Antioxidant and anti-inflammatory activities of the phenolic extracts of Sapium sebiferum (L.) Roxb. leaves.

PubMed

Fu, Rao; Zhang, Yu-Ting; Guo, Yi-Ran; Huang, Qiu-Lan; Peng, Tong; Xu, Ying; Tang, Lin; Chen, Fang

2013-05-20

The leaves of Sapium sebiferum have long been used in Traditional Chinese Medicine (TCM) for the treatment of eczema, shingles, edema, swelling, ascites, scabs, and snakebites, among other maladies. The present study aimed to investigate the antioxidant and anti-inflammatory effects of the phenolic extracts of Sapium sebiferum leaves using in vitro and in vivo models. The in vitro antioxidant activities of the extracts were measured using common chemical methods (total phenolic content; total flavonoid content; scavenging of DPPH·, ABTS+·, superoxide, and nitrite radicals; reducing power; β-carotene bleaching; and FTC assays). The in vivo topical anti-inflammatory activities were tested using the 12-O-tetradecanoylphorbol-13-acetate (TPA)-induced dermatitis animal model. The SOD and CAT activities and the GSH content of ear tissue were also determined using test kits. The extracts of Sapium sebiferum leaves exhibited strong in vitro antioxidant activities. They also showed significant (P<0.001) and dose-dependent anti-inflammatory activities in an acute dermatitis model at the doses of 0.03 mg/ear, 0.1mg/ear, and 0.3mg/ear. The application of Sapium sebiferum leaf extracts increased the SOD and CAT activities and the GSH content relative to those of the TPA treatment group. The anti-inflammatory effect of the Sapium sebiferum leaf extract was positively correlated with its antioxidant activity. These results demonstrate that Sapium sebiferum leaf extract is an effective anti-inflammatory agent in the TPA-induced dermatitis model, and its anti-inflammatory effect is related, at least in part, to its antioxidant activity. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Using internet images to gather distributional data for a newly discovered Caloptilia species (Lepidoptera: Gracillariidae) specializing on Chinese tallow in North America

USDA-ARS?s Scientific Manuscript database

Chinese tallow tree (Triadica sebifera (L.), Euphorbiaceae) is a noxious and highly invasive species that was deliberately introduced to GA in 1772. In early 2009, an unfamiliar caterpillar was independently discovered feeding on T. sebifera trees in Gainesville, FL and Slidell, LA. Adult moths were...

Deep Sequencing of the Fruit Transcriptome and Lipid Accumulation in a Non-Seed Tissue of Chinese Tallow, a Potential Biofuel Crop.

PubMed

Divi, Uday K; Zhou, Xue-Rong; Wang, Penghao; Butlin, Jamie; Zhang, Dong-Mei; Liu, Qing; Vanhercke, Thomas; Petrie, James R; Talbot, Mark; White, Rosemary G; Taylor, Jennifer M; Larkin, Philip; Singh, Surinder P

2016-01-01

Chinese tallow (Triadica sebifera) is a valuable oilseed-producing tree that can grow in a variety of conditions without competing for food production, and is a promising biofuel feedstock candidate. The fruits are unique in that they contain both saturated and unsaturated fat present in the tallow and seed layer, respectively. The tallow layer is poorly studied and is considered only as an external fatty deposition secreted from the seed. In this study we show that tallow is in fact a non-seed cellular tissue capable of triglyceride synthesis. Knowledge of lipid synthesis and storage mechanisms in tissues other than seed is limited but essential to generate oil-rich biomass crops. Here, we describe the annotated transcriptome assembly generated from the fruit coat, tallow and seed tissues of Chinese tallow. The final assembly was functionally annotated, allowing for the identification of candidate genes and reconstruction of lipid pathways. A tallow tissue-specific paralog for the transcription factor gene WRINKLED1 (WRI1) and lipid droplet-associated protein genes, distinct from those expressed in seed tissue, were found to be active in tallow, underpinning the mode of oil synthesis and packaging in this tissue. Our data have established an excellent knowledge base that can provide genetic and biochemical insights for engineering non-seed tissues to accumulate large amounts of oil. In addition to the large data set of annotated transcripts, the study also provides gene-based simple sequence repeat and single nucleotide polymorphism markers. © The Author 2015. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Growth and invasive potential of Sapium sebiferum (Euphorbiaceae) within the coastal prairie region: the effects of soil and moisture regime

USGS Publications Warehouse

Barrilleaux, T.C.; Grace, J.B.

2000-01-01

The introduced tree Sapium sebiferum (Euphorbiaceae) is considered a serious threat to the preservation of the coastal prairie region of Louisiana and Texas, although it is currently uncommon in the western part of the region. The objective of this study was to evaluate the potential effects of location, soils, and available moisture on the growth and survival of S. sebiferum in coastal prairie. In a field experiment, S. sebiferum mortality was significantly greater at a western site than at central and eastern sites. The greatest mortality and least growth of surviving plants occurred on a soil from the western region, regardless of site. A greenhouse study also found that S. sebiferum growth was lowest on the western soil. Watering frequency significantly affected S. sebiferum growth, except on the western soil. Sapium sebiferum growth responded to both nitrogen and phosphorum additions for all soils. Soil analyses revealed the highest sand, sodium, and phosphorus contents, and much higher electrical conductivity in the western soil. It is concluded that the soil examined from the western region is unfavorable for S. sebiferum growth, though not to the extent to preclude S. sebiferum completely. Evidence suggests that soil salinity may be the primary cause of the poor S. sebiferum growth at the western site.

Leaf litter of invasive Chinese tallow (Triadica sebifera) negatively affects hatching success of an aquatic breeding anuran, the southern leopard frog (Lithobates sphenocephalus)

Treesearch

C.K. Adams; D. Saenz

2012-01-01

Chinese tallow (Triadica sebifera (L.) Small) is an aggressive invasive tree species that can be abundant in parts of its non-native range. This tree species has the capability of producing monocultures, by outcompeting native trees, which can be in or near wetlands that are utilized by breeding amphibians. Existing research suggests that leaf litter from invasive...

Metabolizable energy in Chinese tallow fruit for Yellow-rumped Warblers, Northern Cardinals, and American Robins

USGS Publications Warehouse

Baldwin, M.J.; Barrow, W.C.; Jeske, C.; Rohwer, F.C.

2008-01-01

The invasive exotic Chinese tallow tree (Triadica sebifera) produces an abundant fruit crop, which is primarily bird-dispersed. The fruit pulp of tallow is lipid-rich, high in saturated fatty acids, and consumed by many bird species. Long-chained fatty acids can be difficult for many birds to digest and we investigated the ability of tallow consumers to assimilate energy in the pulp. We used the total collection method and compared apparent metabolizable energy (AME) of tallow fruit for three species of birds with differing fruit composition in their natural diets. All birds exhibited nitrogen deficits and lost body mass during the trials. Northern Cardinals (Cardinalis cardinalis) lost more mass (8.73%/day) than Yellow-rumped Warblers (Dendroica coronata) (5.29%/day) and American Robins (Turdus migratorius) (5.48%/day), and had larger nitrogen deficits (-120.1 mg N/g diet) than both species as well (-36.4 mg N/g diet and -68.9 mg N/g diet, respectively). Food intake relative to metabolic body mass was highest in Yellow-rumped Warblers (0.70 g-dry/g 0.75??day). Northern Cardinal and American Robin food intake was lower and did not differ from each other (both species: 0.13 g-dry/g 0.75??day). Nitrogen corrected values of AME were used to make species comparisons. Yellow-rumped-Warblers exhibited the highest values of AME (30.00 kJ/g), followed by American Robins (23.90 kJ/g), and Northern Cardinals (14.34 kJ/g). We suggest tallow may be an important winter food source for Yellow-rumped Warblers where their ranges overlap.

Effects of an invasive plant, Chinese tallow (Triadica sebifera), on development and survival of anuran larvae

Treesearch

Taylor B. Cotten; Matthew A. Kwiatkowski; Daniel Saenz; Michael Collyer

2012-01-01

Amphibians are considered one of the most threatened vertebrate groups. Although numerous studies have addressed the many causes of amphibian population decline, little is known about effects of invasive plants. Chinese tallow (Triadica sebifera) is an exotic deciduous tree that has invaded the southeastern United States. Amphibian larvae in environments invaded by T....

Synergistic effects of the invasive Chinese tallow (Triadica sebifera) and climate change on aquatic amphibian survival

Treesearch

Daniel Saenz; Erin M. Fucik; Matthew A. Kwiatkowski

2013-01-01

Changes in climate and the introduction of invasive species are two major stressors to amphibians, although little is known about the interaction between these two factors with regard to impacts on amphibians. We focused our study on an invasive tree species, the Chinese tallow (Triadica sebifera), that annually sheds its leaves and produces leaf...

Managing an established tree invader: developing control methods for Chinese tallow (Triadica sebifera) in maritime forests

Treesearch

Lauren S. Pile; G. Geoff Wang; Thomas A. Waldrop; Joan L. Walker; William C. Bridges; Patricia A. Layton

2017-01-01

Biological invasions by woody species in forested ecosystems can have significant impacts on forest management and conservation. We designed and tested several management options based on the physiology of Chinese tallow (Triadica sebifera [L.] Small). Specifically, we tested four treatments, including mastication, foliar herbicide, and fire (MH...

Mapping the invasive species, Chinese tallow, with EO1 satellite Hyperion hyperspectral image data and relating tallow occurrences to a classified Landsat Thematic Mapper land cover map

USGS Publications Warehouse

Ramsey, Elijah W.; Rangoonwala, A.; Nelson, G.; Ehrlich, R.

2005-01-01

Our objective was to provide a realistic and accurate representation of the spatial distribution of Chinese tallow (Triadica sebifera) in the Earth Observing 1 (EO1) Hyperion hyperspectral image coverage by using methods designed and tested in previous studies. We transformed, corrected, and normalized Hyperion reflectance image data into composition images with a subpixel extraction model. Composition images were related to green vegetation, senescent foliage and senescing cypress-tupelo forest, senescing Chinese tallow with red leaves ('red tallow'), and a composition image that only corresponded slightly to yellowing vegetation. These statistical and visual comparisons confirmed a successful portrayal of landscape features at the time of the Hyperion image collection. These landscape features were amalgamated in the Landsat Thematic Mapper (TM) pixel, thereby preventing the detection of Chinese tallow occurrences in the Landsat TM classification. With the occurrence in percentage of red tallow (as a surrogate for Chinese tallow) per pixel mapped, we were able to link dominant land covers generated with Landsat TM image data to Chinese tallow occurrences as a first step toward determining the sensitivity and susceptibility of various land covers to tallow establishment. Results suggested that the highest occurrences and widest distribution of red tallow were (1) apparent in disturbed or more open canopy woody wetland deciduous forests (including cypress-tupelo forests), upland woody land evergreen forests (dominantly pines and seedling plantations), and upland woody land deciduous and mixed forests; (2) scattered throughout the fallow fields or located along fence rows separating active and non-active cultivated and grazing fields, (3) found along levees lining the ubiquitous canals within the marsh and on the cheniers near the coastline; and (4) present within the coastal marsh located on the numerous topographic highs. ?? 2005 US Government.

Thermophysical characterization of the seeds of invasive Chinese tallow tree: importance for biofuel production.

