attenuated colitis-associated colorectal tumorigenesis in mice. Taken together, artocarpin, a bioactive component of A. heterophyllus, might merit investigation as a potential colorectal cancer chemopreventive agent.

Guam's forest resources, 2002.

Treesearch

Joseph A. Donnegan; Sarah L. Butler; Walter Grabowiecki; Bruce A. Hiserote; David. Limtiaco

2004-01-01

The Forest Inventory and Analysis Program collected, analyzed, and summarized field data on 46 forested plots on the island of Guam. Estimates of forest area, tree stem volume and biomass, the numbers of trees, tree damages, and the distribution of tree sizes were summarized for this statistical sample. Detailed tables and graphical highlights provide a summary of Guam...

Palau's forest resources, 2003.

Treesearch

Joseph A. Donnegan; Sarah L. Butler; Olaf Kuegler; Brent J. Stroud; Bruce A. Hiserote; Kashgar. Rengulbai

2007-01-01

The Forest Inventory and Analysis Program collected, analyzed, and summarized field data on 54 forested plots on the islands in the Republic of Palau. Estimates of forest area, tree stem volume and biomass, the numbers of trees, tree damages, and the distribution of tree sizes were summarized for this statistical sample. Detailed tables and graphical highlights provide...

Placental Vascular Tree as Biomarker of Autism/ASD Risk

DTIC Science & Technology

2013-09-01

Autism /ASD Risk PRINCIPAL INVESTIGATOR: Carolyn M. Salafia, M.D., M.S...2010 – 14 August 2013 4. TITLE AND SUBTITLE 5a. CONTRACT NUMBER Placental Vascular Tree as Biomarker of Autism /ASD Risk...DISTRIBUTION / AVAILABILITY STATEMENT Approved for Public Release; Distribution Unlimited 13. SUPPLEMENTARY NOTES 14. ABSTRACT Autism Spectrum

Measurement variability error for estimates of volume change

Treesearch

James A. Westfall; Paul L. Patterson

2007-01-01

Using quality assurance data, measurement variability distributions were developed for attributes that affect tree volume prediction. Random deviations from the measurement variability distributions were applied to 19381 remeasured sample trees in Maine. The additional error due to measurement variation and measurement bias was estimated via a simulation study for...

How will climate change affect the potential distribution of Eurasian Tree Sparrows Passer montanus in North America?

USGS Publications Warehouse

Graham, Jim; Jarnevich, Catherine; Young, Nick; Newman, Greg; Stohlgren, Thomas

2011-01-01

Habitat suitability models have been used to predict the present and future potential distribution of a variety of species. Eurasian tree sparrows Passer montanus, native to Eurasia, have established populations in other parts of the world. In North America, their current distribution is limited to a relatively small region around its original introduction to St. Louis, Missouri. We combined data from the Global Biodiversity Information Facility with current and future climate data to create habitat suitability models using Maxent for this species. Under projected climate change scenarios, our models show that the distribution and range of the Eurasian tree sparrow could increase as far as the Pacific Northwest and Newfoundland. This is potentially important information for prioritizing the management and control of this non-native species.

Utilizing random forests imputation of forest plot data for landscape-level wildfire analyses

Treesearch

Karin L. Riley; Isaac C. Grenfell; Mark A. Finney; Nicholas L. Crookston

2014-01-01

Maps of the number, size, and species of trees in forests across the United States are desirable for a number of applications. For landscape-level fire and forest simulations that use the Forest Vegetation Simulator (FVS), a spatial tree-level dataset, or “tree list”, is a necessity. FVS is widely used at the stand level for simulating fire effects on tree mortality,...

Spatially Distributed Dendritic Resonance Selectively Filters Synaptic Input

PubMed Central

Segev, Idan; Shamma, Shihab

2014-01-01

An important task performed by a neuron is the selection of relevant inputs from among thousands of synapses impinging on the dendritic tree. Synaptic plasticity enables this by strenghtening a subset of synapses that are, presumably, functionally relevant to the neuron. A different selection mechanism exploits the resonance of the dendritic membranes to preferentially filter synaptic inputs based on their temporal rates. A widely held view is that a neuron has one resonant frequency and thus can pass through one rate. Here we demonstrate through mathematical analyses and numerical simulations that dendritic resonance is inevitably a spatially distributed property; and therefore the resonance frequency varies along the dendrites, and thus endows neurons with a powerful spatiotemporal selection mechanism that is sensitive both to the dendritic location and the temporal structure of the incoming synaptic inputs. PMID:25144440

Abundance and Size Distribution of Cavity Trees in Second-Growth and Old-Growth Central Hardwood Forests

Treesearch

Zhaofei Fan; Stephen R. Shifley; Martin A. Spetich; Frank R. Thompson III; David R. Larsen

2005-01-01

In central hardwood forests, mean cavity-tree abundance increases with increasing standsize class (seedling/sapling, pole, sawtimber, old-growth). However, within a size class, the number of cavity trees is highly variable among 0.1-ha inventory plots. Plots in young stands are most likely to have no cavity trees, but some plots may have more than 50 cavity trees/ha....

Abundance and size distribution of cavity trees in second-growth and old-growth central hardwood forests

Treesearch

Zhaofei Fan; Stephen R. Shifley; Martin A. Spetich; Frank R. Thompson; David R. Larsen

2005-01-01

In central hardwood forests, mean cavity-tree abundance increases with increasing standsize class (seedling/sapling, pole, sawtimber, old-growth). However, within a size class, the number of cavity trees is highly variable among 0.1-ha inventory plots. Plots in young stands are most likely to have no cavity trees, but some plots may have more than 50 cavity trees/ha....

Unmanned aerial survey of fallen trees in a deciduous broadleaved forest in eastern Japan.

PubMed

Inoue, Tomoharu; Nagai, Shin; Yamashita, Satoshi; Fadaei, Hadi; Ishii, Reiichiro; Okabe, Kimiko; Taki, Hisatomo; Honda, Yoshiaki; Kajiwara, Koji; Suzuki, Rikie

2014-01-01

Since fallen trees are a key factor in biodiversity and biogeochemical cycling, information about their spatial distribution is of use in determining species distribution and nutrient and carbon cycling in forest ecosystems. Ground-based surveys are both time consuming and labour intensive. Remote-sensing technology can reduce these costs. Here, we used high-spatial-resolution aerial photographs (0.5-1.0 cm per pixel) taken from an unmanned aerial vehicle (UAV) to survey fallen trees in a deciduous broadleaved forest in eastern Japan. In nine sub-plots we found a total of 44 fallen trees by ground survey. From the aerial photographs, we identified 80% to 90% of fallen trees that were >30 cm in diameter or >10 m in length, but missed many that were narrower or shorter. This failure may be due to the similarity of fallen trees to trunks and branches of standing trees or masking by standing trees. Views of the same point from different angles may improve the detection rate because they would provide more opportunity to detect fallen trees hidden by standing trees. Our results suggest that UAV surveys will make it possible to monitor the spatial and temporal variations in forest structure and function at lower cost.

Climate threats on growth of rear-edge European beech peripheral populations in Spain.

PubMed

Dorado-Liñán, I; Akhmetzyanov, L; Menzel, A

2017-12-01

European beech (Fagus sylvatica L.) forests in the Iberian Peninsula are a clear example of a temperate forest tree species at the rear edge of its large distribution area in Europe. The expected drier and warmer climate may alter tree growth and species distribution. Consequently, the peripheral populations will most likely be the most threatened ones. Four peripheral beech forests in the Iberian Peninsula were studied in order to assess the climate factors influencing tree growth for the last six decades. The analyses included an individual tree approach in order to detect not only the changes in the sensitivity to climate but also the potential size-mediated sensitivity to climate. Our results revealed a dominant influence of previous and current year summer on tree growth during the last six decades, although the analysis in two equally long periods unveiled changes and shifts in tree sensitivity to climate. The individual tree approach showed that those changes in tree response to climate are not size dependent in most of the cases. We observed a reduced negative effect of warmer winter temperatures at some sites and a generalized increased influence of previous year climatic conditions on current year tree growth. These results highlight the crucial role played by carryover effects and stored carbohydrates for future tree growth and species persistence.

Climate threats on growth of rear-edge European beech peripheral populations in Spain

NASA Astrophysics Data System (ADS)

Dorado-Liñán, I.; Akhmetzyanov, L.; Menzel, A.

2017-12-01

European beech ( Fagus sylvatica L.) forests in the Iberian Peninsula are a clear example of a temperate forest tree species at the rear edge of its large distribution area in Europe. The expected drier and warmer climate may alter tree growth and species distribution. Consequently, the peripheral populations will most likely be the most threatened ones. Four peripheral beech forests in the Iberian Peninsula were studied in order to assess the climate factors influencing tree growth for the last six decades. The analyses included an individual tree approach in order to detect not only the changes in the sensitivity to climate but also the potential size-mediated sensitivity to climate. Our results revealed a dominant influence of previous and current year summer on tree growth during the last six decades, although the analysis in two equally long periods unveiled changes and shifts in tree sensitivity to climate. The individual tree approach showed that those changes in tree response to climate are not size dependent in most of the cases. We observed a reduced negative effect of warmer winter temperatures at some sites and a generalized increased influence of previous year climatic conditions on current year tree growth. These results highlight the crucial role played by carryover effects and stored carbohydrates for future tree growth and species persistence.

Unmanned Aerial Survey of Fallen Trees in a Deciduous Broadleaved Forest in Eastern Japan

PubMed Central

Inoue, Tomoharu; Nagai, Shin; Yamashita, Satoshi; Fadaei, Hadi; Ishii, Reiichiro; Okabe, Kimiko; Taki, Hisatomo; Honda, Yoshiaki; Kajiwara, Koji; Suzuki, Rikie

2014-01-01

Since fallen trees are a key factor in biodiversity and biogeochemical cycling, information about their spatial distribution is of use in determining species distribution and nutrient and carbon cycling in forest ecosystems. Ground-based surveys are both time consuming and labour intensive. Remote-sensing technology can reduce these costs. Here, we used high-spatial-resolution aerial photographs (0.5–1.0 cm per pixel) taken from an unmanned aerial vehicle (UAV) to survey fallen trees in a deciduous broadleaved forest in eastern Japan. In nine sub-plots we found a total of 44 fallen trees by ground survey. From the aerial photographs, we identified 80% to 90% of fallen trees that were >30 cm in diameter or >10 m in length, but missed many that were narrower or shorter. This failure may be due to the similarity of fallen trees to trunks and branches of standing trees or masking by standing trees. Views of the same point from different angles may improve the detection rate because they would provide more opportunity to detect fallen trees hidden by standing trees. Our results suggest that UAV surveys will make it possible to monitor the spatial and temporal variations in forest structure and function at lower cost. PMID:25279817

Spot Anthracnose Disease Caused by Colletotrichum gloeosporioides on Tulip Tree in Korea.

PubMed

Choi, Okryun; Choi, Okhee; Kwak, Youn-Sig; Kim, Jinwoo; Kwon, Jin-Hyeuk

2012-03-01

The tulip tree (Liriodendron chinense) has been widely cultivated in Korea as a street or garden tree for its large flowers, which have a superficial resemblance to tulips. Occurrence of anthracnose disease on the leaves of tulip trees growing on the campus of Gyeongsang National University, Jinju, Korea, has been observed. Based on mycological characteristics, pathogenicity, and internal transcribed spacer sequence, the causal fungus was identified as Colletotrichum gloeosporioides. This is the first report on anthracnose disease caused by C. gloeosporioides on tulip trees in Korea.