PubMed

Picou, Laura; Boldor, Doran

2012-10-16

The limited supply of traditional fossil based fuels, and increased concern about their environmental impact has driven the interest in the utilization of biomass based energy sources, including those that are underutilized or otherwise nuisance species such as Chinese tallow trees (Triadica sebifera [L.]). This species is a prolific seeds producer, and this paper shows that they contain more than 50% lipids by mass that are suitable for conversion into biodiesel. We present here, for the first time, the seeds' thermophysical properties important for biofuel production. The seeds were characterized using thermogravimetric analysis (TGA), differential scanning calorimetry (DSC), and ultimate analysis; their thermal conductivity, thermal diffusivity, and specific heat were determined. The characterization results were correlated to fatty acid composition and lipid content for whole seeds and individual layers, as well as to the protein, hemicellulose, cellulose, and lignin content. The TGA analysis indicated the presence, in addition to lipids, of hemicellulose, cellulose, lignin, and proteins, depending on the layer analyzed. Thermal conductivity and specific heat were, respectively 0.14 ± 0.007 W/mK and 3843.5 ± 171.16 J/kgK for wax, 0.20 ± 0.002 W/mK and 2018.7 ± 5.18 J/kgK for shells, 0.13 ± 0.0 W/mK and 1237 ± 3.15 J/kgK for internal kernel, and 0.13 ± 0.000 W/mK and 2833.9 ± 104.11 J/kgK for whole seeds. These properties and characterization method can be further used in engineering analysis used to determine the most optimum processing method for production of biofuels from this feedstock.

Specificity of extrafloral nectar induction by herbivores differs among native and invasive populations of tallow tree.

PubMed

Wang, Yi; Carrillo, Juli; Siemann, Evan; Wheeler, Gregory S; Zhu, Lin; Gu, Xue; Ding, Jianqing

2013-08-01

Invasive plants can be released from specialist herbivores and encounter novel generalists in their introduced ranges, leading to variation in defence among native and invasive populations. However, few studies have examined how constitutive and induced indirect defences change during plant invasion, especially during the juvenile stage. Constitutive extrafloral nectar (EFN) production of native and invasive populations of juvenile tallow tree (Triadica sebifera) were compared, and leaf clipping, and damage by a native specialist (Noctuid) and two native generalist caterpillars (Noctuid and Limacodid) were used to examine inducible EFN production. Plants from introduced populations had more leaves producing constitutive EFN than did native populations, but the content of soluble solids of EFN did not differ. Herbivores induced EFN production more than simulated herbivory. The specialist (Noctuid) induced more EFN than either generalist for native populations. The content of soluble solids in EFN was higher (2·1 times), with the specialist vs. the generalists causing the stronger response for native populations, but the specialist response was always comparable with the generalist responses for invasive populations. These results suggest that constitutive and induced indirect defences are retained in juvenile plants of invasive populations even during plant establishment, perhaps due to generalist herbivory in the introduced range. However, responses specific to a specialist herbivore may be reduced in the introduced range where specialists are absent. This decreased defence may benefit specialist insects that are introduced for classical biological control of invasive plants.

40 CFR 721.6183 - Amides, from ammonium hydroxide - maleic anhydride polymer and hydrogenated tallow alkyl amines...

Code of Federal Regulations, 2010 CFR

2010-07-01

... - maleic anhydride polymer and hydrogenated tallow alkyl amines, sodium salts, compds. with ethanolamine... Substances § 721.6183 Amides, from ammonium hydroxide - maleic anhydride polymer and hydrogenated tallow... anhydride polymer and hydrogenated tallow alkyl amines, sodium salts, compds. with ethanolamine (PMN P-00...

40 CFR 721.6183 - Amides, from ammonium hydroxide - maleic anhydride polymer and hydrogenated tallow alkyl amines...

Code of Federal Regulations, 2011 CFR

2011-07-01

... - maleic anhydride polymer and hydrogenated tallow alkyl amines, sodium salts, compds. with ethanolamine... Substances § 721.6183 Amides, from ammonium hydroxide - maleic anhydride polymer and hydrogenated tallow... anhydride polymer and hydrogenated tallow alkyl amines, sodium salts, compds. with ethanolamine (PMN P-00...

Atomic force microscopy of the intervessel pit membrane in the stem of Sapium sebiferum (Euphorbiacea)

Treesearch

Thomas C. Pesacreta; Leslie H. Groom; Timothy G. Rials

2005-01-01

Sapwood and juvenile wood of Sapium sebiferum (Euphorbiacea) was collected during 2000-2002. In air-dried vessel elements, the surface of pit membranes (PMs) in the outermost growth ring was coated with plaque-like or interstitial material that was 2-5 nm thick. This coating was phase dark and overlaid a phase bright layer of globules and...

Specificity of extrafloral nectar induction by herbivores differs among native and invasive populations of tallow tree

PubMed Central

Wang, Yi; Carrillo, Juli; Siemann, Evan; Wheeler, Gregory S.; Zhu, Lin; Gu, Xue; Ding, Jianqing

2013-01-01

Background and Aims Invasive plants can be released from specialist herbivores and encounter novel generalists in their introduced ranges, leading to variation in defence among native and invasive populations. However, few studies have examined how constitutive and induced indirect defences change during plant invasion, especially during the juvenile stage. Methods Constitutive extrafloral nectar (EFN) production of native and invasive populations of juvenile tallow tree (Triadica sebifera) were compared, and leaf clipping, and damage by a native specialist (Noctuid) and two native generalist caterpillars (Noctuid and Limacodid) were used to examine inducible EFN production. Key results Plants from introduced populations had more leaves producing constitutive EFN than did native populations, but the content of soluble solids of EFN did not differ. Herbivores induced EFN production more than simulated herbivory. The specialist (Noctuid) induced more EFN than either generalist for native populations. The content of soluble solids in EFN was higher (2·1 times), with the specialist vs. the generalists causing the stronger response for native populations, but the specialist response was always comparable with the generalist responses for invasive populations. Conclusions These results suggest that constitutive and induced indirect defences are retained in juvenile plants of invasive populations even during plant establishment, perhaps due to generalist herbivory in the introduced range. However, responses specific to a specialist herbivore may be reduced in the introduced range where specialists are absent. This decreased defence may benefit specialist insects that are introduced for classical biological control of invasive plants. PMID:23761685

Geographic distribution of genetic variation among native and introduced populations of Chinese tallow tree, Triadica sebifera (Euphorbiaceae).

PubMed

DeWalt, Saara J; Siemann, Evan; Rogers, William E

2011-07-01

Invasive plants often display genetically determined variation in patterns of growth and resource allocation between native and introduced genotypes, as well as among genotypes within different regions of the introduced range. We examined patterns of genetic variation within and among native and introduced populations of the tetraploid Chinese tallow tree (Triadica sebifera, Euphorbiaceae) to determine whether nonselective evolutionary processes or the introduction history could contribute to previously observed phenotypic differences between native and introduced populations as well as among introduced populations. We used six microsatellite markers to study 12 native populations in China, 51 introduced populations in the southeastern USA, and one introduced population in Australia. Genetic diversity was greater within and among native populations than introduced populations. Within the southeastern USA, populations in Georgia and South Carolina differed substantially in their genetic composition and had greater genetic diversity than the rest of the southeastern USA. Greater genetic similarity between some populations in the native range and introduced range indicate a common provenance for Georgia and South Carolina populations that could have come from any of several western or southern Chinese populations and a different provenance for other southeastern USA populations and the Australian population, which were most similar to more northeastern Chinese populations. Differences among introduced populations in potentially adaptive traits (e.g., herbivore tolerance, herbivore resistance, growth rates) may result in part from the introduction history, in particular from differences present among source populations in the native range.

Synergistic effects of the invasive Chinese tallow (Triadica sebifera) and climate change on aquatic amphibian survival

PubMed Central

Saenz, Daniel; Fucik, Erin M; Kwiatkowski, Matthew A

2013-01-01

Changes in climate and the introduction of invasive species are two major stressors to amphibians, although little is known about the interaction between these two factors with regard to impacts on amphibians. We focused our study on an invasive tree species, the Chinese tallow (Triadica sebifera), that annually sheds its leaves and produces leaf litter that is known to negatively impact aquatic amphibian survival. The purpose of our research was to determine whether the timing of leaf fall from Chinese tallow and the timing of amphibian breeding (determined by weather) influence survival of amphibian larvae. We simulated a range of winter weather scenarios, ranging from cold to warm, by altering the relative timing of when leaf litter and amphibian larvae were introduced into aquatic mesocosms. Our results indicate that amphibian larvae survival was greatly affected by the length of time Chinese tallow leaf litter decomposes in water prior to the introduction of the larvae. Larvae in treatments simulating warm winters (early amphibian breeding) were introduced to the mesocosms early in the aquatic decomposition process of the leaf litter and had significantly lower survival compared with cold winters (late amphibian breeding), likely due to significantly lower dissolved oxygen levels. Shifts to earlier breeding phenology, linked to warming climate, have already been observed in many amphibian taxa, and with most climate models predicting a significant warming trend over the next century, the trend toward earlier breeding should continue if not increase. Our results strongly suggest that a warming climate can interact with the effects of invasive plant species, in ways we have not previously considered, to reduce the survival of an already declining group of organisms. PMID:24363907

Synergistic effects of the invasive Chinese tallow (Triadica sebifera) and climate change on aquatic amphibian survival.

PubMed

Saenz, Daniel; Fucik, Erin M; Kwiatkowski, Matthew A

2013-11-01

Changes in climate and the introduction of invasive species are two major stressors to amphibians, although little is known about the interaction between these two factors with regard to impacts on amphibians. We focused our study on an invasive tree species, the Chinese tallow (Triadica sebifera), that annually sheds its leaves and produces leaf litter that is known to negatively impact aquatic amphibian survival. The purpose of our research was to determine whether the timing of leaf fall from Chinese tallow and the timing of amphibian breeding (determined by weather) influence survival of amphibian larvae. We simulated a range of winter weather scenarios, ranging from cold to warm, by altering the relative timing of when leaf litter and amphibian larvae were introduced into aquatic mesocosms. Our results indicate that amphibian larvae survival was greatly affected by the length of time Chinese tallow leaf litter decomposes in water prior to the introduction of the larvae. Larvae in treatments simulating warm winters (early amphibian breeding) were introduced to the mesocosms early in the aquatic decomposition process of the leaf litter and had significantly lower survival compared with cold winters (late amphibian breeding), likely due to significantly lower dissolved oxygen levels. Shifts to earlier breeding phenology, linked to warming climate, have already been observed in many amphibian taxa, and with most climate models predicting a significant warming trend over the next century, the trend toward earlier breeding should continue if not increase. Our results strongly suggest that a warming climate can interact with the effects of invasive plant species, in ways we have not previously considered, to reduce the survival of an already declining group of organisms.

In-situ transesterification of seeds of invasive Chinese tallow trees (Triadica sebifera L.) in a microwave batch system (GREEN(3)) using hexane as co-solvent: Biodiesel production and process optimization.

PubMed

Barekati-Goudarzi, Mohamad; Boldor, Dorin; Nde, Divine B

2016-02-01

In-situ transesterification (simultaneous extraction and transesterification) of Chinese tallow tree seeds into methyl esters using a batch microwave system was investigated in this study. A high degree of oil extraction and efficient conversion of oil to biodiesel were found in the proposed range. The process was further optimized in terms of product yields and conversion rates using Doehlert optimization methodology. Based on the experimental results and statistical analysis, the optimal production yield conditions for this process were determined as: catalyst concentration of 1.74wt.%, solvent ratio about 3 (v/w), reaction time of 20min and temperature of 58.1°C. H(+)NMR was used to calculate reaction conversion. All methyl esters produced using this method met ASTM biodiesel quality specifications. Copyright © 2015 Elsevier Ltd. All rights reserved.

40 CFR 721.6183 - Amides, from ammonium hydroxide - maleic anhydride polymer and hydrogenated tallow alkyl amines...

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 31 2014-07-01 2014-07-01 false Amides, from ammonium hydroxide - maleic anhydride polymer and hydrogenated tallow alkyl amines, sodium salts, compds. with ethanolamine... Substances § 721.6183 Amides, from ammonium hydroxide - maleic anhydride polymer and hydrogenated tallow...

40 CFR 721.6183 - Amides, from ammonium hydroxide - maleic anhydride polymer and hydrogenated tallow alkyl amines...

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 32 2012-07-01 2012-07-01 false Amides, from ammonium hydroxide - maleic anhydride polymer and hydrogenated tallow alkyl amines, sodium salts, compds. with ethanolamine... Substances § 721.6183 Amides, from ammonium hydroxide - maleic anhydride polymer and hydrogenated tallow...

40 CFR 721.6183 - Amides, from ammonium hydroxide - maleic anhydride polymer and hydrogenated tallow alkyl amines...

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 32 2013-07-01 2013-07-01 false Amides, from ammonium hydroxide - maleic anhydride polymer and hydrogenated tallow alkyl amines, sodium salts, compds. with ethanolamine... Substances § 721.6183 Amides, from ammonium hydroxide - maleic anhydride polymer and hydrogenated tallow...

Biology and host range of Heterapoderopsis bicallosicollis; a potential biological control agent for Chinese tallow Triadica sebifera

USDA-ARS?s Scientific Manuscript database

Chinese tallow, Triadica sebifera, is an invasive weed that infests natural and agricultural areas of the southeastern USA. A candidate for biological control of Chinese tallow has been studied under quarantine conditions. The biology and host range of a primitive leaf feeding beetle, Heterapoderops...

Robust new NIRS coupled with multivariate methods for the detection and quantification of tallow adulteration in clarified butter samples.

PubMed

Mabood, Fazal; Abbas, Ghulam; Jabeen, Farah; Naureen, Zakira; Al-Harrasi, Ahmed; Hamaed, Ahmad M; Hussain, Javid; Al-Nabhani, Mahmood; Al Shukaili, Maryam S; Khan, Alamgir; Manzoor, Suryyia

2018-03-01

Cows' butterfat may be adulterated with animal fat materials like tallow which causes increased serum cholesterol and triglycerides levels upon consumption. There is no reliable technique to detect and quantify tallow adulteration in butter samples in a feasible way. In this study a highly sensitive near-infrared (NIR) spectroscopy combined with chemometric methods was developed to detect as well as quantify the level of tallow adulterant in clarified butter samples. For this investigation the pure clarified butter samples were intentionally adulterated with tallow at the following percentage levels: 1%, 3%, 5%, 7%, 9%, 11%, 13%, 15%, 17% and 20% (wt/wt). Altogether 99 clarified butter samples were used including nine pure samples (un-adulterated clarified butter) and 90 clarified butter samples adulterated with tallow. Each sample was analysed by using NIR spectroscopy in the reflection mode in the range 10,000-4000 cm -1 , at 2 cm -1 resolution and using the transflectance sample accessory which provided a total path length of 0.5 mm. Chemometric models including principal components analysis (PCA), partial least-squares discriminant analysis (PLSDA), and partial least-squares regressions (PLSR) were applied for statistical treatment of the obtained NIR spectral data. The PLSDA model was employed to differentiate pure butter samples from those adulterated with tallow. The employed model was then externally cross-validated by using a test set which included 30% of the total butter samples. The excellent performance of the model was proved by the low RMSEP value of 1.537% and the high correlation factor of 0.95. This newly developed method is robust, non-destructive, highly sensitive, and economical with very minor sample preparation and good ability to quantify less than 1.5% of tallow adulteration in clarified butter samples.

Metabolism of Some Anionic Tallow-based Detergents by Sewage Microorganisms1

PubMed Central

Cordon, Theone C.; Maurer, Elmer W.; Nuñez-Ponzoa, M. V.; Stirton, A. J.

1968-01-01

A method in which the test detergent was the sole source of carbon was used to study the metabolism of several tallow-based detergents. These were tallow alcohol sulfates, long-chain ether alcohol sulfates, and esters of α-sulfo fatty acids. Sodium p-(1-methylundecyl)benzenesulfonate (LAS) was used as a reference material. The alcohol sulfates were the most rapidly and completely metabolized (96 to 99%), and one ether alcohol sulfate was 94% degraded. The other compounds were metabolized to the extent of 61 to 87%; LAS was 80% degraded. Except for the alcohol sulfates, loss of methylene blue activity (MBAS) occurred long before the chemical oxygen demand (COD) values had reached a minimum; with the alcohol sulfates, MBAS and COD decreased simultaneously. PMID:5636472

Timing of favorable conditions, competition and fertility interact to govern recruitment of invasive Chinese tallow tree in stressful environments.

PubMed

Gabler, Christopher A; Siemann, Evan

2013-01-01

The rate of new exotic recruitment following removal of adult invaders (reinvasion pressure) influences restoration outcomes and costs but is highly variable and poorly understood. We hypothesize that broad variation in average reinvasion pressure of Triadica sebifera (Chinese tallow tree, a major invader) arises from differences among habitats in spatiotemporal availability of realized recruitment windows. These windows are periods of variable duration long enough to permit establishment given local environmental conditions. We tested this hypothesis via a greenhouse mesocosm experiment that quantified how the duration of favorable moisture conditions prior to flood or drought stress (window duration), competition and nutrient availability influenced Triadica success in high stress environments. Window duration influenced pre-stress seedling abundance and size, growth during stress and final abundance; it interacted with other factors to affect final biomass and germination during stress. Stress type and competition impacted final size and biomass, plus germination, mortality and changes in size during stress. Final abundance also depended on competition and the interaction of window duration, stress type and competition. Fertilization interacted with competition and stress to influence biomass and changes in height, respectively, but did not affect Triadica abundance. Overall, longer window durations promoted Triadica establishment, competition and drought (relative to flood) suppressed establishment, and fertilization had weak effects. Interactions among factors frequently produced different effects in specific contexts. Results support our 'outgrow the stress' hypothesis and show that temporal availability of abiotic windows and factors that influence growth rates govern Triadica recruitment in stressful environments. These findings suggest that native seed addition can effectively suppress superior competitors in stressful environments. We also describe

Timing of Favorable Conditions, Competition and Fertility Interact to Govern Recruitment of Invasive Chinese Tallow Tree in Stressful Environments

PubMed Central

Gabler, Christopher A.; Siemann, Evan

2013-01-01

The rate of new exotic recruitment following removal of adult invaders (reinvasion pressure) influences restoration outcomes and costs but is highly variable and poorly understood. We hypothesize that broad variation in average reinvasion pressure of Triadica sebifera (Chinese tallow tree, a major invader) arises from differences among habitats in spatiotemporal availability of realized recruitment windows. These windows are periods of variable duration long enough to permit establishment given local environmental conditions. We tested this hypothesis via a greenhouse mesocosm experiment that quantified how the duration of favorable moisture conditions prior to flood or drought stress (window duration), competition and nutrient availability influenced Triadica success in high stress environments. Window duration influenced pre-stress seedling abundance and size, growth during stress and final abundance; it interacted with other factors to affect final biomass and germination during stress. Stress type and competition impacted final size and biomass, plus germination, mortality and changes in size during stress. Final abundance also depended on competition and the interaction of window duration, stress type and competition. Fertilization interacted with competition and stress to influence biomass and changes in height, respectively, but did not affect Triadica abundance. Overall, longer window durations promoted Triadica establishment, competition and drought (relative to flood) suppressed establishment, and fertilization had weak effects. Interactions among factors frequently produced different effects in specific contexts. Results support our ‘outgrow the stress’ hypothesis and show that temporal availability of abiotic windows and factors that influence growth rates govern Triadica recruitment in stressful environments. These findings suggest that native seed addition can effectively suppress superior competitors in stressful environments. We also describe

Identification, characterization and structure analysis of a type I ribosome-inactivating protein from Sapium sebiferum (Euphorbiaceae)

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

Wu, Ying; School of Life Sciences, University of Science and Technology of China, Hefei 230027, Anhui; College of Food and Bioengineering, Henan University of Science and Technology, Luoyang 471023, Henan

2015-08-07

Ribosome-inactivating proteins (RIPs) are N-glycosidases (EC3.2.2.22) that universally inactivate the ribosome, thereby inhibiting protein biosynthesis. In this study, a novel type I RIPs named SEBIN was identified in Sapium sebiferum. Nuclear acid depurine experiment showed that SEBIN had rRNA N-Glycosidase activity. Further experiment indicated that SEBIN significantly inhibited Caenorhabditis elegans development as well as resulted in worm cell apoptosis. This is the first report to evaluate RIPs toxicity using C. elegans. We proposed that SEBIN may impaire C. elegans reproduction in a DNA-damage manner besides traditional protein synthesis inhibition approach. The predicted 3D structure was modeled using threading and ab initio modeling,more » and the r-RNA binding residue of SEBIN was identified through the protein-ligand docking approach. It showed the amino acid residues, Glu195, Asn81, Ala82, Tyr83, Glu164, Ser163, Ile159 and Arg167, played critical roles in catalytic process. Our results provided the theoretical foundation of structure–function relationships between enzymatic properties, toxicity and structural characterization of SEBIN. - Graphical abstract: Superposition of main chains of ricin (cyan) and SEBIN (brown), and adenine binding site residues of SEBIN. - Highlights: • A Ribosome-inactivating proteins gene (SEBIN) was isolated from Sapium sebiferum. • SEBIN had DNase activity besides widely reported ribosome inactivation via N-glycosidases activity. • SEBIN significantly inhibited Caenorhabditis elegans development in vivo. • SEBIN may impaire C. elegans reproduction in a DNA-damage manner with the aid of mutant strains hus-1 and clk-2. • The possible active sites between SEBIN and the adenine of rRNA were predicted.« less

Antimicrobial and cytotoxic constituents from leaves of Sapium baccatum.

PubMed

Ahmed, Yunus; Sohrab, Md Hossain; Al-Reza, Sharif M; Tareq, Faqir Shahidulla; Hasan, Choudhury M; Sattar, M A

2010-02-01

Six compounds, namely, Lupeol (1), Betulin (2), beta-Taraxerol (3), Taraxerone (4), Stigmasterol (5) and beta-Sitosterol (6) were isolated from the petroleum ether extract of the leaves of Sapium baccatum based on spectroscopic evidence. Lupeol (1), Betulin (2) and Stigmasterol (5) were isolated for the first time from this plant. The cytotoxic potential of the different solvent extracts (methanol, petroleum ether, carbon-tetrachloride and dichloromethane); six column fractions (F-4, F-7, F-10, F-12, F-18 and F-22) of petroleum ether extract and three pure compounds 1, 4 and 6 were determined by using brine shrimp lethality bioassay. The LC50 of all the tested samples were showed to be lethal to brine shrimp nauplii. However, petroleum ether, carbon-tetrachloride extract, column fractions F-4 and F-18 of petroleum ether extract and pure compound 6 showed quite potent activity in brine shrimp lethality bioassay with LC50 1.33, 1.35, 1.40, 1.58 and 1.58 microg/ml, respectively. These result suggested that they might be contain antitumor or pesticidal activity. Further, the methanol extract and four column fractions (F-7, F-12, F-18 and F-22) of petroleum ether showed significant activity against the tested microorganisms. Copyright 2009 Elsevier Ltd. All rights reserved.