On Tree-Based Phylogenetic Networks.

PubMed

Zhang, Louxin

2016-07-01

A large class of phylogenetic networks can be obtained from trees by the addition of horizontal edges between the tree edges. These networks are called tree-based networks. We present a simple necessary and sufficient condition for tree-based networks and prove that a universal tree-based network exists for any number of taxa that contains as its base every phylogenetic tree on the same set of taxa. This answers two problems posted by Francis and Steel recently. A byproduct is a computer program for generating random binary phylogenetic networks under the uniform distribution model.

Accessible light detection and ranging: estimating large tree density for habitat identification

Treesearch

Heather A. Kramer; Brandon M. Collins; Claire V. Gallagher; John Keane; Scott L. Stephens; Maggi Kelly

2016-01-01

Large trees are important to a wide variety of wildlife, including many species of conservation concern, such as the California spotted owl (Strix occidentalis occidentalis). Light detection and ranging (LiDAR) has been successfully utilized to identify the density of large-diameter trees, either by segmenting the LiDAR point cloud into...

Testing tree seeds for vigor: a review

Treesearch

F.T. Bonner

1998-01-01

This review examines the use of vigor tests for tree seeds. It suggests that precise evaluations of these tests and their application with seeds of woody plants is not yet possible. This is due to the wide genetic variation, primarily manifested in variable maturity and dormancy, that exists in most tree seed lots. Sensitive measurements of germination rate during...

Survival and growth of deep-planted, in-leaf grafts in a germplasm repository of canker-resistant butternut

Treesearch

J. W. Van Sambeek; Michael E. Ostry; James J. Zaczek

2003-01-01

Butternut (Juglans cinerea L.), highly valued for its timber and nuts, occurs as widely scattered trees or isolated stands throughout the Central Hardwood region (Rink 1990). The introduced fungus Sirococcus clavigignenti-juglandacearum has rapidly cankered, girdled, and killed most of the butternut trees; however, a few trees that...

Breeding trees resistant to insects and diseases: putting theory into application

Treesearch

Richard A. Sniezko; Jennifer Koch

2017-01-01

Tree species world-wide are under increasing threat from diseases and insects, many of which are non-native. The integrity of our natural, urban and plantation forest ecosystems, and the services they provide are seriously imperiled. Breeding programs that harness the natural genetic resistance within tree species can provide a durable solution to these threats. In...

Distribution of green infrastructure along walkable roads ...

EPA Pesticide Factsheets

Low-income and minority neighborhoods frequently lack healthful resources to which wealthier communities have access. Though important, the addition of facilities such as recreation centers can be costly and take time to implement. Urban green infrastructure, such as street trees and other green space, can be a low-cost alternative to promote frequency and duration of outdoor physical activity. Street trees and other green space may increase outdoor physical activity levels by providing shade, improving aesthetics, and promoting social engagement. Though street trees and green space provide many benefits and are publicly accessible at all times, these resources are not evenly distributed between neighborhoods. An objective analysis of street tree cover and green space in 6,407 block groups across 10 urban areas was conducted using fine-scale land cover data. Distribution of green infrastructure was then analyzed by minority status, income, car ownership, housing density, and employment density. The objective measure of street tree cover and green space is based on 1-meter resolution land cover data from the U.S. EPA-led EnviroAtlas. Tree cover was analyzed along each side of walkable road centerlines in the areas where sidewalks are estimated to be. Green space was calculated within 25 meters of road centerlines. Percent tree cover and green space per city block were then summarized to census block group (CBG). CBG demographics from the U.S. Census and built env

National Assessment of Tree City USA Participation According to Geography and Socioeconomic Characteristics

EPA Science Inventory

Tree City USA is a national program that recognizes municipal commitment to community forestry. In return for meeting program requirements, Tree City USA participants expect social, economic, and/or environmental benefits. Understandingthe geographic distribution and socioeconomi...

Distribution of cavity trees in midwestern old-growth and second-growth forests

Treesearch

Zhaofei Fan; Stephen R. Shifley; Martin A. Spetich; Frank R. Thompson; David R. Larsen

2003-01-01

We used classification and regression tree analysis to determine the primary variables associated with the occurrence of cavity trees and the hierarchical structure among those variables. We applied that information to develop logistic models predicting cavity tree probability as a function of diameter, species group, and decay class. Inventories of cavity abundance in...

Distribution of cavity trees in midwesternold-growth and second-growth forests

Treesearch

Zhaofei Fan; Stephen R. Shifley; Martin A. Spetich; Frank R., III Thompson; David R. Larsen

2003-01-01

We used classification and regression tree analysis to determine the primary variables associated with the occurrence of cavity trees and the hierarchical structure among those variables. We applied that information to develop logistic models predicting cavity tree probability as a function of diameter, species group, and decay class. Inventories of cavity abundance in...

Federated States of Micronesia's forest resources, 2006

Treesearch

Joseph A. Donnegan; Sarah L. Butler; Olaf Kuegler; Bruce A. Hiserote

2011-01-01

The Forest Inventory and Analysis program collected, analyzed, and summarized field data on 73 forested field plots on the islands of Kosrae, Chuuk, Pohnpei, and Yap in the Federated States of Micronesia (FSM). Estimates of forest area, tree stem volume and biomass, the numbers of trees, tree damages, and the distribution of tree sizes were summarized for this...

Commonwealth of the Northern Mariana Islands' forest resources, 2004

Treesearch

Joseph A. Donnegan; Sarah L. Butler; Olaf Kuegler; Bruce A. Hiserote

2011-01-01

The Forest Inventory and Analysis program collected, analyzed, and summarized field data on 37 field plots on the islands of Rota, Tinian, and Saipan in the Commonwealth of the Northern Mariana Islands (CNMI). Estimates of forest area, tree stem volume and biomass, the numbers of trees, tree damages, and the distribution of tree sizes were summarized for this...

Estimating tree cavity distributions from historical FIA data

Treesearch

Mark D. Nelson; Charlotte Roy

2012-01-01

Tree cavities provide important habitat features for a variety of wildlife species. We describe an approach for using historical FIA data to estimate the number of trees containing cavities during the 1990s in seven states of the Upper Midwest. We estimated a total of 280 million cavity-containing trees. Iowa and Missouri had the highest percentages of cavity-...

Topographic Distributions of Emergent Trees in Tropical Forests of the Osa Peninsula, Costa Rica

NASA Astrophysics Data System (ADS)

Balzotti, C.; Asner, G. P.; Taylor, P.; Cole, R. J.; Osborne, B. B.; Cleveland, C. C.; Porder, S.; Townsend, A. R.

2015-12-01

Tropical rainforests are reservoirs of terrestrial carbon and biodiversity. Large and often emergent trees store disproportionately large amounts of aboveground carbon and greatly influence the structure and functioning of tropical rainforests. Despite their importance, controls on the abundance and distribution of emergent trees are largely unknown across tropical landscapes. Conventional field approaches are limited in their ability to characterize patterns in emergent trees across vast landscapes with varying environmental conditions and floristic composition. Here we used a high-resolution light detection and ranging (LiDAR) sensor, aboard the Carnegie Airborne Observatory Airborne Taxonomic Mapping System (CAO-AToMS), to examine the abundance and distribution of tall emergent tree canopies (ETC) relative to surrounding tree canopies (STC), across the Osa Peninsula, a geologically and topographically diverse region of Costa Rica. The abundance of ETC was clearly influenced by fine-scale topographic variation, with distribution patterns that held across a variety of geologic substrates. Specifically, the density of ETC was much greater on lower slopes and in valleys, compared to upper slopes and ridges. Furthermore, using the CAO high-fidelity imaging spectrometer, ETC had a different spectral signature than that of the STC. Most notably, ETC had lower foliar N than STC, which was verified with an independent field survey of canopy leaf chemistry. The underlying mechanisms to explain the topographic-dependence of ETCs and linkages to canopy N are unknown, and remain an important area of research.

Oxygen Distributions-Evaluation of Computational Methods, Using a Stochastic Model for Large Tumour Vasculature, to Elucidate the Importance of Considering a Complete Vascular Network.

PubMed

Lagerlöf, Jakob H; Bernhardt, Peter

2016-01-01

To develop a general model that utilises a stochastic method to generate a vessel tree based on experimental data, and an associated irregular, macroscopic tumour. These will be used to evaluate two different methods for computing oxygen distribution. A vessel tree structure, and an associated tumour of 127 cm3, were generated, using a stochastic method and Bresenham's line algorithm to develop trees on two different scales and fusing them together. The vessel dimensions were adjusted through convolution and thresholding and each vessel voxel was assigned an oxygen value. Diffusion and consumption were modelled using a Green's function approach together with Michaelis-Menten kinetics. The computations were performed using a combined tree method (CTM) and an individual tree method (ITM). Five tumour sub-sections were compared, to evaluate the methods. The oxygen distributions of the same tissue samples, using different methods of computation, were considerably less similar (root mean square deviation, RMSD≈0.02) than the distributions of different samples using CTM (0.001< RMSD<0.01). The deviations of ITM from CTM increase with lower oxygen values, resulting in ITM severely underestimating the level of hypoxia in the tumour. Kolmogorov Smirnov (KS) tests showed that millimetre-scale samples may not represent the whole. The stochastic model managed to capture the heterogeneous nature of hypoxic fractions and, even though the simplified computation did not considerably alter the oxygen distribution, it leads to an evident underestimation of tumour hypoxia, and thereby radioresistance. For a trustworthy computation of tumour oxygenation, the interaction between adjacent microvessel trees must not be neglected, why evaluation should be made using high resolution and the CTM, applied to the entire tumour.

The ecology, distribution, conservation and management of large old trees.

PubMed

Lindenmayer, David B; Laurance, William F

2017-08-01

Large old trees are some of the most iconic biota on earth and are integral parts of many terrestrial ecosystems including those in tropical, temperate and boreal forests, deserts, savannas, agro-ecological areas, and urban environments. In this review, we provide new insights into the ecology, function, evolution and management of large old trees through broad cross-disciplinary perspectives from literatures in plant physiology, growth and development, evolution, habitat value for fauna and flora, and conservation management. Our review reveals that the diameter, height and longevity of large old trees varies greatly on an inter-specific basis, thereby creating serious challenges in defining large old trees and demanding an ecosystem- and species-specific definition that will only rarely be readily transferable to other species or ecosystems. Such variation is also manifested by marked inter-specific differences in the key attributes of large old trees (beyond diameter and height) such as the extent of buttressing, canopy architecture, the extent of bark micro-environments and the prevalence of cavities. We found that large old trees play an extraordinary range of critical ecological roles including in hydrological regimes, nutrient cycles and numerous ecosystem processes. Large old trees strongly influence the spatial and temporal distribution and abundance of individuals of the same species and populations of numerous other plant and animal species. We suggest many key characteristics of large old trees such as extreme height, prolonged lifespans, and the presence of cavities - which confer competitive and evolutionary advantages in undisturbed environments - can render such trees highly susceptible to a range of human influences. Large old trees are vulnerable to threats ranging from droughts, fire, pests and pathogens, to logging, land clearing, landscape fragmentation and climate change. Tackling such diverse threats is challenging because they often interact and manifest in different ways in different ecosystems, demanding targeted species- or ecosystem-specific responses. We argue that novel management actions will often be required to protect existing large old trees and ensure the recruitment of new cohorts of such trees. For example, fine-scale tree-level conservation such as buffering individual stems will be required in many environments such as in agricultural areas and urban environments. Landscape-level approaches like protecting places where large old trees are most likely to occur will be needed. However, this brings challenges associated with likely changes in tree distributions associated with climate change, because long-lived trees may presently exist in places unsuitable for the development of new cohorts of the same species. Appropriate future environmental domains for a species could exist in new locations where it has never previously occurred. The future distribution and persistence of large old trees may require controversial responses including assisted migration via seed or seedling establishment in new locales. However, the effectiveness of such approaches may be limited where key ecological features of large old trees (such as cavity presence) depend on other species such as termites, fungi and bacteria. Unless other species with similar ecological roles are present to fulfil these functions, these taxa might need to be moved concurrently with the target tree species. © 2016 Cambridge Philosophical Society.