40 CFR 721.630 - Salt of a modified tallow alkylenediamine (generic).

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 30 2010-07-01 2010-07-01 false Salt of a modified tallow alkylenediamine (generic). 721.630 Section 721.630 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) TOXIC SUBSTANCES CONTROL ACT SIGNIFICANT NEW USES OF CHEMICAL SUBSTANCES Significant New Uses for Specific Chemical Substances § 721.630 Sal...

LC-MS guided isolation of diterpenoids from Sapium insigne with α-glucosidase inhibitory activities.

PubMed

Yan, De-Xiu; Geng, Chang-An; Yang, Tong-Hua; Huang, Xiao-Yan; Li, Tian-Ze; Gao, Zhen; Ma, Yun-Bao; Peng, Hua; Zhang, Xue-Mei; Chen, Ji-Jun

2018-04-08

Ten new (1-10) and ten known (11-20) diterpenoids involving ent-atisane, ent-seco-atisane, ent-kaurane and ent-seco-kaurane types were isolated from Sapium insigne under the guidance of LCMS-IT-TOF analyses. Their structures were characterized by extensive spectroscopic analyses (HRESIMS, UV, IR, 1D and 2D NMR). A putative biosynthetic pathway was proposed for ent-seco-atisane diterpenoids. Their inhibitory activities on α-glucosidase in vitro were tested for the first time. Compound 4 showed moderate inhibitory effect on α-glucosidase with an IC 50 value of 0.34 mM via a noncompetitive inhibition mechanism (K i  = 0.27 mM). The preliminary structure-activity relationships of the ent-atisane diterpenoids inhibiting α-glucosidase were discussed. Copyright © 2018 Elsevier B.V. All rights reserved.

Enhancing freezing tolerance of Brassica napus L. by overexpression of a stearoyl-acyl carrier protein desaturase gene (SAD) from Sapium sebiferum (L.) Roxb.

PubMed

Peng, Dan; Zhou, Bo; Jiang, Yueqiao; Tan, XiaoFeng; Yuan, DeYi; Zhang, Lin

2018-07-01

Sapium sebiferum (L.) Roxb. is an important woody oil tree and traditional herbal medicine in China. Stearoyl-acyl carrier protein desaturase (SAD) is a dehydrogenase enzyme that plays a key role in the transformation of saturated fatty acids into unsaturated fatty acids in oil; these fatty acids greatly influence the freezing tolerance of plants. However, it remains unclear whether freezing tolerance can be regulated by the expression level of SsSAD in S. sebiferum L. Our research indicated that SsSAD expression in S. sebiferum L. increased under freezing stress. To further confirm this result, we constructed a pEGAD-SsSAD vector and transformed it into B. napus L. W10 by Agrobacterium tumefaciens-mediated transformation. Transgenic plants that overexpressed the SsSAD gene exhibited significantly higher linoleic (18:2) and linolenic acid (18:3) content and advanced freezing tolerance. These results suggest that SsSAD overexpression in B. napus L. can increase the content of polyunsaturated fatty acids (PUFAs) such as linoleic (18:2) and linolenic acid (18:3), which are likely pivotal in improving freezing tolerance in B. napus L. plants. Thus, SsSAD overexpression could be useful in the production of freeze-tolerant varieties of B. napus L. Copyright © 2018 Elsevier B.V. All rights reserved.

Gene expression of insulin signal-transduction pathway intermediates is lower in rats fed a beef tallow diet than in rats fed a safflower oil diet.

PubMed

Kim, Y B; Nakajima, R; Matsuo, T; Inoue, T; Sekine, T; Komuro, M; Tamura, T; Tokuyama, K; Suzuki, M

1996-09-01

To elucidate the effects of dietary fatty acid composition on the insulin signaling pathway, we measured the gene expression of the earliest steps in the insulin action pathway in skeletal muscle of rats fed a safflower oil diet or a beef tallow diet. Rats were meal-fed an isoenergetic diet based on either safflower oil or beef tallow for 8 weeks. Both diets provided 45%, 35%, and 20% of energy as fat, carbohydrate, and protein, respectively. Insulin resistance, assessed from the diurnal rhythm of plasma glucose and insulin and the oral glucose tolerance test (OGTT), developed in rats fed a beef tallow diet. Body fat content was greater in rats fed a beef tallow diet versus a safflower oil diet. The level of insulin receptor mRNA, relative expression of the insulin receptor mRNA isoforms, and receptor protein were not affected by the composition of dietary fatty acids. The abundance of insulin receptor substrate-1 (IRS-1) and phosphatidylinositol (PI) 3-kinase mRNA and protein was significantly lower in rats fed a beef tallow diet versus a safflower oil diet. We conclude that long-term feeding of a high-fat diet with saturated fatty acids induces decrease in IRS-1 and PI 3-kinase mRNA and protein levels, causing insulin resistance in skeletal muscle.

Risk assessment: progress of quarantine biocontrol research on Chinese Tallow, Melaleuca, and Downy Rose Myrtle

USDA-ARS?s Scientific Manuscript database

Risk assessments of two biocontrol candidates for Chinese tallow, Triadica sebifera (Euphoriales: Euphorbiaceae), and one for Melaleuca, Melaleuca quinquenervia (Myrtales: Myrtaceae), were conducted during 2009 and continuing into 2010 by USDA scientists located at the Florida Department of Agricul...

Enzyme-catalyzed synthesis and kinetics of ultrasonic-assisted biodiesel production from waste tallow.

PubMed

Adewale, Peter; Dumont, Marie-Josée; Ngadi, Michael

2015-11-01

The use of ultrasonic processing was evaluated for its ability to achieve adequate mixing while providing sufficient activation energy for the enzymatic transesterification of waste tallow. The effects of ultrasonic parameters (amplitude, cycle and pulse) and major reaction factors (molar ratio and enzyme concentration) on the reaction kinetics of biodiesel generation from waste tallow bio-catalyzed by immobilized lipase [Candida antarctica lipase B (CALB)] were investigated. Three sets of experiments namely A, B, and C were conducted. In experiment set A, two factors (ultrasonic amplitude and cycle) were investigated at three levels; in experiment set B, two factors (molar ratio and enzyme concentration) were examined at three levels; and in experiment set C, two factors (ultrasonic amplitude and reaction time) were investigated at five levels. A Ping Pong Bi Bi kinetic model approach was employed to study the effect of ultrasonic amplitude on the enzymatic transesterification. Kinetic constants of transesterification reaction were determined at different ultrasonic amplitudes (30%, 35%, 40%, 45%, and 50%) and enzyme concentrations (4, 6, and 8 wt.% of fat) at constant molar ratio (fat:methanol); 1:6, and ultrasonic cycle; 5 Hz. Optimal conditions for ultrasound-assisted biodiesel production from waste tallow were fat:methanol molar ratio, 1:4; catalyst level 6% (w/w of fat); reaction time, 20 min (30 times less than conventional batch processes); ultrasonic amplitude 40% at 5 Hz. The kinetic model results revealed interesting features of ultrasound assisted enzyme-catalyzed transesterification (as compared to conventional system): at ultrasonic amplitude 40%, the reaction activities within the system seemed to be steady after 20 min which means the reaction could proceed with or without ultrasonic mixing. Reversed phase high performance liquid chromatography indicated the biodiesel yield to be 85.6±0.08%. Copyright © 2015 Elsevier B.V. All rights reserved.

Effects of Chinese tallow leaf litter on water chemistry and surfacing behaviour of anuran larvae

Treesearch

Daniel Saenz; Cory K. Adams

2017-01-01

The establishment of exotic invasive species, including plants, has been linked to the decline of some amphibian populations. Of particular concern with invasive plants, from an amphibian conservation perspective, is that they are disproportionately wetland or riparian species. Recent evidence suggests that Chinese tallow (Triadica sebifera), an...

Nutritional value of raw soybeans, extruded soybeans, roasted soybeans and tallow as fat sources in early lactating dairy cows.

PubMed

Amanlou, H; Maheri-Sis, N; Bassiri, S; Mirza-Aghazadeh, A; Salamatdust, R; Moosavi, A; Karimi, V

2012-01-01

Thirty multiparous Holstein cows (29.8 ± 4.01days in milk; 671.6 ± 31.47 kg of body weight) were used in a completely randomized design to compare nutritional value of four fat sources including tallow, raw soybeans, extruded soybeans and roasted soybeans for 8 weeks. Experimental diets were a control containing 27.4 % alfalfa silage, 22.5% corn silage, and 50.1% concentrate, and four diets with either tallow, raw soybean, extruded soybean, or roasted soybean added to provide 1.93% supplemental fat. Dry matter and NEL intakes were similar among treatments, while cows fed fat diets had significantly (P<0.05) high NEL intakes when compared to control with no fat. Supplemental fat, whether tallow or full fat soybeans increased milk production (1.89-2.45 kg/d; P<0.01) and FCM production (1.05-2.79; P<0.01). Milk fat yield and percentage of cows fed fat-supplemented diets were significantly (P<0.01 and P<0.05 respectively) higher than control. Between fat-supplemented diets, roasted soybean caused highest milk fat yield and extruded soybean caused lowest milk fat yield. There was no significant effect of supplemental fat on the milk protein and lactose content and yield. Feed efficiency of fat-supplemented diets was significantly (P<0.01) higher than control. Body weight, body weight change and BCS (body condition score) of cows, as well as energy balance and energy efficiency were similar between treatments. In conclusion, while there was no significant effect of fat sources on production response of cows, fat originating from heat-treated soybean help to minimize imported RUP (rumen undegradable protein) sources level as fish meal in comparison with tallow and raw soybean oil. In the Current study, there was no statistical significance among nutritional values of oil from extruded soybeans and roasted soybeans.

Chinese Tallow (Triadica sebifera (L.) Small) Population expansion in Louisiana, East Texas, and Mississippi

Treesearch

Sonja N. Oswalt

2010-01-01

Chinese tallow (Triadica sebifera) is a nonnative invasive species with high fecundity rates that has naturalized from the coastal prairies of east Texas along the Gulf and Atlantic coasts as far north as North Carolina. Population differences were computed for two forest inventory periods (mid-1990s and late 2000s) in Louisiana, east Texas, and Mississippi using data...

9 CFR 315.1 - Carcasses and parts passed for cooking; rendering into lard or tallow.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 9 Animals and Animal Products 2 2010-01-01 2010-01-01 false Carcasses and parts passed for cooking... PARTS PASSED FOR COOKING § 315.1 Carcasses and parts passed for cooking; rendering into lard or tallow. Carcasses and parts passed for cooking may be rendered into lard in accordance with § 319.702 of this...

Hybrid striped bass feeds based on fish oil, beef tallow, and eicosapentaenoic acid/docosahexaenoic acid supplements: Insight regarding fish oil sparing and demand for -3 long-chain polyunsaturated fatty acids.