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

PubMed

Junier, Thomas; Zdobnov, Evgeny M

2010-07-01

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

[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.

a Novel Approach of Indexing and Retrieving Spatial Polygons for Efficient Spatial Region Queries

NASA Astrophysics Data System (ADS)

Zhao, J. H.; Wang, X. Z.; Wang, F. Y.; Shen, Z. H.; Zhou, Y. C.; Wang, Y. L.

2017-10-01

Spatial region queries are more and more widely used in web-based applications. Mechanisms to provide efficient query processing over geospatial data are essential. However, due to the massive geospatial data volume, heavy geometric computation, and high access concurrency, it is difficult to get response in real time. Spatial indexes are usually used in this situation. In this paper, based on k-d tree, we introduce a distributed KD-Tree (DKD-Tree) suitbable for polygon data, and a two-step query algorithm. The spatial index construction is recursive and iterative, and the query is an in memory process. Both the index and query methods can be processed in parallel, and are implemented based on HDFS, Spark and Redis. Experiments on a large volume of Remote Sensing images metadata have been carried out, and the advantages of our method are investigated by comparing with spatial region queries executed on PostgreSQL and PostGIS. Results show that our approach not only greatly improves the efficiency of spatial region query, but also has good scalability, Moreover, the two-step spatial range query algorithm can also save cluster resources to support a large number of concurrent queries. Therefore, this method is very useful when building large geographic information systems.

Practical (?) considerations for implementing assisted migration strategies for trees in North America

NASA Astrophysics Data System (ADS)

McKenney, D.; Pedlar, J.

2011-12-01

Climate is one of the major influences on forests and much effort has gone into projecting the impacts of rapid climate change on forest distribution and productivity. Such efforts are premised on the notion that the current generation of Global Climate Models (GCMs) provide reasonably accurate representations of future climate. But what is the appropriate level of faith to put in these projections when making relatively fine-scale resource management decisions such as the movement of plant genetic material? In this talk we review recent outcomes of climate envelope models for North American tree species that suggest optimal climate regimes could move on average ~700km within the next 100 years. Newer generation GCMs seem to confirm these results but much uncertainty remains for practical decision-making. Despite these uncertainties, assisted migration has been suggested as a climate change adaptation tool wherein populations of trees are moved up to a few hundred kilometers north (or a few hundred meters upslope) to keep pace with the anticipated changes in optimal climate regimes. A continent-wide web based tool (SEEDWHERE) is presented, which assists in identifying appropriate translocation distances for assisted migration initiatives. We finish with some suggestions for future work on the topic of forest regeneration decisions under an evolving and uncertain future climate.

Rethinking Ginkgo biloba L.: Medicinal uses and conservation

PubMed Central

Isah, Tasiu

2015-01-01

Ginkgo biloba (G. biloba) is an ancient medicinal tree species that has been in existence for millennia without undergoing modifications due to its resistance to environmental stresses. Palaeobotanical history showed a wide distribution of the species across the globe but declined over geological time, becoming restricted to narrow geographical range with few surviving individuals in the modern day. The tree is slow growing, adapted to many ecological conditions and shows numerous adaptation in developmental patterns. Medicinal use of the species is attracting research interest, especially the various parts of the tree that are used in orthodox or traditional medicine to treat diseases due to the many bioactive compounds. The primary compounds receiving increasing research interest are the triterpene lactones and flavonoids; these are the target of biotechnological strategies being employed to enhance production. Many genetic and environmental factors have contributed to the endangered status of the species; conservation measures are required to protect it from extinction. In many countries, the cultivation of plantations for the supply of ginkgo leaf-based pharmaceutical formulations is in progress, and efforts to standardize ginkgo leaf extract as herbal medication for human use are being made. Microcuttings and cuttings, cryopreservation, and plant tissue culture have all aided to conserve G. biloba. PMID:26392712

A conceptual approach to approximate tree root architecture in infinite slope models

NASA Astrophysics Data System (ADS)

Schmaltz, Elmar; Glade, Thomas

2016-04-01

Vegetation-related properties - particularly tree root distribution and coherent hydrologic and mechanical effects on the underlying soil mantle - are commonly not considered in infinite slope models. Indeed, from a geotechnical point of view, these effects appear to be difficult to be reproduced reliably in a physically-based modelling approach. The growth of a tree and the expansion of its root architecture are directly connected with both intrinsic properties such as species and age, and extrinsic factors like topography, availability of nutrients, climate and soil type. These parameters control four main issues of the tree root architecture: 1) Type of rooting; 2) maximum growing distance to the tree stem (radius r); 3) maximum growing depth (height h); and 4) potential deformation of the root system. Geometric solids are able to approximate the distribution of a tree root system. The objective of this paper is to investigate whether it is possible to implement root systems and the connected hydrological and mechanical attributes sufficiently in a 3-dimensional slope stability model. Hereby, a spatio-dynamic vegetation module should cope with the demands of performance, computation time and significance. However, in this presentation, we focus only on the distribution of roots. The assumption is that the horizontal root distribution around a tree stem on a 2-dimensional plane can be described by a circle with the stem located at the centroid and a distinct radius r that is dependent on age and species. We classified three main types of tree root systems and reproduced the species-age-related root distribution with three respective mathematical solids in a synthetic 3-dimensional hillslope ambience. Thus, two solids in an Euclidian space were distinguished to represent the three root systems: i) cylinders with radius r and height h, whilst the dimension of latter defines the shape of a taproot-system or a shallow-root-system respectively; ii) elliptic paraboloids represent a cordate-root-system with radius r, height h and a constant, species-independent curvature. This procedure simplifies the classification of tree species into the three defined geometric solids. In this study we introduce a conceptual approach to estimate the 2- and 3-dimensional distribution of different tree root systems, and to implement it in a raster environment, as it is used in infinite slope models. Hereto we used the PCRaster extension in a python framework. The results show that root distribution and root growth are spatially reproducible in a simple raster framework. The outputs exhibit significant effects for a synthetically generated slope on local scale for equal time-steps. The preliminary results depict an initial step to develop a vegetation module that can be coupled with hydro-mechanical slope stability models. This approach is expected to yield a valuable contribution to the implementation of vegetation-related properties, in particular effects of root-reinforcement, into physically-based approaches using infinite slope models.

Self-organization, the cascade model, and natural hazards.

PubMed

Turcotte, Donald L; Malamud, Bruce D; Guzzetti, Fausto; Reichenbach, Paola

2002-02-19

We consider the frequency-size statistics of two natural hazards, forest fires and landslides. Both appear to satisfy power-law (fractal) distributions to a good approximation under a wide variety of conditions. Two simple cellular-automata models have been proposed as analogs for this observed behavior, the forest fire model for forest fires and the sand pile model for landslides. The behavior of these models can be understood in terms of a self-similar inverse cascade. For the forest fire model the cascade consists of the coalescence of clusters of trees; for the sand pile model the cascade consists of the coalescence of metastable regions.

Self-organization, the cascade model, and natural hazards

PubMed Central

Turcotte, Donald L.; Malamud, Bruce D.; Guzzetti, Fausto; Reichenbach, Paola

2002-01-01

We consider the frequency-size statistics of two natural hazards, forest fires and landslides. Both appear to satisfy power-law (fractal) distributions to a good approximation under a wide variety of conditions. Two simple cellular-automata models have been proposed as analogs for this observed behavior, the forest fire model for forest fires and the sand pile model for landslides. The behavior of these models can be understood in terms of a self-similar inverse cascade. For the forest fire model the cascade consists of the coalescence of clusters of trees; for the sand pile model the cascade consists of the coalescence of metastable regions. PMID:11875206

Distribution of biomass and nutrients in lodgepole pine/bitterbrush ecosystems in central Oregon.

Treesearch

Susan N. Little; Laurl J. Shainsky

1992-01-01

We investigated the distribution of biomass and nutrients in lodgepole pine (Pinus contorta var. murryana Dougl.) ecosystems on pumice soils in south-central Oregon. Sixty-three trees were sampled to develop equations for estimating dry weights of tree crowns, boles, bark, and coarse roots from diameter at breast height and...

SEASONAL PATTERNS OF FINE ROOT PRODUCTION AND TURNOVER IN PONDEROSA PINE STANDS OF DIFFERENT AGES

EPA Science Inventory

Root minirhizotron tubes were installed in two ponderosa pine (Pinus ponderosa Laws.) stands around three different tree age classes (16, 45, and > 250 yr old) to examine root spatial distribution in relation to canopy size and tree distribution, and to determine if rates of fine...

Improving quantum state transfer efficiency and entanglement distribution in binary tree spin network through incomplete collapsing measurements

NASA Astrophysics Data System (ADS)

Behzadi, Naghi; Ahansaz, Bahram

2018-04-01

We propose a mechanism for quantum state transfer (QST) over a binary tree spin network on the basis of incomplete collapsing measurements. To this aim, we perform initially a weak measurement (WM) on the central qubit of the binary tree network where the state of our concern has been prepared on that qubit. After the time evolution of the whole system, a quantum measurement reversal (QMR) is performed on a chosen target qubit. By taking optimal value for the strength of QMR, it is shown that the QST quality from the sending qubit to any typical target qubit on the binary tree is considerably improved in terms of the WM strength. Also, we show that how high-quality entanglement distribution over the binary tree network is achievable by using this approach.

Root location in random trees: a polarity property of all sampling consistent phylogenetic models except one.

PubMed

Steel, Mike

2012-10-01

Neutral macroevolutionary models, such as the Yule model, give rise to a probability distribution on the set of discrete rooted binary trees over a given leaf set. Such models can provide a signal as to the approximate location of the root when only the unrooted phylogenetic tree is known, and this signal becomes relatively more significant as the number of leaves grows. In this short note, we show that among models that treat all taxa equally, and are sampling consistent (i.e. the distribution on trees is not affected by taxa yet to be included), all such models, except one (the so-called PDA model), convey some information as to the location of the ancestral root in an unrooted tree. Copyright © 2012 Elsevier Inc. All rights reserved.

A molecular phylogeny of scaly tree ferns (Cyatheaceae).

PubMed

Korall, Petra; Conant, David S; Metzgar, Jordan S; Schneider, Harald; Pryer, Kathleen M

2007-05-01

Tree ferns recently were identified as the closest sister group to the hyperdiverse clade of ferns, the polypods. Although most of the 600 species of tree ferns are arborescent, the group encompasses a wide range of morphological variability, from diminutive members to the giant scaly tree ferns, Cyatheaceae. This well-known family comprises most of the tree fern diversity (∼500 species) and is widespread in tropical, subtropical, and south temperate regions of the world. Here we investigate the phylogenetic relationships of scaly tree ferns based on DNA sequence data from five plastid regions (rbcL, rbcL-accD IGS, rbcL-atpB IGS, trnG-trnR, and trnL-trnF). A basal dichotomy resolves Sphaeropteris as sister to all other taxa and scale features support these two clades: Sphaeropteris has conform scales, whereas all other taxa have marginate scales. The marginate-scaled clade consists of a basal trichotomy, with the three groups here termed (1) Cyathea (including Cnemidaria, Hymenophyllopsis, Trichipteris), (2) Alsophila sensu stricto, and (3) Gymnosphaera (previously recognized as a section within Alsophila) + A. capensis. Scaly tree ferns display a wide range of indusial structures, and although indusium shape is homoplastic it does contain useful phylogenetic information that supports some of the larger clades recognised.