PubMed

Bowzer, J; Jackson, C; Trushenski, J

2016-03-01

Previous research suggests that saturated (SFA) and monounsaturated fatty acid (MUFA) rich lipids, including beef tallow, can make utilization or diet-to-tissue transfer of long-chain polyunsaturated fatty acids (LC-PUFA) more efficient. We hypothesized that using beef tallow as an alternative to fish oil may effectively reduce the LC-PUFA demand of hybrid striped bass × and allow for greater fish oil sparing. Accordingly, we evaluated growth performance and tissue fatty acid profiles of juvenile fish (23.7 ± 0.3 g) fed diets containing menhaden fish oil (considered an ideal source of LC-PUFA for this taxon), beef tallow (BEEF ONLY), or beef tallow amended with purified sources of eicosapentaenoic acid (EPA) and/or docosahexaenoic acid (DHA) to achieve levels corresponding to 50 or 100% of those observed in the FISH ONLY feed. Diets were randomly assigned to quadruplicate tanks of fish ( = 4; 10 fish/tank), and fish were fed assigned diets to apparent satiation once daily for 10 wk. Survival (98-100%) was equivalent among treatments, but weight gain (117-180%), specific growth rate (1.1-1.5% BW/d), feed intake (1.4-1.8% BW/d), thermal growth coefficient (0.50-0.70), and feed conversion ratio (FCR; 1.1-1.4, DM basis) varied. Except for FCR, no differences were observed between the FISH ONLY and BEEF ONLY treatments, but performance was generally numerically superior among fish fed the diets containing beef tallow supplemented with DHA at the 100% or both EPA and DHA at the 50% or 100% level. Tissue fatty acid composition was significantly distorted in favor among fish fed the beef tallow-based feeds; however, profile distortion was most overt in peripheral tissues. Results suggest that beef tallow may be used as a primary lipid source in practical diets for hybrid striped bass, but performance may be improved by supplementation with LC-PUFA, particularly DHA. Furthermore, our results suggest that -3 LC-PUFA requirements reported for hybrid striped bass may not be

Chinese tallow (Triadica sebifera) invasion in maritime forests: the role of anthropogenic disturbance and its management implication

Treesearch

Lauren S. Pile; G. Geoff Wang; Benjamin O. Knapp; Joan L. Walker; Michael C. Stambaugh

2017-01-01

Land-use and forest management practices may facilitate the invasion success of non-native plants in forests. In this study, we tested if agricultural land abandonment and subsequent forest management contributed to the invasion success of Chinese tallow (Triadica sebifera (L.) Small) in the maritime forest of Parris Island, SC. We compared the...

Integrating spread dynamics and economics of timber production to manage Chinese Tallow invasions in southern U.S

Treesearch

Hsiao-Hsuan Wang; William E. Grant; Jianbang Gan; William E. Rogers; Todd M. Swannack; Tomasz E. Koralewski; James H. Miller; John W. Taylor

2012-01-01

Economic costs associated with the invasion of nonnative species are of global concern. We estimated expected costs of Chinese tallow (Triadica sebifera (L.) Small) invasions related to timber production in southern U.S. forestlands under different management strategies. Expected costs were confined to the value of timber production losses plus costs for search and...

Beef Tallow, but Not Perilla or Corn Oil, Promotion of Rat Prostate and Intestinal Carcinogenesis by 3,2‐Dimethyl‐4‐aminobiphenyl

PubMed Central

Mori, Toshio; Imaida, Katsumi; Tamano, Seiko; Sano, Masashi; Takahashi, Satoru; Asamoto, Makoto; Takeshita, Masazumi; Ueda, Hiroshi

2001-01-01

The modifying effects of three kinds of fat (corn oil, beef tallow or perilla oil, each at 20% in the diet) on F344 rat prostate carcinogenesis induced by 3,2‐dimethyl‐4‐aminobiphenyl (DMAB) were investigated. Non‐invasive carcinomas of the ventral prostate were induced by DMAB alone and invasive carcinomas of the other prostate lobes and seminal vesicles by DMAB and testosterone propionate (TP). Eight groups of F344 rats were initiated with 50 mg/kg body weight of DMAB at 2‐week intervals for the first 20 weeks, four also receiving TP, extended until week 60. The animals received basal chow powder diet or one of three high fat diets throughout the experiment (60 weeks). One further group served as a non‐carcinogen‐treated control maintained on basal chow powder diet. Beef tallow significantly increased the development of ventral prostate carcinomas with DMAB alone (from 15 to 45%, P<0.05), while perilla oil reduced the incidence of prostatic intraepithelial neoplasia (PIN) in the ventral lobe of rats given DMAB + TP (from 70 to 10%, P<0.01), but not in those given DMAB alone. No other effects of high fats were observed regarding PIN or invasive cancers of the dorsolateral and anterior prostate or seminal vesicles. A satellite experiment demonstrated that all high fat diets for 4 weeks increased the 5‐bromo‐2‐deoxyuridine (BrdU) labeling index of prostate epithelial cells, suggesting that a high fat intake, irrespective of the fatty acid composition, may accelerate cell kinetics in the prostate. Of the three high fat diets, beef tallow was also found to increase intestinal carcinogenesis. Thus, the present data revealed carcinogenesis in the prostate and intestine to be promoted by beef tallow. PMID:11676852

Delayed tree mortality in the Atchafalaya Basin of Southern Louisiana following Hurricane Andrew

USGS Publications Warehouse

Keeland, B.D.; Gorham, L.E.

2009-01-01

Hurricanes can damage trees in forested wetlands, and the potential for mortality related to these storms exists due to the effects of tree damage over time. In August 1992, Hurricane Andrew passed through the forested wetlands of southern Louisiana with winds in excess of 225 kph. Although more than 78 of the basal area was destroyed in some areas, most trees greater than 2.5 cm dbh were alive and resprouting prolifically the following year (98.8). Survival of most tree species was similarly high two years after the hurricane, but mortality rates of some species increased dramatically. For example, Populus heterophylla (swamp cottonwood) mortality increased from 7.8 to 59.2 (n 76) and Salix interior (sandbar willow) mortality increased from 4.5 to 57.1 (n 21). Stem sprouts on many up-rooted hardwood trees of other species were still alive in 1998, 6 years after the hurricane. Due to the understory tree species composition, regeneration, and high levels of resprouting, there was little change in species composition or perhaps a slight shift toward more shade and flood tolerant species six years following the hurricane event. Triadica sebifera (Chinese tallow) was found on some of the sites heavily disturbed by Hurricane Andrew, and may proliferate at the expense of native tree species. ?? 2009 The Society of Wetland Scientists.

[Effects of waterlogging on the growth and energy-metabolic enzyme activities of different tree species].

PubMed

Wang, Gui-Bin; Cao, Fu-Liang; Zhang, Xiao-Yan; Zhang, Wang-Xiang

2010-03-01

Aimed to understand the waterlogging tolerance and adaptation mechanisms of different tree species, a simulated field experiment was conducted to study the growth and energy-metabolic enzyme activities of one-year-old seedlings of Taxodium distichum, Carya illinoensis, and Sapium sebiferum. Three treatments were installed, i. e., CK, waterlogging, and flooding, with the treatment duration being 60 days. Under waterlogging and flooding, the relative growth of test tree species was in the order of T. distichum > C. illinoensis > S. sebiferum, indicating that T. distichum had the strongest tolerance against waterlogging and flooding, while S. sebiferum had the weakest one. Also under waterlogging and flooding, the root/crown ratio of the three tree species increased significantly, suggesting that more photosynthates were allocated in roots, and the lactate dehydrogenase (LDH) and alcohol dehydrogenase (ADH) activities of the tree species also had a significant increase. Among the test tree species, T. distichum had the lowest increment of LDH and ADH activities under waterlogging and flooding, but the increment could maintain at a higher level in the treatment duration, while for C. illinoensis and S. sebiferum, the increment was larger during the initial and medium period, but declined rapidly during the later period of treatment. The malate dehydrogenase (MDH), phosphohexose (HPI), and glucose-6-phosphate dehydrogenase (G6PDH) -6-phosphogluconate dehydrogenase (6PGDH) activities of the tree species under waterlogging and flooding had a significant decrease, and the decrement was the largest for T. distichum, being 35.6% for MDH, 21.0% for HPI, and 22.7% for G6PDH - 6PGDH under flooding. It was suggested that under waterlogging and flooding, the tree species with strong waterlogging tolerance had a higher ability to maintain energy-metabolic balance, and thus, its growth could be maintained at a certain level.

Pre-release assessment of Gadirtha inexacta a proposed biological control agent of Chinese tallow (Triadica sebifera) in the United States

USDA-ARS?s Scientific Manuscript database

Native to China, Chinese tallow, Triadica sebifera (Euphorbiaceae) is an aggressive woody invader in the southeastern United States. The noctuid, Gadirtha inexacta, is a multivoltine herbivore attacking this plant in China. To evaluate its potential as a biological control agent in the United States...

Influence of high dose of phytase and an emulsifier on performance, apparent metabolisable energy and nitrogen retention in broilers fed on diets containing soy oil or tallow.

PubMed

Zaefarian, F; Romero, L F; Ravindran, V

2015-01-01

The effects of high dose of microbial phytase and an emulsifier on the performance, apparent metabolisable energy (AME) and nitrogen (N) retention in broilers fed on diets containing different fat sources were examined in a 5-week trial. Two fat sources (soy oil and tallow), two inclusion levels of E. coli phytase (500 or 1000 phytase units (FTU)/kg diet) and two inclusion levels of lysolecithin emulsifier (0 or 3.5 g/kg of diet) were evaluated in a 2 × 2 × 2 factorial arrangement of treatments. Throughout the 5-week trial, soy oil supplementation improved weight gain and feed per gain compared with tallow, but had no effect on feed intake. The high dose of phytase increased the weight gain and feed intake and lowered the feed per gain during d 1-21, but had no effect on performance parameters over the whole trial period. An effect of emulsifier was observed for feed intake during d 1-21 and over the whole trial period. Addition of emulsifier increased feed intake compared with diets without emulsifier. During weeks 1, 2, 3 and 5, birds fed on soy oil-based diets had higher nitrogen-corrected AME (AMEN) compared with those fed on tallow-based diets. During weeks 2, 3 and 5, the effect of phytase was significant for AMEN, with the high dose increasing the AMEN. During week 2, AMEN was increased with emulsifier addition. During weeks 1, 2, 3 and 5, birds fed on soy oil-based diets had higher fat retention compared with those fed on tallow-based diets. The high dose of phytase improved the retention of fat during week 5 and the addition of emulsifier resulted in higher fat retention during week 1. During weeks 2, 3 and 5, an interaction between fat source × phytase × emulsifier was observed for N retention. In soy oil-based diets, emulsifier plus 1000 FTU/kg phytase increased N retention compared with other groups, while in tallow-based diets, emulsifier addition increased N retention in diets with 500 FTU/kg, but not in 1000 FTU/kg diet. Overall, the

A new species of Gadirtha Walker (Nolidae: Collomeninae): a proposed biological control agent of Chinese tallow (Triadica sebifera (L.) Small) (Euphorbiaceae) in the United States

USDA-ARS?s Scientific Manuscript database

Gadirtha fusca, new species, is described from Hong Kong. Adult, male and female genitalia, larva, and pupa are described, illustrated, and compared with Gadirtha impingens Walker. Species is a possible biological control agent for Chinese tallow (Triadica sebifera (L.) Small, Euphorbiaceae) in the ...

Lower resistance and higher tolerance of invasive host plants: biocontrol agents reach high densities but exert weak control.