Soft context clustering for F0 modeling in HMM-based speech synthesis

NASA Astrophysics Data System (ADS)

Khorram, Soheil; Sameti, Hossein; King, Simon

2015-12-01

This paper proposes the use of a new binary decision tree, which we call a soft decision tree, to improve generalization performance compared to the conventional `hard' decision tree method that is used to cluster context-dependent model parameters in statistical parametric speech synthesis. We apply the method to improve the modeling of fundamental frequency, which is an important factor in synthesizing natural-sounding high-quality speech. Conventionally, hard decision tree-clustered hidden Markov models (HMMs) are used, in which each model parameter is assigned to a single leaf node. However, this `divide-and-conquer' approach leads to data sparsity, with the consequence that it suffers from poor generalization, meaning that it is unable to accurately predict parameters for models of unseen contexts: the hard decision tree is a weak function approximator. To alleviate this, we propose the soft decision tree, which is a binary decision tree with soft decisions at the internal nodes. In this soft clustering method, internal nodes select both their children with certain membership degrees; therefore, each node can be viewed as a fuzzy set with a context-dependent membership function. The soft decision tree improves model generalization and provides a superior function approximator because it is able to assign each context to several overlapped leaves. In order to use such a soft decision tree to predict the parameters of the HMM output probability distribution, we derive the smoothest (maximum entropy) distribution which captures all partial first-order moments and a global second-order moment of the training samples. Employing such a soft decision tree architecture with maximum entropy distributions, a novel speech synthesis system is trained using maximum likelihood (ML) parameter re-estimation and synthesis is achieved via maximum output probability parameter generation. In addition, a soft decision tree construction algorithm optimizing a log-likelihood measure is developed. Both subjective and objective evaluations were conducted and indicate a considerable improvement over the conventional method.

Vascular Epiphyte Diversity Differs with Host Crown Zone and Diameter, but Not Orientation in a Tropical Cloud Forest

PubMed Central

Wang, Xixi; Long, Wenxing; Schamp, Brandon S.; Yang, Xiaobo; Kang, Yong; Xie, Zhixu; Xiong, Menghui

2016-01-01

Vascular epiphytes are important components of biological diversity in tropical forests. We measured the species richness and abundance of vascular epiphytes along four vertical crown zones and five horizontal orientations on 376 trees, as well as the diameter at breast height (DBH) of host trees in tropical cloud forests in Bawangling, Hainan, China. The relationship between vascular epiphyte species richness and host tree DBH was assessed using a generalized linear model. There were 1,453 vascular individual epiphytes attributed to 9 families, 24 genera and 35 species, with orchids and pteridophytes dominating. Both the species richness and abundance of epiphytes significantly differed among the four crown zones for all collections and each host tree, suggesting that vertical microhabitats contribute to the distribution of epiphytes on host trees. Neither epiphyte abundance nor species richness differed among the eastern, southern, western, and northern orientations for all host trees; however, both richness and abundance were significantly higher for epiphytes that encircled host tree trunks. This suggests that morphological and physiological characteristics of the tree, but not microclimates probably contribute to the distribution of epiphytes on host trees. Epiphyte species richness was positively correlated with tree DBH across the six host tree species studied, with increases in DBH among smaller trees resulting in larger increases in richness, while increases in DBH among larger host trees resulting in more modest increases in ephiphyte richness. Our findings contribute support for a positive relationship between epiphyte species richness and host tree DBH and provide important guidance for future surveys of epiphyte community development. PMID:27391217

Tropical dry forest trees and lianas differ in leaf economic spectrum traits but have overlapping water-use strategies.

PubMed

Werden, Leland K; Waring, Bonnie G; Smith-Martin, Christina M; Powers, Jennifer S

2018-04-01

Tree species in tropical dry forests employ a wide range of strategies to cope with seasonal drought, including regulation of hydraulic function. However, it is uncertain if co-occurring lianas also possess a diversity of strategies. For a taxonomically diverse group of 14 tree and 7 liana species, we measured morphological and hydraulic functional traits during an unusual drought and under non-drought conditions to determine (i) if trees have different water-use strategies than lianas and (ii) if relationships among these traits can be used to better understand how tree and liana species regulate diurnal leaf water potential (Ψdiurnal). In this Costa Rican tropical dry forest, lianas and trees had overlapping water-use strategies, but differed in many leaf economic spectrum traits. Specifically, we found that both lianas and trees employed a diversity of Ψdiurnal regulation strategies, which did not differ statistically. However, lianas and trees did significantly differ in terms of certain traits including leaf area, specific leaf area, petiole length, wood vessel diameter and xylem vessel density. All liana and tree species we measured fell along a continuum of isohydric (partial) to anisohydric (strict or extreme) Ψdiurnal regulation strategies, and leaf area, petiole length, stomatal conductance and wood vessel diameter correlated with these strategies. These findings contribute to a trait-based understanding of how plants regulate Ψdiurnal under both drought stress and sufficient water availability, and underscore that lianas and trees employ a similarly wide range of Ψdiurnal regulation strategies, despite having vastly different growth forms.

Hybridization among distantly related species: Examples from the polyploid genus Curcuma (Zingiberaceae).

PubMed

Záveská, Eliška; Fér, Tomáš; Šída, Otakar; Marhold, Karol; Leong-Škorničková, Jana

2016-07-01

Discerning relationships among species evolved by reticulate and/or polyploid evolution is not an easy task, although it is widely discussed. The economically important genus Curcuma (ca. 120 spp.; Zingiberaceae), broadly distributed in tropical SE Asia, is a particularly interesting example of a group of palaeopolyploid origin whose evolution is driven mainly by hybridization and polyploidization. Although a phylogeny and a new infrageneric classification of Curcuma, based on commonly used molecular markers (ITS and cpDNA), have recently been proposed, significant evolutionary questions remain unresolved. We applied a multilocus approach and a combination of modern analytical methods to this genus to distinguish causes of gene tree incongruence and to identify hybrids and their parental species. Five independent regions of nuclear DNA (DCS, GAPDH, GLOBOSA3, LEAFY, ITS) and four non-coding cpDNA regions (trnL-trnF, trnT-trnL, psbA-trnH and matK), analysed as a single locus, were employed to construct a species tree and hybrid species trees using (*)BEAST and STEM-hy. Detection of hybridogenous species in the dataset was also conducted using the posterior predictive checking approach as implemented in JML. The resulting species tree outlines the relationships among major evolutionary lineages within Curcuma, which were previously unresolved or which conflicted depending upon whether they were based on ITS or cpDNA markers. Moreover, by using the additional markers in tests of plausible topologies of hybrid species trees for C. vamana, C. candida, C. roscoeana and C. myanmarensis suggested by previous molecular and morphological evidence, we found strong evidence that all the species except C. candida are of subgeneric hybrid origin. Copyright © 2016 Elsevier Inc. All rights reserved.

Tree-hierarchy of DNA and distribution of Holliday junctions.

PubMed

Rozikov, U A

2017-12-01

We define a DNA as a sequence of [Formula: see text]'s and embed it on a path of Cayley tree. Using group representation of the Cayley tree, we give a hierarchy of a countable set of DNAs each of which 'lives' on the same Cayley tree. This hierarchy has property that each vertex of the Cayley tree belongs only to one of DNA. Then we give a model (energy, Hamiltonian) of this set of DNAs by an analogue of Ising model with three spin values (considered as DNA base pairs) on a set of admissible configurations. To study thermodynamic properties of the model of DNAs we describe corresponding translation invariant Gibbs measures (TIGM) of the model on the Cayley tree of order two. We show that there is a critical temperature [Formula: see text] such that (i) if temperature [Formula: see text] then there exists unique TIGM; (ii) if [Formula: see text] then there are two TIGMs; (iii) if [Formula: see text] then there are three TIGMs. Each such measure describes a phase of the set of DNAs. We use these results to study distributions of Holliday junctions and branches of DNAs. In case of very high and very low temperatures we give stationary distributions and typical configurations of the Holliday junctions.

Know your limits? Climate extremes impact the range of Scots pine in unexpected places

PubMed Central

Julio Camarero, J.; Gazol, Antonio; Sancho-Benages, Santiago; Sangüesa-Barreda, Gabriel

2015-01-01

Background and Aims Although extreme climatic events such as drought are known to modify forest dynamics by triggering tree dieback, the impact of extreme cold events, especially at the low-latitude margin (‘rear edge’) of species distributional ranges, has received little attention. The aim of this study was to examine the impact of one such extreme cold event on a population of Scots pine (Pinus sylvestris) along the species’ European southern rear-edge range limit and to determine how such events can be incorporated into species distribution models (SDMs). Methods A combination of dendrochronology and field observation was used to quantify how an extreme cold event in 2001 in eastern Spain affected growth, needle loss and mortality of Scots pine. Long-term European climatic data sets were used to contextualize the severity of the 2001 event, and an SDM for Scots pine in Europe was used to predict climatic range limits. Key Results The 2001 winter reached record minimum temperatures (equivalent to the maximum European-wide diurnal ranges) and, for trees already stressed by a preceding dry summer and autumn, this caused dieback and large-scale mortality. Needle loss and mortality were particularly evident in south-facing sites, where post-event recovery was greatly reduced. The SDM predicted European Scots pine distribution mainly on the basis of responses to maximum and minimum monthly temperatures, but in comparison with this the observed effects of the 2001 cold event at the southerly edge of the range limit were unforeseen. Conclusions The results suggest that in order to better forecast how anthropogenic climate change might affect future forest distributions, distribution modelling techniques such as SDMs must incorporate climatic extremes. For Scots pine, this study shows that the effects of cold extremes should be included across the entire distribution margin, including the southern ‘rear edge’, in order to avoid biased predictions based solely on warmer climatic scenarios. PMID:26292992

Biotic interactions mediate the expansion of black mangrove (Avicennia germinans) into salt marshes under climate change.

PubMed

Guo, Hongyu; Zhang, Yihui; Lan, Zhenjiang; Pennings, Steven C

2013-09-01

Many species are expanding their distributions to higher latitudes due to global warming. Understanding the mechanisms underlying these distribution shifts is critical for better understanding the impacts of climate changes. The climate envelope approach is widely used to model and predict species distribution shifts with changing climates. Biotic interactions between species, however, may also influence species distributions, and a better understanding of biotic interactions could improve predictions based solely on climate envelope models. Along the northern Gulf of Mexico coast, USA, subtropical black mangrove (Avicennia germinans) at the northern limit of its distribution grows sympatrically with temperate salt marsh plants in Florida, Louisiana, and Texas. In recent decades, freeze-free winters have led to an expansion of black mangrove into salt marshes. We examined how biotic interactions between black mangrove and salt marsh vegetation along the Texas coast varied across (i) a latitudinal gradient (associated with a winter-temperature gradient); (ii) the elevational gradient within each marsh (which creates different marsh habitats); and (iii) different life history stages of black mangroves (seedlings vs. juvenile trees). Each of these variables affected the strength or nature of biotic interactions between black mangrove and salt marsh vegetation: (i) Salt marsh vegetation facilitated black mangrove seedlings at their high-latitude distribution limit, but inhibited black mangrove seedlings at lower latitudes; (ii) mangroves performed well at intermediate elevations, but grew and survived poorly in high- and low-marsh habitats; and (iii) the effect of salt marsh vegetation on black mangroves switched from negative to neutral as black mangroves grew from seedlings into juvenile trees. These results indicate that the expansion of black mangroves is mediated by complex biotic interactions. A better understanding of the impacts of climate change on ecological communities requires incorporating context-dependent biotic interactions into species range models. © 2013 John Wiley & Sons Ltd.