PubMed

Wang, Yi; Huang, Wei; Siemann, Evan; Zou, Jianwen; Wheeler, Gregory S; Carrillo, Juli; Ding, Jianqing

2011-04-01

Invasive plants often have novel biotic interactions in their introduced ranges. Their defense to herbivory may differ from their native counterparts, potentially influencing the effectiveness of biological control. If invasive plants have decreased resistance but increased tolerance to enemies, insect herbivores may rapidly build up their populations but exert weak control. Moreover, resource availability to plants may affect the efficacy of biological control agents. We tested these predictions using Chinese tallow tree (Triadica sebifera) and two specialist herbivores (Heterapoderopsis bicallosicollis and Gadirtha inexacta) that are candidates for biological control. We performed a pair of field common garden experiments in China in which Triadica seedlings from the native or introduced range were grown in low or high light conditions and subjected to different levels of herbivory by each herbivore in a factorial design. We found that Heterapoderopsis achieved greater densities on tallow trees from the introduced range or when trees were grown in high light conditions. When Gadirtha was raised in the lab on tallow tree foliage we found that it performed better (larger pupal size) when fed foliage from introduced populations. However, introduced populations generally had greater herbivore tolerance such that the impact of each agent on plant performance was lower than on native populations despite higher herbivore loads. Tallow trees grew more slowly and achieved smaller sizes in lower light levels, but the impact of biological control agents was comparable to that found for higher light levels. Plants from introduced populations grew larger than those from native populations in all conditions. Our results suggest that reduced resistance and increased tolerance to herbivory in introduced populations may impede success of biological control programs. Biological control practitioners should include plants from the introduced range in the prerelease evaluation

Integrating spread dynamics and economics of timber production to manage Chinese tallow invasions in southern U.S. forestlands.

PubMed

Wang, Hsiao-Hsuan; Grant, William E; Gan, Jianbang; Rogers, William E; Swannack, Todd M; Koralewski, Tomasz E; Miller, James H; Taylor, John W

2012-01-01

Economic costs associated with the invasion of nonnative species are of global concern. We estimated expected costs of Chinese tallow (Triadica sebifera (L.) Small) invasions related to timber production in southern U.S. forestlands under different management strategies. Expected costs were confined to the value of timber production losses plus costs for search and control. We simulated management strategies including (1) no control (NC), and control beginning as soon as the percentage of invaded forest land exceeded (2) 60 (Low Control), (3) 25 (Medium Control), or (4) 0 (High Control) using a spatially-explicit, stochastic, bioeconomic model. With NC, simulated invasions spread northward and westward into Arkansas and along the Gulf of Mexico to occupy ≈1.2 million hectares within 20 years, with associated expected total costs increasing exponentially to ≈$300 million. With LC, MC, and HC, invaded areas reached ≈275, 34, and 2 thousand hectares after 20 years, respectively, with associated expected costs reaching ≈$400, $230, and $200 million. Complete eradication would not be cost-effective; the minimum expected total cost was achieved when control began as soon as the percentage of invaded land exceeded 5%. These results suggest the importance of early detection and control of Chinese tallow, and emphasize the importance of integrating spread dynamics and economics to manage invasive species.

Integrating Spread Dynamics and Economics of Timber Production to Manage Chinese Tallow Invasions in Southern U.S. Forestlands

PubMed Central

Wang, Hsiao-Hsuan; Grant, William E.; Gan, Jianbang; Rogers, William E.; Swannack, Todd M.; Koralewski, Tomasz E.; Miller, James H.; Taylor, John W.

2012-01-01

Economic costs associated with the invasion of nonnative species are of global concern. We estimated expected costs of Chinese tallow (Triadica sebifera (L.) Small) invasions related to timber production in southern U.S. forestlands under different management strategies. Expected costs were confined to the value of timber production losses plus costs for search and control. We simulated management strategies including (1) no control (NC), and control beginning as soon as the percentage of invaded forest land exceeded (2) 60 (Low Control), (3) 25 (Medium Control), or (4) 0 (High Control) using a spatially-explicit, stochastic, bioeconomic model. With NC, simulated invasions spread northward and westward into Arkansas and along the Gulf of Mexico to occupy ≈1.2 million hectares within 20 years, with associated expected total costs increasing exponentially to ≈$300 million. With LC, MC, and HC, invaded areas reached ≈275, 34, and 2 thousand hectares after 20 years, respectively, with associated expected costs reaching ≈$400, $230, and $200 million. Complete eradication would not be cost-effective; the minimum expected total cost was achieved when control began as soon as the percentage of invaded land exceeded 5%. These results suggest the importance of early detection and control of Chinese tallow, and emphasize the importance of integrating spread dynamics and economics to manage invasive species. PMID:22442731

Antibacterial activity of tannins isolated from Sapium baccatum extract and use for control of tomato bacterial wilt.

PubMed

Vu, Thuy Thu; Kim, Hun; Tran, Vu Khac; Vu, Hoang Dinh; Hoang, Tien Xuan; Han, Jae Woo; Choi, Yong Ho; Jang, Kyoung Soo; Choi, Gyung Ja; Kim, Jin-Cheol

2017-01-01

In the search for new antibacterial agents from natural sources, we revealed that a crude methanol extract of Sapium baccatum was highly active against Ralstonia solanacearum, a causal agent of a serious disease called bacterial wilt of tomato. The bioassay-guided fractionation of this extract resulted in the isolation of seven known active compounds, including gallic acid, methyl gallate, corilagin, tercatain, chebulagic acid, chebulinic acid, and quercetin 3-O-α-L-arabinopyranoside. Their chemical structures were determined by electrospray ionization mass spectrometry and nuclear magnetic resonance spectroscopy. An in vitro antibacterial bioassay using a broth microdilution method revealed that, except for quercetin 3-O-α-L-arabinopyranoside (MIC = 250 μg/mL), the isolated compounds exhibited strong antibacterial activity against R. solanacearum (MIC = 26-52 μg/mL). Among the seven compounds, methyl gallate exhibited the strongest broad-spectrum activity against most of the plant pathogenic bacteria tested (MIC = 26-250 μg/mL). In the in vivo experiments, the crude extract of S. baccatum at 2000 and 1000 μg/mL reduced the development of tomato bacterial wilt by 83 and 63%, respectively, under greenhouse conditions after 14 days of infection. The results suggested that the extracts of S. baccatum or isolated tannins could be used as natural bactericides for the control of bacterial wilt of tomato.

Antibacterial activity of tannins isolated from Sapium baccatum extract and use for control of tomato bacterial wilt

PubMed Central

Vu, Thuy Thu; Kim, Hun; Tran, Vu Khac; Vu, Hoang Dinh; Hoang, Tien Xuan; Han, Jae Woo; Choi, Yong Ho; Jang, Kyoung Soo; Choi, Gyung Ja

2017-01-01

In the search for new antibacterial agents from natural sources, we revealed that a crude methanol extract of Sapium baccatum was highly active against Ralstonia solanacearum, a causal agent of a serious disease called bacterial wilt of tomato. The bioassay-guided fractionation of this extract resulted in the isolation of seven known active compounds, including gallic acid, methyl gallate, corilagin, tercatain, chebulagic acid, chebulinic acid, and quercetin 3-O-α-L-arabinopyranoside. Their chemical structures were determined by electrospray ionization mass spectrometry and nuclear magnetic resonance spectroscopy. An in vitro antibacterial bioassay using a broth microdilution method revealed that, except for quercetin 3-O-α-L-arabinopyranoside (MIC = 250 μg/mL), the isolated compounds exhibited strong antibacterial activity against R. solanacearum (MIC = 26–52 μg/mL). Among the seven compounds, methyl gallate exhibited the strongest broad-spectrum activity against most of the plant pathogenic bacteria tested (MIC = 26–250 μg/mL). In the in vivo experiments, the crude extract of S. baccatum at 2000 and 1000 μg/mL reduced the development of tomato bacterial wilt by 83 and 63%, respectively, under greenhouse conditions after 14 days of infection. The results suggested that the extracts of S. baccatum or isolated tannins could be used as natural bactericides for the control of bacterial wilt of tomato. PMID:28742863

The host range and impact of Bikasha collaris (Coleoptera: Chrysomelidae), a promising candidate agent for biological control of Chinese tallow, Triadica sebifera (Euphorbiaceae) in the United States

USDA-ARS?s Scientific Manuscript database

Native to China, the Chinese tallow, Triadica sebifera (Euphorbiaceae) is an aggressive woody invader in the southeastern United States. The flea beetle, Bikasha collaris (Coleoptera: Chrysomelidae), is a common herbivore attacking this plant in China. To evaluate its potential as a biological contr...

Level of selected toxic elements in meat, liver, tallow and bone marrow of young semi-domesticated reindeer (Rangifer tarandus tarandus L.) from Northern Norway

PubMed Central

Hassan, Ammar Ali; Rylander, Charlotta; Brustad, Magritt; Sandanger, Torkjel M.

2012-01-01

Objectives To gain knowledge on toxic elements in semi-domesticated reindeer and their distribution in meat, liver, tallow and bone marrow. The correlations between concentrations in meat and liver, as well as the use of the latter as an indicator for toxic elements in meat, were also investigated. Study design Cross-sectional study on population of semi-domesticated reindeer from 2 northern Norwegian counties (Finnmark and Nordland). Methods Semi-domesticated reindeer carcasses (n=31) were randomly selected, from which meat, liver, tallow and bone marrow samples were collected. Selected toxic elements (cadmium, lead, arsenic, nickel and vanadium) were studied. Results Liver was the organ with the highest level of all elements except for nickel, which was highest in bone marrow. Meat had the lowest levels, whereas levels in tallow and bone marrow were between those of meat and liver. Concentrations of cadmium, lead and arsenic were significantly different (p<0.05) between meat and liver, while only arsenic and cadmium were significantly correlated in meat (rs=0.71, p<0.01) and liver (rs=0.72, p<0.01). The cadmium level exceeded the European Commission's (EC) maximum level set for bovine meat and live in 52% of the liver samples (n=29). Nevertheless, the estimated monthly cadmium intake from liver of 2.29 µg/kg body weight was well below the provisional tolerable monthly intake of 25 µg/kg body weight set by the FAO/WHO Joint Expert Committee on Food Additives. Conclusions Based on the measured levels and their relation to the maximum level and to the provisional tolerable weekly/monthly intake limits, it could be inferred that consumption of reindeer meat is not associated with any health risk related to the studied toxic elements for consumers. PMID:22564461

Coconut oil and beef tallow, but not tricaprylin, can replace menhaden oil in the diet of red drum (Sciaenops ocellatus) without adversely affecting growth or fatty acid composition.

PubMed

Craig, S R; Gatlin, D M

1995-12-01

The ability of juvenile red drum (Sciaenops ocellatus) to utilize medium-chain triglycerides (MCT) and other saturated dietary lipids was investigated in two 6-wk feeding experiments. Diets contained solvent-extracted menhaden fish meal to which menhaden fish oil (control), coconut oil, corn oil, beef tallow or various levels of MCT as tricaprylin (30, 46, 65 and 80% of total lipid) were added. Diets were fed to triplicate groups of juvenile red drum in aquaria containing brackish (6%) water. In the first feeding experiment, red drum fed the control diet had the greatest weight gains and feed efficiencies. Weight gain, but not feed was slightly, of fish fed corn oil and fish fed coconut oil was slightly (P < 0.05) lower. In the second feeding experiment, fish fed coconut oil and those fed beef tallow had significantly higher weight gains and feed efficiencies than did fish fed the control diet. Fish fed the diets containing tricaprylin at all inclusion levels in both feeding experiments had significantly lower weight gains and feed efficiencies and higher levels of beta-hydroxybutyric acid in plasma. Fish fed diets with high levels of MCT also had lower (n-3) and greater (n-6) fatty acid levels in the neutral lipid fraction of muscle tissue compared with fish fed the control diet. Coconut oil and beef tallow consistently resulted in greater liver lipid deposition but had variable effects on other tissue indices. Saturated dietary lipids had variable effects on fatty acid composition of muscle polar and neutral lipid fractions.(ABSTRACT TRUNCATED AT 250 WORDS)

Enzymatically interesterified fats based on mutton tallow and walnut oil suitable for cosmetic emulsions.