Tree growth acceleration and expansion of alpine forests: The synergistic effect of atmospheric and edaphic change.

PubMed

Silva, Lucas C R; Sun, Geng; Zhu-Barker, Xia; Liang, Qianlong; Wu, Ning; Horwath, William R

2016-08-01

Many forest ecosystems have experienced recent declines in productivity; however, in some alpine regions, tree growth and forest expansion are increasing at marked rates. Dendrochronological analyses at the upper limit of alpine forests in the Tibetan Plateau show a steady increase in tree growth since the early 1900s, which intensified during the 1930s and 1960s, and have reached unprecedented levels since 1760. This recent growth acceleration was observed in small/young and large/old trees and coincided with the establishment of trees outside the forest range, reflecting a connection between the physiological performance of dominant species and shifts in forest distribution. Measurements of stable isotopes (carbon, oxygen, and nitrogen) in tree rings indicate that tree growth has been stimulated by the synergistic effect of rising atmospheric CO2 and a warming-induced increase in water and nutrient availability from thawing permafrost. These findings illustrate the importance of considering soil-plant-atmosphere interactions to understand current and anticipate future changes in productivity and distribution of forest ecosystems.

Mixed-up trees: the structure of phylogenetic mixtures.

PubMed

Matsen, Frederick A; Mossel, Elchanan; Steel, Mike

2008-05-01

In this paper, we apply new geometric and combinatorial methods to the study of phylogenetic mixtures. The focus of the geometric approach is to describe the geometry of phylogenetic mixture distributions for the two state random cluster model, which is a generalization of the two state symmetric (CFN) model. In particular, we show that the set of mixture distributions forms a convex polytope and we calculate its dimension; corollaries include a simple criterion for when a mixture of branch lengths on the star tree can mimic the site pattern frequency vector of a resolved quartet tree. Furthermore, by computing volumes of polytopes we can clarify how "common" non-identifiable mixtures are under the CFN model. We also present a new combinatorial result which extends any identifiability result for a specific pair of trees of size six to arbitrary pairs of trees. Next we present a positive result showing identifiability of rates-across-sites models. Finally, we answer a question raised in a previous paper concerning "mixed branch repulsion" on trees larger than quartet trees under the CFN model.

Tree growth acceleration and expansion of alpine forests: The synergistic effect of atmospheric and edaphic change

PubMed Central

Silva, Lucas C. R.; Sun, Geng; Zhu-Barker, Xia; Liang, Qianlong; Wu, Ning; Horwath, William R.

2016-01-01

Many forest ecosystems have experienced recent declines in productivity; however, in some alpine regions, tree growth and forest expansion are increasing at marked rates. Dendrochronological analyses at the upper limit of alpine forests in the Tibetan Plateau show a steady increase in tree growth since the early 1900s, which intensified during the 1930s and 1960s, and have reached unprecedented levels since 1760. This recent growth acceleration was observed in small/young and large/old trees and coincided with the establishment of trees outside the forest range, reflecting a connection between the physiological performance of dominant species and shifts in forest distribution. Measurements of stable isotopes (carbon, oxygen, and nitrogen) in tree rings indicate that tree growth has been stimulated by the synergistic effect of rising atmospheric CO2 and a warming-induced increase in water and nutrient availability from thawing permafrost. These findings illustrate the importance of considering soil-plant-atmosphere interactions to understand current and anticipate future changes in productivity and distribution of forest ecosystems. PMID:27652334

Change in Mesoherbivore Browsing Is Mediated by Elephant and Hillslope Position.

PubMed

Lagendijk, D D Georgette; Thaker, Maria; de Boer, Willem F; Page, Bruce R; Prins, Herbert H T; Slotow, Rob

2015-01-01

Elephant are considered major drivers of ecosystems, but their effects within small-scale landscape features and on other herbivores still remain unclear. Elephant impact on vegetation has been widely studied in areas where elephant have been present for many years. We therefore examined the combined effect of short-term elephant presence (< 4 years) and hillslope position on tree species assemblages, resource availability, browsing intensity and soil properties. Short-term elephant presence did not affect woody species assemblages, but did affect height distribution, with greater sapling densities in elephant access areas. Overall tree and stem densities were also not affected by elephant. By contrast, slope position affected woody species assemblages, but not height distributions and densities. Variation in species assemblages was statistically best explained by levels of total cations, Zinc, sand and clay. Although elephant and mesoherbivore browsing intensities were unaffected by slope position, we found lower mesoherbivore browsing intensity on crests with high elephant browsing intensity. Thus, elephant appear to indirectly facilitate the survival of saplings, via the displacement of mesoherbivores, providing a window of opportunity for saplings to grow into taller trees. In the short-term, effects of elephant can be minor and in the opposite direction of expectation. In addition, such behavioural displacement promotes recruitment of saplings into larger height classes. The interaction between slope position and elephant effect found here is in contrast with other studies, and illustrates the importance of examining ecosystem complexity as a function of variation in species presence and topography. The absence of a direct effect of elephant on vegetation, but the presence of an effect on mesoherbivore browsing, is relevant for conservation areas especially where both herbivore groups are actively managed.

Change in Mesoherbivore Browsing Is Mediated by Elephant and Hillslope Position

PubMed Central

Lagendijk, D. D. Georgette; Thaker, Maria; de Boer, Willem F.; Page, Bruce R.; Prins, Herbert H. T.; Slotow, Rob

2015-01-01

Elephant are considered major drivers of ecosystems, but their effects within small-scale landscape features and on other herbivores still remain unclear. Elephant impact on vegetation has been widely studied in areas where elephant have been present for many years. We therefore examined the combined effect of short-term elephant presence (< 4 years) and hillslope position on tree species assemblages, resource availability, browsing intensity and soil properties. Short-term elephant presence did not affect woody species assemblages, but did affect height distribution, with greater sapling densities in elephant access areas. Overall tree and stem densities were also not affected by elephant. By contrast, slope position affected woody species assemblages, but not height distributions and densities. Variation in species assemblages was statistically best explained by levels of total cations, Zinc, sand and clay. Although elephant and mesoherbivore browsing intensities were unaffected by slope position, we found lower mesoherbivore browsing intensity on crests with high elephant browsing intensity. Thus, elephant appear to indirectly facilitate the survival of saplings, via the displacement of mesoherbivores, providing a window of opportunity for saplings to grow into taller trees. In the short-term, effects of elephant can be minor and in the opposite direction of expectation. In addition, such behavioural displacement promotes recruitment of saplings into larger height classes. The interaction between slope position and elephant effect found here is in contrast with other studies, and illustrates the importance of examining ecosystem complexity as a function of variation in species presence and topography. The absence of a direct effect of elephant on vegetation, but the presence of an effect on mesoherbivore browsing, is relevant for conservation areas especially where both herbivore groups are actively managed. PMID:26083248

Environmental constraints on the invasion of Triadica sebifera in the eastern United States: an experimental field assessment.

PubMed

Pattison, Robert R; Mack, Richard N

2009-01-01

Identifying the environmental constraints that affect the distribution of an invasive species is fundamental to its effective control. Triadica sebifera (Chinese tallow tree) has invaded the southeastern United States, but its potential for further range and habitat extension has been unresolved. We explored experimentally environmental factors in macro- and microhabitats that affect its persistence at five widely separated sites along the Atlantic seaboard of the United States and at two sites inland; three sites occur well beyond the tree's current range. At each site, seeds and young vegetative plants (0.5-0.65 m tall) of T. sebifera were placed in four microhabitats (closed-canopy upland, closed-canopy lowland, open-canopy upland, and open-canopy lowland). Plant growth, leaf CO(2) assimilation rates, leaf N concentrations and delta(13)C ratios, and stem water potential were measured for two growing seasons. Percent seed germination was consistently higher in open-canopy microhabitats and lowest at northern and inland sites. T. sebifera grew in all open-canopy microhabitats, even 300-500 km beyond its current distribution. Plant growth in closed-canopy habitats was lower, attributable to lower carbon gain per unit leaf area in shaded compared with open-canopy environments, especially at northern and inland sites. Neither competition, other than canopy shade, nor grazing was a key constraint on distribution at any scale. Our results demonstrate that T. sebifera is dispersal limited at landscape scales but limited locally by dispersal and overstory shade; it has yet to occupy the full extent of its new range in North America. Quantifying environmental factors both within and well beyond a species' current range can effectively highlight the limits on its distribution.

Steady-state distributions of probability fluxes on complex networks

NASA Astrophysics Data System (ADS)

Chełminiak, Przemysław; Kurzyński, Michał

2017-02-01

We consider a simple model of the Markovian stochastic dynamics on complex networks to examine the statistical properties of the probability fluxes. The additional transition, called hereafter a gate, powered by the external constant force breaks a detailed balance in the network. We argue, using a theoretical approach and numerical simulations, that the stationary distributions of the probability fluxes emergent under such conditions converge to the Gaussian distribution. By virtue of the stationary fluctuation theorem, its standard deviation depends directly on the square root of the mean flux. In turn, the nonlinear relation between the mean flux and the external force, which provides the key result of the present study, allows us to calculate the two parameters that entirely characterize the Gaussian distribution of the probability fluxes both close to as well as far from the equilibrium state. Also, the other effects that modify these parameters, such as the addition of shortcuts to the tree-like network, the extension and configuration of the gate and a change in the network size studied by means of computer simulations are widely discussed in terms of the rigorous theoretical predictions.

Detection of Single Standing Dead Trees from Aerial Color Infrared Imagery by Segmentation with Shape and Intensity Priors

NASA Astrophysics Data System (ADS)

Polewski, P.; Yao, W.; Heurich, M.; Krzystek, P.; Stilla, U.

2015-03-01

Standing dead trees, known as snags, are an essential factor in maintaining biodiversity in forest ecosystems. Combined with their role as carbon sinks, this makes for a compelling reason to study their spatial distribution. This paper presents an integrated method to detect and delineate individual dead tree crowns from color infrared aerial imagery. Our approach consists of two steps which incorporate statistical information about prior distributions of both the image intensities and the shapes of the target objects. In the first step, we perform a Gaussian Mixture Model clustering in the pixel color space with priors on the cluster means, obtaining up to 3 components corresponding to dead trees, living trees, and shadows. We then refine the dead tree regions using a level set segmentation method enriched with a generative model of the dead trees' shape distribution as well as a discriminative model of their pixel intensity distribution. The iterative application of the statistical shape template yields the set of delineated dead crowns. The prior information enforces the consistency of the template's shape variation with the shape manifold defined by manually labeled training examples, which makes it possible to separate crowns located in close proximity and prevents the formation of large crown clusters. Also, the statistical information built into the segmentation gives rise to an implicit detection scheme, because the shape template evolves towards an empty contour if not enough evidence for the object is present in the image. We test our method on 3 sample plots from the Bavarian Forest National Park with reference data obtained by manually marking individual dead tree polygons in the images. Our results are scenario-dependent and range from a correctness/completeness of 0.71/0.81 up to 0.77/1, with an average center-of-gravity displacement of 3-5 pixels between the detected and reference polygons.