PubMed

Kowalska, M; Mendrycka, M; Zbikowska, A; Stawarz, S

2015-02-01

Formation of emulsion systems based on interesterified fats was the objective of the study. Enzymatic interesterification was carried out between enzymatic mutton tallow and walnut oil in the proportions 2 : 3 (w/w) to produce fats not available in nature. At the beginning of the interesterification process, the balance between the interesterification and fat hydrolysis was intentionally disturbed by adding more water to the catalyst (Lipozyme IR MR) of the reaction to produce more of the polar fraction monoacylglycerols [MAGs] and diacylglycerols [DAGs]. To obtain a greater quantity of MAGs and DAGs in the reaction environment via hydrolysis, water was added (11, 13, 14, 16 w-%) to the enzymatic preparation. The obtained fats were used to form emulsions. The emulsions were evaluated with respect to sensory and skin moisturizing properties by 83 respondents. Determination of emulsion stability using temperature and centrifugal tests was carried out. Morphology and the type of emulsions were determined. The respondents described the skin to which the emulsions in testing were applied as smooth, pleasant to touch and adequately moisturized. The work has demonstrated that interesterification of a mutton tallow and walnut oil blend resulted in new fats with very interesting characteristics of triacylglycerols that are not present in the environment. The results of the present work indicate the possibility of application of fats with the largest quantity of MAGs and DAGs as a fat base of emulsions in the cosmetic industries. The hypothesis assumed in this work of producing additional quantities of MAGs and DAGs (in the process of enzymatic interesterification) responsible for the stability of the system was confirmed. It should be pointed out that the emulsions based on interesterified fats exhibited a greater level of moisturization of the skin than the emulsions containing non-interesterified fat. Also, in the respondents' opinion, the emulsion containing fat, which

A new species of Gadirtha Walker (Nolidae, Eligminae): a proposed biological control agent of Chinese tallow (Triadica sebifera (L.) Small) (Euphorbiaceae) in the United States.

PubMed

Pogue, Michael G

2014-01-01

Gadirtha fusca sp. n., is described from Guangxi Province, China. Gadirtha fusca differs in forewing color and pattern, male and female genitalia, and in larval pattern from all other species of Gadirtha. Gadirtha fusca has been evaluated as a potential biological control agent for Chinese tallow (Triadica sebifera (L.) Small, Euphorbiaceae) in the southeastern United States. Adult, male and female genitalia, larva, and pupa are described, illustrated, and compared with Gadirtha impingens Walker.

Iron utilization and liver mineral concentrations in rats fed safflower oil, flaxseed oil, olive oil, or beef tallow in combination with different concentrations of dietary iron.

PubMed

Shotton, Andrea D; Droke, Elizabeth A

2004-03-01

Diets with a higher proportion of polyunsaturated fatty acids (i.e., linoleic acid) have decreased iron absorption and utilization compared with diets containing a higher proportion of the saturated fatty acid stearic acid (e.g., beef tallow). However, less is known regarding the influence of other polyunsaturated or monounsaturated fatty acids, along with higher dietary iron, on iron absorption and utilization. The present study was conducted to compare the effects of dietary fat sources known to vary in (n-3), (n-6), and (n-9) fatty acids on iron utilization and liver mineral concentrations. Male weanling rats were fed a diet containing 10, 35, or 100 microg/g iron in combination with safflower oil, flaxseed oil, olive oil, or beef tallow for 8 wk. Indicators of iron status, iron utilization, and liver iron concentrations were unaffected by an interaction between the fat source and iron concentration. Plasma copper was the only variable affected by an interaction between the fat source and dietary iron. Findings of this study demonstrate that flaxseed oil and olive oil may alter tissue minerals and affect iron utilization. Further studies should be conducted to establish the effect of varying (n-3), (n-6), and (n-9) fatty acids on trace mineral status and iron utilization.

A new species of Gadirtha Walker (Nolidae, Eligminae): a proposed biological control agent of Chinese tallow (Triadica sebifera (L.) Small) (Euphorbiaceae) in the United States

PubMed Central

Pogue, Michael G.

2014-01-01

Abstract Gadirtha fusca sp. n., is described from Guangxi Province, China. Gadirtha fusca differs in forewing color and pattern, male and female genitalia, and in larval pattern from all other species of Gadirtha. Gadirtha fusca has been evaluated as a potential biological control agent for Chinese tallow (Triadica sebifera (L.) Small, Euphorbiaceae) in the southeastern United States. Adult, male and female genitalia, larva, and pupa are described, illustrated, and compared with Gadirtha impingens Walker. PMID:24624017

Effects of tallow, choice white grease, palm oil, corn oil, or soybean oil on apparent total tract digestibility of minerals in diets fed to growing pigs.

PubMed

Merriman, L A; Walk, C L; Parsons, C M; Stein, H H

2016-10-01

An experiment was conducted to determine the effect of supplementing diets fed to growing pigs with fat sources differing in their composition of fatty acids on the apparent total tract digestibility (ATTD) of minerals. A diet based on corn, potato protein isolate, and 7% sucrose was formulated. Five additional diets that were similar to the previous diet with the exception that sucrose was replaced by 7% tallow, choice white grease, palm oil, corn oil, or soybean oil were also formulated. Diets were formulated to contain 0.70% Ca and 0.33% standardized total tract digestible P. Growing barrows ( = 60; 15.99 ± 1.48 kg initial BW) were allotted to a randomized complete block design with 2 blocks of 30 pigs, 6 dietary treatments, and 10 replicate pigs per treatment. Experimental diets were provided for 12 d with the initial 5 d being the adaptation period. Total feces were collected for a 5-d collection period using the marker-to-marker approach, and the ATTD of minerals, ether extract, and acid hydrolyzed ether extract was calculated for all diets. Digestibility of DM was greater ( < 0.05) in the diet containing soybean oil compared with the diet containing choice white grease or the basal diet, with all other diets being intermediate. The ATTD of Ca, S, and P was greater ( < 0.05) for pigs fed diets containing soybean oil, corn oil, palm oil, or tallow than for pigs fed the basal diet or the diet containing choice white grease. The ATTD of Mg, Zn, Mn, Na, and K were not different among dietary treatments. The ATTD of ether extract was greater ( < 0.05) in diets containing palm oil, corn oil, or soybean oil compared with the diet containing choice white grease, and the ATTD of acid hydrolyzed ether extract in the diet containing soybean oil was also greater ( < 0.05) than in the diet containing choice white grease. In conclusion, supplementation of a basal diet with tallow, palm oil, corn oil, or soybean oil may increase the ATTD of some macrominerals, but that

Final Environmental Assessment: Hurlburt Field Skeet & Trap Club

DTIC Science & Technology

2008-07-01

Invasive Species). To date, 18 Category I and 8 Category II species have been documented on Eglin AFB. Chinese tallow, or popcorn tree ( Triadica ... sebifera ), cogon grass (Imperata cylindrical), Japanese climbing fern (Lygodium japonicum), Chinese privet/hedge (Ligustrum sinense), and torpedo grass

Actions to Abate Critical Threats, Such as Encroachment and Invasive Species, Using GIS and Conservation Area Planning Across the Gulf Coastal Plain Ecosystem Partnership (GCPEP) Landscape, Phase 1

DTIC Science & Technology

2006-12-22

invasive species include cogongrass ( Imperata cylindrica ), Chinese tallowtree (Sapium sebiferum), Japanese climbing fern (Lygodium japonicum), Chinese...Species in bold letter were identified as the top invasives across the partnership. Plants Animals 10 Cogon Grass( Imperata cylindrica ) 10...problematic invasive species include cogongrass ( Imperata cylindrica ), Chinese tallowtree (Sapium sebiferum), Japanese climbing fern (Lygodium japonicum

Adsorption of N-tallow 1,3-propanediamine-dioleate collector on albite and quartz minerals, and selective flotation of albite from greek stefania feldspar ore.

PubMed

Vidyadhar, A; Hanumantha Rao, K; Forssberg, K S E

2002-04-01

The adsorption behavior of tallow 1,3-propanediamine-dioleate (Duomeen TDO) collector on albite and quartz minerals is assessed through Hallimond flotation, zeta potential, and diffuse reflectance FTIR investigations, together with the species distribution of the collector. The collector performance on albite separation from a natural feldspar material is evaluated in bench scale flotation tests. The Hallimond flotation responses of the minerals as a function of pH and collector concentration indicate that albite can be selectively floated from quartz at pH 2 where the doubly positively charged collector species adsorb on albite but not on quartz. However, the zeta potential and infrared spectra reveal that the adsorption behavior of the collector is similar on both minerals. The discrepancy in the flotation and adsorption results is attributed to the coarse and fine particle size fractions, and the shorter and longer equilibration periods employed in these studies respectively. The comparable adsorption on fine particles of albite and quartz at pH 2 is explained by the interaction of ammonium ions on silanol groups by hydrogen bonding as well as electrostatic interactions. The changes in zeta potentials are in good agreement with the formation of ionic species and free molecular forms of the collector. The IR spectra show the coexistence of neutral oleic acid together with charged amine species at low pH values in accordance with the species distribution diagram. Selective flotation of albite is accomplished from a natural feldspar material with tallow diamine-dioleate collector at pH 2 using sulfuric acid, only when the feed is deslimed prior to the bench scale flotation tests. An albite recovery exceeding 85% is achieved from a feed material containing about 50% albite.

Physicochemical characterization of lignin recovered from microwave-assisted delignified lignocellulosic biomass for use in biobased materials

Treesearch

Jiulong Xie; Chung-Yun Hse; Todd F. Shupe; Tingxing Hu

2015-01-01

Lignocellulosic biomass (Moso Bamboo, Chinese tallow tree wood, switchgrass, and pine wood) was subjected to a novel delignification process using microwave energy in a binary glycerol/methanol solvent. The physicochemical properties of the recovered lignin were analyzed prior to its application in the fabrication of polylactic acid (PLA)–lignin composites. The results...

Phytotoxic Potential of Secondary Metabolites and Semisynthetic Compounds from Endophytic Fungus Xylaria feejeensis Strain SM3e-1b Isolated from Sapium macrocarpum.

PubMed

García-Méndez, Marbella Claudia; Macías-Ruvalcaba, Norma A; Lappe-Oliveras, Patricia; Hernández-Ortega, Simón; Macías-Rubalcava, Martha Lydia

2016-06-01

Bioactivity-directed fractionation of the combined culture medium and mycelium extract of the endophytic fungus Xylaria feejeensis strain SM3e-1b, isolated from Sapium macrocarpum, led to the isolation of three known natural products: (4S,5S,6S)-4-hydroxy-3-methoxy-5-methyl-5,6-epoxycyclohex-2-enone or coriloxine, 1; 2-hydroxy-5-methoxy-3-methylcyclohexa-2,5-diene-1,4-dione, 2; and 2,6-dihydroxy-5-methoxy-3-methylcyclohexa-2,5-diene-1,4-dione or fumiquinone B, 3. This is the first report of compound 3 being isolated from this species. Additionally, four new derivatives of coriloxine were prepared: (4R,5S,6R)-6-chloro-4,5-dihydroxy-3-methoxy-5-methylcyclohex-2-enone, 4; 6-hydroxy-5-methyl-3-(methylamino)cyclohexa-2,5- diene-1,4-dione, 5; (4R,5R,6R)-4,5-dihydroxy-3-methoxy-5-methyl-6-(phenylamino)cyclohex-2-enone, 6; and 2-((4-butylphenyl)amino)-5-methoxy-3-methylcyclohexa-2,5-diene-1,4-dione, 7. X-ray analysis allowed us to unambiguously determine the structures and absolute configuration of semisynthetic derivatives 4, 5, and 6. The phytotoxic activity of the three isolated natural products and the coriloxine derivatives is reported. Germination of the seed, root growth, and oxygen uptake of the seedlings of Trifolium pratense, Medicago sativa, Panicum miliaceum, and Amaranthus hypochondriacus were significantly inhibited by all of the tested compounds. In general, they were more effective inhibiting root elongation than suppressing the germination and seedling oxygen uptake processes as shown by their IC50 values.