Thinning northern hardwoods in New England by dominant-tree removal — early results

Treesearch

William Leak

2007-01-01

Commercial thinning is a widely accepted practice in northern hardwood stands of New England. Commercial thinning guidelines for eastern hardwoods generally recommend releasing selected crop trees or the removal of trees in less-than-dominant crown classes unless they are of poor health or quality. However, many northern hardwood stands in New England have a dominant...

An evaluation of the STEMS tree growth projection system.

Treesearch

Margaret R. Holdaway; Gary J. Brand

1983-01-01

STEMS (Stand and Tree Evaluation and Modeling System) is a tree growth projection system. This paper (1) compares the performance of the current version of STEMS developed for the Lake States with that of the original model and (2) reports the results of an analysis of the current model over a wide range of conditions and identifies its main strengths and weaknesses...

Recent climate warming forces contrasting growth responses of white spruce at treeline in Alaska through temperature thresholds

Treesearch

Martin Wilmking; Glenn P. Juday; Valerie A. Barber; Harold S.J. Zald

2004-01-01

Northern and high-latitude alpine treelines are generally thought to be limited by available warmth. Most studies of tree-growth-climate interaction at treeline as well as climate reconstructions using dendrochronology report positive growth response of treeline trees to warmer temperatures. However, population-wide responses of treeline trees to climate remain largely...

Response of dwarf mistletoe-infested ponderosa pine to thinning: 2. Dwarf mistletoe propagation.

Treesearch

Lewis F. Roth; James W. Barrett

1985-01-01

Propagation of dwarf mistletoe in ponderosa pine saplings is little influenced by thinning overly dense stands to 250 trees per acre. Numerous plants that appear soon after thinning develop from formerly latent plants in the suppressed under-story. Subsequently, dwarf mistletoe propagates nearly as fast as tree crowns enlarge but the rate differs widely among trees....

The value of information in conservation planning: Selecting retention trees for lichen conservation

Treesearch

Karin Perhans; Robert G. Haight; Lena Gustafsson

2014-01-01

Conservation planning studies at small scales such as forest stands and below are uncommon. However, for retention forestry, developed during the last two decades and with current wide and increasing application in boreal and temperate regions, the need for cost-effective selection of individual trees is evident. In retention forestry certain trees are left at final...

Comparison of protein profiles of beech bark disease-resistant or beech bark disease-susceptible American beech

Treesearch

Mary E. Mason; Marek Krasowski; Judy Loo; Jennifer. Koch

2011-01-01

Proteomic analysis of beech bark proteins from trees resistant and susceptible to beech bark disease (BBD) was conducted. Sixteen trees from eight geographically isolated stands, 10 resistant (healthy) and 6 susceptible (diseased/infested) trees, were studied. The genetic complexity of the sample unit, the sampling across a wide geographic area, and the complexity of...

Habitat Preferences of Boros schneideri (Coleoptera: Boridae) in the Natural Tree Stands of the Białowieża Forest

PubMed Central

Gutowski, Jerzy M.; Sućko, Krzysztof; Zub, Karol; Bohdan, Adam

2014-01-01

Abstract We analyzed habitat requirements of Boros schneideri (Panzer, 1796) (Coleoptera: Boridae) in the natural forests of the continental biogeographical region, using data collected in the Białowieża Forest. This species has been found on the six host trees, but it preferred dead, standing pine trees, characterized by large diameter, moderately moist and moist phloem but avoided trees in sunny locations. It occurred mostly in mesic and wet coniferous forests. This species demonstrated preferences for old tree stands (over 140-yr old), and its occurrence in younger tree-stand age classes (minimum 31–40-yr old) was not significantly different from random distribution. B. schneideri occupied more frequently locations distant from the forest edge, which were less affected by logging. Considering habitat requirements, character of occurrence, and decreasing number of occupied locations in the whole range of distribution, this species can be treated as relict of primeval forests. PMID:25527586

Genetic and ecological insights into glacial refugia of walnut (Juglans regia L.)

PubMed Central

Aradhya, Mallikarjuna; Ibrahimov, Zakir; Toktoraliev, Biimyrza; Maghradze, David; Musayev, Mirza; Bobokashvili, Zviadi; Preece, John E.

2017-01-01

The distribution and survival of trees during the last glacial maximum (LGM) has been of interest to paleoecologists, biogeographers, and geneticists. Ecological niche models that associate species occurrence and abundance with climatic variables are widely used to gain ecological and evolutionary insights and to predict species distributions over space and time. The present study deals with the glacial history of walnut to address questions related to past distributions through genetic analysis and ecological modeling of the present, LGM and Last Interglacial (LIG) periods. A maximum entropy method was used to project the current walnut distribution model on to the LGM (21–18 kyr BP) and LIG (130–116 kyr BP) climatic conditions. Model tuning identified the walnut data set filtered at 10 km spatial resolution as the best for modeling the current distribution and to hindcast past (LGM and LIG) distributions of walnut. The current distribution model predicted southern Caucasus, parts of West and Central Asia extending into South Asia encompassing northern Afghanistan, Pakistan, northwestern Himalayan region, and southwestern Tibet, as the favorable climatic niche matching the modern distribution of walnut. The hindcast of distributions suggested the occurrence of walnut during LGM was somewhat limited to southern latitudes from southern Caucasus, Central and South Asian regions extending into southwestern Tibet, northeastern India, Himalayan region of Sikkim and Bhutan, and southeastern China. Both CCSM and MIROC projections overlapped, except that MIROC projected a significant presence of walnut in the Balkan Peninsula during the LGM. In contrast, genetic analysis of the current walnut distribution suggested a much narrower area in northern Pakistan and the surrounding areas of Afghanistan, northwestern India, and southern Tajikistan as a plausible hotspot of diversity where walnut may have survived glaciations. Overall, the findings suggest that walnut perhaps survived the last glaciations in several refugia across a wide geographic area between 30° and 45° North latitude. However, humans probably played a significant role in the recent history and modern distribution of walnut. PMID:29023476

Genetic and ecological insights into glacial refugia of walnut (Juglans regia L.).

PubMed

Aradhya, Mallikarjuna; Velasco, Dianne; Ibrahimov, Zakir; Toktoraliev, Biimyrza; Maghradze, David; Musayev, Mirza; Bobokashvili, Zviadi; Preece, John E

2017-01-01

The distribution and survival of trees during the last glacial maximum (LGM) has been of interest to paleoecologists, biogeographers, and geneticists. Ecological niche models that associate species occurrence and abundance with climatic variables are widely used to gain ecological and evolutionary insights and to predict species distributions over space and time. The present study deals with the glacial history of walnut to address questions related to past distributions through genetic analysis and ecological modeling of the present, LGM and Last Interglacial (LIG) periods. A maximum entropy method was used to project the current walnut distribution model on to the LGM (21-18 kyr BP) and LIG (130-116 kyr BP) climatic conditions. Model tuning identified the walnut data set filtered at 10 km spatial resolution as the best for modeling the current distribution and to hindcast past (LGM and LIG) distributions of walnut. The current distribution model predicted southern Caucasus, parts of West and Central Asia extending into South Asia encompassing northern Afghanistan, Pakistan, northwestern Himalayan region, and southwestern Tibet, as the favorable climatic niche matching the modern distribution of walnut. The hindcast of distributions suggested the occurrence of walnut during LGM was somewhat limited to southern latitudes from southern Caucasus, Central and South Asian regions extending into southwestern Tibet, northeastern India, Himalayan region of Sikkim and Bhutan, and southeastern China. Both CCSM and MIROC projections overlapped, except that MIROC projected a significant presence of walnut in the Balkan Peninsula during the LGM. In contrast, genetic analysis of the current walnut distribution suggested a much narrower area in northern Pakistan and the surrounding areas of Afghanistan, northwestern India, and southern Tajikistan as a plausible hotspot of diversity where walnut may have survived glaciations. Overall, the findings suggest that walnut perhaps survived the last glaciations in several refugia across a wide geographic area between 30° and 45° North latitude. However, humans probably played a significant role in the recent history and modern distribution of walnut.

Common Lognormal Behavior in Legal Systems

NASA Astrophysics Data System (ADS)

Yamamoto, Ken

2017-07-01

This study characterizes a statistical property of legal systems: the distribution of the number of articles in a law follows a lognormal distribution. This property is common to the Japanese, German, and Singaporean laws. To explain this lognormal behavior, tree structure of the law is analyzed. If the depth of a tree follows a normal distribution, the lognormal distribution of the number of articles can be theoretically derived. We analyze the structure of the Japanese laws using chapters, sections, and other levels of organization, and this analysis demonstrates that the proposed model is quantitatively reasonable.

Potential impacts of climate change on bird and tree habitats within the Appalachian Mountains

Treesearch

Stephen Matthews; Louis Iverson; Anantha Prasad; Matthew. Peters

2010-01-01

The habitats associated with the distributions of bird and tree species vary with the resolution of investigation and regional context, and especially within high-elevation forests. Our understanding of how bird distributions may shift with climate change was advanced by our understanding of how climate shapes the boundaries of a species' range.

Distribution and mixing of old and new nonstructural carbon in two temperate trees

Treesearch

Andrew D. Richardson; Mariah S. Carbone; Brett A. Huggett; Morgan E. Furze; Claudia I. Czimczik; Jennifer C. Walker; Xiaomei Xu; Paul G. Schaberg; Paula Murakami

2015-01-01

We know surprisingly little about whole-tree nonstructural carbon (NSC; primarily sugars and starch) budgets. Even less well understood is the mixing between recent photosynthetic assimilates (new NSC) and previously stored reserves. And, NSC turnover times are poorly constrained. We characterized the distribution of NSC in the stemwood, branches, and roots of two...

Determining suitable locations for seed transfer under climate change: a global quantitative method

Treesearch

Kevin M. Potter; William W. Hargrove

2012-01-01

Changing climate conditions will complicate efforts to match seed sources with the environments to which they are best adapted. Tree species distributions may have to shift to match new environmental conditions, potentially requiring the establishment of some species entirely outside of their current distributions to thrive. Even within the portions of tree species...

Distributed Contour Trees

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

Morozov, Dmitriy; Weber, Gunther H.

2014-03-31

Topological techniques provide robust tools for data analysis. They are used, for example, for feature extraction, for data de-noising, and for comparison of data sets. This chapter concerns contour trees, a topological descriptor that records the connectivity of the isosurfaces of scalar functions. These trees are fundamental to analysis and visualization of physical phenomena modeled by real-valued measurements. We study the parallel analysis of contour trees. After describing a particular representation of a contour tree, called local{global representation, we illustrate how di erent problems that rely on contour trees can be solved in parallel with minimal communication.

Phyto-toponyms of Arbutus unedo L. and their distribution in Sardinia (Italy)

PubMed Central

Pinna, Claudia; Carta, Luisa; Deiana, Vitale; Camarda, Ignazio

2017-01-01

The study shows the results of an inventory of place names connected to Arbutus unedo L., a Mediterranean species, widespread throughout Sardinia. The main aim was to compare the past distribution of place names, referring to the strawberry tree, to the current distribution of the species on the island. In addition, we investigated the meaning and the diversity of these local place names in the various communities. The result was a collection of 432 phyto-toponyms. 248 of them were used for an analysis of their distribution in the habitats, indicated on the Map of the Nature System in Sardinia, defined on the basis of the current vegetation typology. The persistence of the species in the various habitats was either confirmed or negated with in site investigations and interviews. 47.5% of municipalities have place names related to the strawberry tree. Of the 248 phyto-toponyms, 127 fall in the habitats where the species currently persists proving a correspondence between their regional distribution and the current distribution of the species. The remaining 121 phyto-toponyms fall in habitats where the strawberry tree is currently absent. Most of them are found in man-made habitats where man has transformed the forest cover which previously included the strawberry tree. This study also contributes to promoting and conserving the linguistic heritage of local communities. PMID:28704491

How much does climate change threaten European forest tree species distributions?

PubMed

Dyderski, Marcin K; Paź, Sonia; Frelich, Lee E; Jagodziński, Andrzej M

2018-03-01

Although numerous species distribution models have been developed, most were based on insufficient distribution data or used older climate change scenarios. We aimed to quantify changes in projected ranges and threat level by the years 2061-2080, for 12 European forest tree species under three climate change scenarios. We combined tree distribution data from the Global Biodiversity Information Facility, EUFORGEN, and forest inventories, and we developed species distribution models using MaxEnt and 19 bioclimatic variables. Models were developed for three climate change scenarios-optimistic (RCP2.6), moderate (RCP4.5), and pessimistic (RPC8.5)-using three General Circulation Models, for the period 2061-2080. Our study revealed different responses of tree species to projected climate change. The species may be divided into three groups: "winners"-mostly late-successional species: Abies alba, Fagus sylvatica, Fraxinus excelsior, Quercus robur, and Quercus petraea; "losers"-mostly pioneer species: Betula pendula, Larix decidua, Picea abies, and Pinus sylvestris; and alien species-Pseudotsuga menziesii, Quercus rubra, and Robinia pseudoacacia, which may be also considered as "winners." Assuming limited migration, most of the species studied would face a significant decrease in suitable habitat area. The threat level was highest for species that currently have the northernmost distribution centers. Ecological consequences of the projected range contractions would be serious for both forest management and nature conservation. © 2017 John Wiley & Sons Ltd.

Riparian Ficus Tree Communities: The Distribution and Abundance of Riparian Fig Trees in Northern Thailand

PubMed Central

Pothasin, Pornwiwan; Compton, Stephen G.; Wangpakapattanawong, Prasit

2014-01-01

Fig trees (Ficus) are often ecologically significant keystone species because they sustain populations of the many seed-dispersing animals that feed on their fruits. They are prominent components of riparian zones where they may also contribute to bank stability as well as supporting associated animals. The diversity and distributions of riparian fig trees in deciduous and evergreen forests in Chiang Mai Province, Northern Thailand were investigated in 2010–2012. To record the diversity and abundance of riparian fig trees, we (1) calculated stem density, species richness, and diversity indices in 20×50 m randomly selected quadrats along four streams and (2) measured the distances of individual trees from four streams to determine if species exhibit distinct distribution patterns within riparian zones. A total of 1169 individuals (from c. 4 ha) were recorded in the quadrats, representing 33 Ficus species (13 monoecious and 20 dioecious) from six sub-genera and about 70% of all the species recorded from northern Thailand. All 33 species had at least some stems in close proximity to the streams, but they varied in their typical proximity, with F. squamosa Roxb. and F. ischnopoda Miq the most strictly stream-side species. The riparian forests in Northern Thailand support a rich diversity and high density of Ficus species and our results emphasise the importance of fig tree within the broader priorities of riparian area conservation. Plans to maintain or restore properly functioning riparian forests need to take into account their significance. PMID:25310189

Distribution of 'Candidatus Liberibacter asiaticus' Above and Below Ground in Texas Citrus.

PubMed

Louzada, Eliezer S; Vazquez, Omar Ed; Braswell, W Evan; Yanev, George; Devanaboina, Madhavi; Kunta, Madhurababu

2016-07-01

Detection of 'Candidatus Liberibacter asiaticus' represents one of the most difficult, yet critical, steps of controlling Huanglongbing disease. Efficient detection relies on understanding the underlying distribution of bacteria within trees. To that end, we studied the distribution of 'Ca. L. asiaticus' in leaves of 'Rio Red' grapefruit trees and in roots of 'Valencia' sweet orange trees grafted onto sour orange rootstock. We performed two sets of leaf collection on grapefruit trees; the first a selective sampling targeting symptomatic leaves and their neighbors and the second a systematic collection disregarding symptomology. From uprooted orange trees, we exhaustively sampled fibrous roots. In this study, the presence of 'Ca. L. asiaticus' was detected in leaves using real-time polymerase chain reaction (PCR) targeting the 16S ribosomal gene and in roots using the rpIJ/rpIL ribosomal protein genes and was confirmed with conventional PCR and sequencing of the rpIJ/rpIL gene in both tissues. Among randomly collected leaves, 'Ca. L. asiaticus' was distributed in a patchy fashion. Detection of 'Ca. L. asiaticus' varied with leaf symptomology with symptomatic leaves showing the highest frequency (74%) followed by their neighboring asymptomatic leaves (30%), while randomly distributed asymptomatic leaves had the lowest frequency (20%). Among symptomatic leaves, we found statistically significant differences in mean number of bacterial cells with respect to both increasing distance of the leaf from the trunk and cardinal direction. The titer of 'Ca. L. asiaticus' cells was significantly greater on the north side of trees than on the south and west sides. Moreover, these directions showed different spatial distributions of 'Ca. L. asiaticus' with higher titers near the trunk on the south and west sides as opposed to further from the trunk on the north side. Similarly, we found spatial variation in 'Ca. L. asiaticus' distribution among root samples. 'Ca. L. asiaticus' was detected more frequently and bacterial abundances were higher among horizontally growing roots just under the soil surface (96%) than among deeper vertically growing roots (78%). Bacterial abundance declined slightly with distance from the trunk. These results point to paths of research that will likely prove useful to combating this devastating disease.

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

PubMed Central

Junier, Thomas; Zdobnov, Evgeny M.

2010-01-01

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

Long-term changes of tree species composition and distribution in Korean mountain forests

NASA Astrophysics Data System (ADS)

Lee, Boknam; Lee, Hoontaek; Cho, Sunhee; Yoon, Jongguk; Park, Jongyoung; Kim, Hyun Seok

2017-04-01

Long-term changes in the abundance and distribution of tree species in the temperate forests of South Korea remain poorly understood. We investigated how tree species composition and stand distribution change across temperate mountainous forests using the species composition and DBH size collected over the past 15 years (1998-2012) across 130 permanent forest plots of 0.1 ha in Jiri and Baegun mountains in South Korea. The overall net change of tree communities over the years showed positive in terms of stand density, richness, diversity, and evenness. At the species level, the change of relative species composition has been led by intermediate and shade-tolerant species, such as Quercus mongolica, Carpinus laxiflora, Quercus serrate, Quercus variabilis, Styrax japonicus, Lindera erythrocarpa, and Pinus densiflora and was categorized into five species communities, representing gradual increase or decrease, establishment, extinction, fluctuation of species population. At the community level, the change in species composition appeared to have consistent and directional patterns of increase in the annual rate of change in the mean species traits including species density, pole growth rate, adult growth rate, and adult stature. Based on the additive models, the distribution of species diversity was significantly related to topographical variables including elevation, latitude, longitude, slope, topographic wetness index, and curvature where elevation was the most significant driver, followed by latitude and longitude. However, the change in distribution of species diversity was only significantly influenced by latitude and longitude. This is the first study to reveal the long-term dynamics of change in tree species composition and distribution, which are important to broaden our understanding of temperate mountainous forest ecosystem in South Korea.

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.

[Biomass distribution patterns of Alnus hirsuta and Betula platyphylla-swamp ecotone communities in Changbai Mountains].

PubMed

Mu, Changcheng; Wan, Shucheng; Su, Ping; Song, Hongwen; Sun, Zhihu

2004-12-01

In order to reveal the growth patterns of dominant tree species and the distribution patterns of community biomass along the horizontal environmental gradients or among the vertical layers of communities in Changbai Mountains, this paper studied the biomass distribution patterns of Alnus hirsuta-swamp and Betula platyphylla-swamp ecotone communities. The results showed that there were some differences in growth rate and in adaptability to habitats between A. hirsuta and B. platyphylla. In the wetland habitats of the ecotone, A. hirsuta grew 1-2 times faster than B. platyphylla, but along the gradient from swamp to forest, it grew slowly, while B. platyphylla grew fast. Therefore, A. hirsuta was a favorite tree species in wetland habitats. The distribution pattern of organ biomass was similar between A. hirsute and B. platyphylla, the trunk being 1/2, tree root 1/4, branch 1/10, bark 1.5/20, and leaf 1/20. The vertical distribution pattern of biomass was also similar between A. hirsute-swamp and B. platyphylla-swamp ecotone communities, the tree, shrub, and herbage layer accounted for 87%-90%, 7%-9%, and 2%-3%, respectively in the whole ecotone communities. The community biomass increased linearly from swamp to forest with the change of environment factors.

Conservation, Divergence, and Genome-Wide Distribution of PAL and POX A Gene Families in Plants.

PubMed

Rawal, H C; Singh, N K; Sharma, T R

2013-01-01

Genome-wide identification and phylogenetic and syntenic comparison were performed for the genes responsible for phenylalanine ammonia lyase (PAL) and peroxidase A (POX A) enzymes in nine plant species representing very diverse groups like legumes (Glycine max and Medicago truncatula), fruits (Vitis vinifera), cereals (Sorghum bicolor, Zea mays, and Oryza sativa), trees (Populus trichocarpa), and model dicot (Arabidopsis thaliana) and monocot (Brachypodium distachyon) species. A total of 87 and 1045 genes in PAL and POX A gene families, respectively, have been identified in these species. The phylogenetic and syntenic comparison along with motif distributions shows a high degree of conservation of PAL genes, suggesting that these genes may predate monocot/eudicot divergence. The POX A family genes, present in clusters at the subtelomeric regions of chromosomes, might be evolving and expanding with higher rate than the PAL gene family. Our analysis showed that during the expansion of POX A gene family, many groups and subgroups have evolved, resulting in a high level of functional divergence among monocots and dicots. These results will act as a first step toward the understanding of monocot/eudicot evolution and functional characterization of these gene families in the future.

Conservation, Divergence, and Genome-Wide Distribution of PAL and POX A Gene Families in Plants

PubMed Central

Rawal, H. C.; Singh, N. K.; Sharma, T. R.

2013-01-01

Genome-wide identification and phylogenetic and syntenic comparison were performed for the genes responsible for phenylalanine ammonia lyase (PAL) and peroxidase A (POX A) enzymes in nine plant species representing very diverse groups like legumes (Glycine max and Medicago truncatula), fruits (Vitis vinifera), cereals (Sorghum bicolor, Zea mays, and Oryza sativa), trees (Populus trichocarpa), and model dicot (Arabidopsis thaliana) and monocot (Brachypodium distachyon) species. A total of 87 and 1045 genes in PAL and POX A gene families, respectively, have been identified in these species. The phylogenetic and syntenic comparison along with motif distributions shows a high degree of conservation of PAL genes, suggesting that these genes may predate monocot/eudicot divergence. The POX A family genes, present in clusters at the subtelomeric regions of chromosomes, might be evolving and expanding with higher rate than the PAL gene family. Our analysis showed that during the expansion of POX A gene family, many groups and subgroups have evolved, resulting in a high level of functional divergence among monocots and dicots. These results will act as a first step toward the understanding of monocot/eudicot evolution and functional characterization of these gene families in the future. PMID:23671845

Modeling of air pollutant removal by dry deposition to urban trees using a WRF/CMAQ/i-Tree Eco coupled system

Treesearch

Maria Theresa I. Cabaraban; Charles N. Kroll; Satoshi Hirabayashi; David J. Nowak

2013-01-01

A distributed adaptation of i-Tree Eco was used to simulate dry deposition in an urban area. This investigation focused on the effects of varying temperature, LAI, and NO2 concentration inputs on estimated NO2 dry deposition to trees in Baltimore, MD. A coupled modeling system is described, wherein WRF provided temperature...

Height-diameter equations for young-growth red fir in California and southern Oregon

Treesearch

K. Leroy Dolph

1989-01-01

Total tree height of young-growth red fir can be estimated from the relation of total tree height to diameter outside bark at breast height (DOB). Total tree heights and corresponding diameters were obtained from stem analyses of 562 trees distributed across 56 sampling locations in the true fir forest type of California and Oregon. The resulting equations can predict...

A nearest-neighbor imputation approach to mapping tree species over large areas using forest inventory plots and moderate resolution raster data

Treesearch

B. Tyler Wilson; Andrew J. Lister; Rachel I. Riemann

2012-01-01

The paper describes an efficient approach for mapping multiple individual tree species over large spatial domains. The method integrates vegetation phenology derived from MODIS imagery and raster data describing relevant environmental parameters with extensive field plot data of tree species basal area to create maps of tree species abundance and distribution at a 250-...

Simulated cavity tree dynamics under alternative timber harvest regimes

Treesearch

Zhaofei Fan; Stephen R Shifley; Frank R Thompson; David R Larsen

2004-01-01

We modeled cavity tree abundance on a landscape as a function of forest stand age classes and as a function of aggregate stand size classes.We explored the impact of five timber harvest regimes on cavity tree abundance on a 3261 ha landscape in southeast Missouri, USA, by linking the stand level cavity tree distribution model to the landscape age structure simulated by...

Tree specific traits vs. stand level characteristics - assessing the source depths of plant water uptake in a mixed forest stand

NASA Astrophysics Data System (ADS)

Seeger, Stefan; Brinkmann, Nadine; Kahmen, Ansgar; Weiler, Markus

2017-04-01

Due to differences in fine root distributions, physiological root characteristics and plant plasticity, the spatial and temporal characteristics of plant water uptake are expected to vary between different tree species. This has implications on the overall water budget of a forest stand as well as on the drought sensitivity of particular trees. A four-year time series of climate data, soil moisture, and stable water isotopes in soil and tree xylem was used to investigate plant water uptake dynamics of four tree species (beech - Fagus sylvatica, spruce - Picea abies, ash - Fraxinus excelsior and maple - Acer pseudoplatanus) in a mixed forest stand. Modeling with a modified version of the soil hydrological model Hydrus-1D allowed us to simulate continuous time series of stable water isotopes in plant water uptake, which were compared to the measured values in tree xylem water and soil water. We found that different estimated species specific fine root distributions and root water uptake parameters lead to very similar simulated water balances and soil water isotope depth profiles for all four species. According to our simulations, differences in evaporative demand (i.e. LAI) had the biggest influence on water uptake and soil water distributions. Comparing the isotopic signatures of simulated root water uptake and measured xylem water, the simulations for beech were most suited to predict the observed signatures of all four species. This indicates that isolated, tree specific parametrized 1-D simulations are not suited to predict actual water uptake of different trees in a mixed stand. Due to overlapping root spaces dominant trees (in our case beeches with an LAI of around 5.5) may influence the soil water storage below accompanying trees (spruces, ashes and maples with LAIs between 1.8 and 3.1) in a degree that their actual water uptake cannot be predicted with 1-D simulations based on their smaller LAI values. Consequently, for a mixed forest stand the interplay of trees with different traits has to be accounted for in order to correctly model plant water uptake of single trees.

The Mouse-colored Tyrannulet (Phaeomyias murina) is a species complex that includes the Cocos Flycatcher (Nesotriccus ridgwayi), an island form that underwent a population bottleneck.

PubMed

Zucker, Marc R; Harvey, Michael G; Oswald, Jessica A; Cuervo, Andrés; Derryberry, Elizabeth; Brumfield, Robb T

2016-08-01

Simultaneous examination of evolutionary history in island forms and closely related mainland relatives can provide reciprocal insight into the evolution of island and mainland faunas. The Cocos Flycatcher (Nesotriccus ridgwayi) is a small tyrant flycatcher (Tyrannidae) endemic to Cocos Island, an oceanic island in the eastern Pacific Ocean. We first established its close relationship to the mainland species Mouse-colored Tyrannulet (Phaeomyias murina) using a phylogeny from genome-wide ultraconserved elements and exons. We then used mitochondrial DNA to explore the relationships between Nesotriccus and Phaeomyias populations from across its distribution in Central and South America. We found that Nesotriccus is nested within the Phaeomyias evolutionary tree, and that Phaeomyias represents a complex of at least four evolutionarily distinct species that differ in plumage, voice, and habitat association. Nesotriccus underwent a population bottleneck subsequent to its divergence from Central American and northern South American Phaeomyias populations in the middle Pleistocene. The 46 UCE loci containing alleles that are fixed between the two species are widely distributed across the genome, which suggests that selective or neutral processes responsible for divergence have occurred genome-wide. Overall, our simultaneous examination of Phaeomyias and Nesotriccus revealed divergent levels of genetic diversity and evolutionary histories between island and mainland forms. Copyright © 2016 Elsevier Inc. All rights reserved.

Quantifying geomorphic controls on riparian forest dynamics using a linked physical-biological model: implications for river corridor conservation

NASA Astrophysics Data System (ADS)

Stella, J. C.; Harper, E. B.; Fremier, A. K.; Hayden, M. K.; Battles, J. J.

2009-12-01

In high-order alluvial river systems, physical factors of flooding and channel migration are particularly important drivers of riparian forest dynamics because they regulate habitat creation, resource fluxes of water, nutrients and light that are critical for growth, and mortality from fluvial disturbance. Predicting vegetation composition and dynamics at individual sites in this setting is challenging, both because of the stochastic nature of the flood regime and the spatial variability of flood events. Ecological models that correlate environmental factors with species’ occurrence and abundance (e.g., ’niche models’) often work well in infrequently-disturbed upland habitats, but are less useful in river corridors and other dynamic zones where environmental conditions fluctuate greatly and selection pressures on disturbance-adapted organisms are complex. In an effort to help conserve critical riparian forest habitat along the middle Sacramento River, CA, we are taking a mechanistic approach to quantify linkages between fluvial and biotic processes for Fremont cottonwood (Populus fremontii), a keystone pioneer tree in dryland rivers ecosystems of the U.S. Southwest. To predict the corridor-wide population effects of projected changes to the disturbance regime from flow regulation, climate change, and landscape modifications, we have coupled a physical model of channel meandering with a patch-based population model that incorporates the climatic, hydrologic, and topographic factors critical for tree recruitment and survival. We employed these linked simulations to study the relative influence of the two most critical habitat types--point bars and abandoned channels--in sustaining the corridor-wide cottonwood population over a 175-year period. The physical model uses discharge data and channel planform to predict the spatial distribution of new habitat patches; the population model runs on top of this physical template to track tree colonization and survival on each patch. Model parameters of tree life-history traits (e.g., dispersal timing) and hydrogeomorphic processes (e.g., sedimentation rate) were determined by field and experimental studies, and aerial LIDAR, with separate range of values for point bar versus floodplain habitats. In most runs, abandoned channels were colonized one third as frequently as point bars, but supported much larger forest patches when colonization was successful (from 15-99% of forest area, depending on point bar success). Independent evaluation of aerial photos confirm that cottonwood forest stands associated with abandoned channels were less frequent (38% of all stands) but more extensive (53% of all forest area) relative to those caused by migrating point bars. Results indicate that changes to the rate and scale of river migration, and particularly channel abandonment, from human and climatic alterations to the flow regime will likely influence riparian corridor-wide tree population structure and forest dynamics, with consequences for the community of organisms that depend on this habitat.

Book review: A new view on the species abundance distribution

USGS Publications Warehouse

DeAngelis, Donald L.

2018-01-01

The sampled relative abundances of species of a taxonomic group, whether birds, trees, or moths, in a natural community at a particular place vary in a way that suggests a consistent underlying pattern, referred to as the species abundance distribution (SAD). Preston [1] conjectured that the numbers of species, plotted as a histogram of logarithmic abundance classes called octaves, seemed to fit a lognormal distribution; that is, the histograms look like normal distributions, although truncated on the left-hand, or low-species-abundance, end. Although other specific curves for the SAD have been proposed in the literature, Preston’s lognormal distribution is widely cited in textbooks and has stimulated attempts at explanation. An important aspect of Preston’s lognormal distribution is the ‘veil line’, a vertical line drawn exactly at the point of the left-hand truncation in the distribution, to the left of which would be species missing from the sample. Dewdney rejects the lognormal conjecture. Instead, starting with the long-recognized fact that the number of species sampled from a community, when plotted as histograms against population abundance, resembles an inverted J, he presents a mathematical description of an alternative that he calls the ‘J distribution’, a hyperbolic density function truncated at both ends. When multiplied by species richness, R, it becomes the SAD of the sample.

Bacterial Leaf Scorch of Amenity Trees a Wide-Spread Problem of Economic Significance to the Urban Forest

Treesearch

James Lashomb; Alan Iskra; Ann Brooks Gould; George Hamilton

2003-01-01

Bacterial leaf scorch (BLS) of amenity trees is caused by the bacterium Xylella fastidiosa, a xylem-limited pathogen that causes water stress resulting in leaf scorch, decline, and eventual death of affected trees. Recent surveys indicate that BLS is widespread throughout the eastern half of the United States. In New Jersey, BLS primarily affects red and pin oaks...

A bark-shaving technique to deter rat snakes from climbing red-cockaded woodpecker cavity trees

Treesearch

Daniel Saenz; Christopher S. Collins; Richard N. Conner

1999-01-01

We developed a bark-shaving technique to deter rat snakes (Elaphe obsoleta) from climbing red-cockaded woodpecker (Picoides borealis) trees as an aesthetically pleasing, more cost-effective, and safer alternative to other snake excluder devices. We used a drawknife to carefully shave the bark around the circumference of 4 treatment trees in a l-m-wide band to...

Predicting past and future diameter growth for trees in the northeastern United States

Treesearch

James A. Westfall

2006-01-01

Tree diameter growth models are widely used in forestry applications, often to predict tree size at a future point in time. Also, there are instances where projections of past diameters are needed. A relative diameter growth model was developed to allow prediction of both future and past growth rates. Coefficients were estimated for 15 species groups that cover most...

Genome-wide analysis of oleosin gene family in 22 tree species: An accelerator for metabolic engineering of biofuel crops and agrigenomics industrial applications?

USDA-ARS?s Scientific Manuscript database

Triacylglycerols (TAGs) are the major molecules of energy storage in eukaryotes. Trees contribute to part of enormous plant oil reserves because fruits and kernels of many trees contain up to 50-80% of oil. TAGs accumulate in oil bodies in plants, similar to oil droplets in animals. Oleosins (OLEs) ...