Comparative transcriptome analysis reveals the regulatory networks of cytokinin in promoting the floral feminization in the oil plant Sapium sebiferum.

PubMed

Ni, Jun; Shah, Faheem Afzal; Liu, Wenbo; Wang, Qiaojian; Wang, Dongdong; Zhao, Weiwei; Lu, Weili; Huang, Shengwei; Fu, Songling; Wu, Lifang

2018-05-30

Sapium sebiferum, whose seeds contain high level of fatty acids, has been considered as one of the most important oil plants. However, the high male to female flower ratio limited the seed yield improvement and its industrial potentials. Thus, the study of the sex determination in S. sebiferum is of significant importance in increasing the seed yield. In this study, we demonstrated that in S. sebiferum, cytokinin (CK) had strong feminization effects on the floral development. Exogenous application with 6-benzylaminopurine (6-BA) or thidiazuron (TDZ) significantly induced the development of female flowers and increased the fruit number. Interestingly, the feminization effects of cytokinin were also detected on the androecious genotype of S. sebiferum which only produce male flowers. To further investigate the mechanism underlying the role of cytokinin in the flower development and sex differentiation, we performed the comparative transcriptome analysis of the floral buds of the androecious plants subjected to 6-BA. The results showed that there were separately 129, 352 and 642 genes differentially expressed at 6 h, 12 h and 24 h after 6-BA treatment. Functional analysis of the differentially expressed genes (DEGs) showed that many genes are related to the hormonal biosynthesis and signaling, nutrients translocation and cell cycle. Moreover, there were twenty one flowering-related genes identified to be differentially regulated by 6-BA treatment. Specifically, the gynoecium development-related genes SPATULA (SPT), KANADI 2 (KAN2), JAGGED (JAG) and Cytochrome P450 78A9 (CYP79A9) were significantly up-regulated, whereas the expression of PISTILLATA (PI), TATA Box Associated Factor II 59 (TAFII59) and MYB Domain Protein 108 (MYB108) that were important for male organ development was down-regulated in response to 6-BA treatment, demonstrating that cytokinin could directly target the floral organ identity genes to regulate the flower sex. Our work demonstrated that

Effect of red pepper Capsicum annuum var. conoides and garlic Allium sativum on plasma lipid levels and cecal microflora in mice fed beef tallow.

PubMed

Kuda, Takashi; Iwai, Akiko; Yano, Toshihiro

2004-10-01

Antihyperlipidemia or hypocholesterolaemic and antibacterial activities of red hot pepper and garlic are well known. To determine the effect of the dietary spices ingested to suppress blood lipids on the intestinal condition, we examined plasma lipid levels and cecal microflora in mice that were fed diets containing 19% (w/w) beef tallow and 2% red pepper Capsicum annuum var. conoides 'Takanotume' (RP) or garlic Allium sativum 'White' (GP) for 4-weeks. Plasma triacylglyceride level was suppressed by the spices. RP lowered cecal bacteroidaceae, a predominant bacterial group (from 9.4 to 9.0 log CFU/g), bifidobacteria (from 8.7 to 7.6 log CFU/g), and staphylococci. Although GP increased the cecal weight including their contents, significant differences were not shown in the cecal microflora. These results suggest that RP can affect the intestinal condition and host health through the disturbance of intestinal microflora. Copyright 2004 Elsevier Ltd.

Characterization of polyoxyethylene tallow amine surfactants in technical mixtures and glyphosate formulations using ultra-high performance liquid chromatography and triple quadrupole mass spectrometry

USGS Publications Warehouse

Tush, Daniel; Loftin, Keith A.; Meyer, Michael T.

2013-01-01

Little is known about the occurrence, fate, and effects of the ancillary additives in pesticide formulations. Polyoxyethylene tallow amine (POEA) is a non-ionic surfactant used in many glyphosate formulations, a widely applied herbicide both in agricultural and urban environments. POEA has not been previously well characterized, but has been shown to be toxic to various aquatic organisms. Characterization of technical mixtures using ultra-high performance liquid chromatography (UHPLC) and mass spectrometry shows POEA is a complex combination of homologs of different aliphatic moieties and ranges of ethoxylate units. Tandem mass spectrometry experiments indicate that POEA homologs generate no product ions readily suitable for quantitative analysis due to poor sensitivity. A comparison of multiple high performance liquid chromatography (HPLC) and UHPLC analytical columns indicates that the stationary phase is more important in column selection than other parameters for the separation of POEA. Analysis of several agricultural and household glyphosate formulations confirms that POEA is a common ingredient but ethoxylate distributions among formulations vary.

Categorizing Ideas about Trees: A Tree of Trees

PubMed Central

Fisler, Marie; Lecointre, Guillaume

2013-01-01

The aim of this study is to explore whether matrices and MP trees used to produce systematic categories of organisms could be useful to produce categories of ideas in history of science. We study the history of the use of trees in systematics to represent the diversity of life from 1766 to 1991. We apply to those ideas a method inspired from coding homologous parts of organisms. We discretize conceptual parts of ideas, writings and drawings about trees contained in 41 main writings; we detect shared parts among authors and code them into a 91-characters matrix and use a tree representation to show who shares what with whom. In other words, we propose a hierarchical representation of the shared ideas about trees among authors: this produces a “tree of trees.” Then, we categorize schools of tree-representations. Classical schools like “cladists” and “pheneticists” are recovered but others are not: “gradists” are separated into two blocks, one of them being called here “grade theoreticians.” We propose new interesting categories like the “buffonian school,” the “metaphoricians,” and those using “strictly genealogical classifications.” We consider that networks are not useful to represent shared ideas at the present step of the study. A cladogram is made for showing who is sharing what with whom, but also heterobathmy and homoplasy of characters. The present cladogram is not modelling processes of transmission of ideas about trees, and here it is mostly used to test for proximity of ideas of the same age and for categorization. PMID:23950877

Inclusion of tallow and soybean oil to calf starters fed to dairy calves from birth to four months of age on calf performance and digestion.

PubMed

Hill, T M; Bateman, H G; Aldrich, J M; Quigley, J D; Schlotterbeck, R L

2015-07-01

Energy demands for calves can increase during periods of heat and cold stress. One way to potentially increase energy intake is to increase the energy density of the feed with fat. Trial 1a compared a control starter with no added fat or oil (CON) to starters with 2% tallow (TAL) and 2% soybean oil (SBO). Starters were 20% crude protein (CP) and 45 to 47% starch. Male Holstein calves that were initially 3 to 5d of age were fed a 27% CP, 17% fat milk replacer at 0.66kg of dry matter daily and fully weaned by 42d of a 56-d trial. Trial 1b estimated the digestion of the diets (employed chromic oxide as an indigestible digesta flow marker) using a subset of 5 weaned calves per treatment between d 52 and 56. Trial 2 used Holstein calves initially 59 to 61d of age fed starters CON and SBO blended with 5% chopped grass hay over a 56-d trial. Trial 3 used Holstein calves initially 59 to 61d of age fed starters CON and TAL blended with 5% chopped grass hay over a 56-d trial. Treatments were compared using repeated measures (where appropriate) in a completely randomized design. In trials 1a and 1b, preplanned contrasts compared CON versus TAL and CON versus SBO. Compared with CON, calves fed SBO had reduced starter intake, average daily gain, and digestion of dry matter, organic matter, and CP before 8wk of age. Compared with CON, calves fed SBO had reduced average daily gain and change in hip width from 2 to 4 mo of age. Compared with CON, calves fed TAL had reduced average daily gain and tended to have reduced change in hip width from 2 to 4 mo of age. Calculated metabolizable energy intake was not increased in any trial by added fat or oil. Tallow and soybean oil inclusion at 2% of the starter feed was not advantageous for calf growth before 4 mo of age. Copyright © 2015 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Improving the Cold Temperature Properties of Tallow-Based Methyl Ester Mixtures Using Fractionation, Blending, and Additives

NASA Astrophysics Data System (ADS)

Elwell, Caleb

Beef tallow is a less common feedstock source for biodiesel than soy or canola oil, but it can have economic benefits in comparison to these traditional feedstocks. However, tallow methyl ester (TME) has the major disadvantage of poor cold temperature properties. Cloud point (CP) is an standard industry metric for evaluating the cold temperature performance of biodiesel and is directly related to the thermodynamic properties of the fuel's constituents. TME has a CP of 14.5°C compared with 2.3°C for soy methyl ester (SME) and -8.3°C for canola methyl ester (CME). In this study, three methods were evaluated to reduce the CP of TME: fractionation, blending with SME and CME, and using polymer additives. TME fractionation (i.e. removal of specific methyl ester constituents) was simulated by creating FAME mixtures to match the FAME profiles of fractionated TME. The fractionation yield was found to be highest at the eutectic point of methyl palmitate (MP) and methyl stearate (MS), which was empirically determined to be at a MP/(MP+MS) ratio of approximately 82%. Since unmodified TME has a MP/(MP+MS) ratio of 59%, initially only MS should be removed to produce a ratio closer to the eutectic point to reduce CP and maximize yield. Graphs relating yield (with 4:1 methyl stearate to methyl oleate carryover) to CP were produced to determine the economic viability of this approach. To evaluate the effect of blending TME with other methyl esters, SME and CME were blended with TME at blend ratios of 0 to 100%. Both the SME/TME and CME/TME blends exhibited decreased CPs with increasing levels of SME and CME. Although the CP of the SME/TME blends varied linearly with SME content, the CP of the CME/TME blends varied quadratically with CME content. To evaluate the potential of fuel additives to reduce the CP of TME, 11 different polymer additives were tested. Although all of these additives were specifically marketed to enhance the cold temperature properties of petroleum diesel or

What Makes a Tree a Tree?

ERIC Educational Resources Information Center

NatureScope, 1986

1986-01-01

Provides: (1) background information on trees, focusing on the parts of trees and how they differ from other plants; (2) eight activities; and (3) ready-to-copy pages dealing with tree identification and tree rings. Activities include objective(s), recommended age level(s), subject area(s), list of materials needed, and procedures. (JN)

TreeCmp: Comparison of Trees in Polynomial Time

PubMed Central

Bogdanowicz, Damian; Giaro, Krzysztof; Wróbel, Borys

2012-01-01

When a phylogenetic reconstruction does not result in one tree but in several, tree metrics permit finding out how far the reconstructed trees are from one another. They also permit to assess the accuracy of a reconstruction if a true tree is known. TreeCmp implements eight metrics that can be calculated in polynomial time for arbitrary (not only bifurcating) trees: four for unrooted (Matching Split metric, which we have recently proposed, Robinson-Foulds, Path Difference, Quartet) and four for rooted trees (Matching Cluster, Robinson-Foulds cluster, Nodal Splitted and Triple). TreeCmp is the first implementation of Matching Split/Cluster metrics and the first efficient and convenient implementation of Nodal Splitted. It allows to compare relatively large trees. We provide an example of the application of TreeCmp to compare the accuracy of ten approaches to phylogenetic reconstruction with trees up to 5000 external nodes, using a measure of accuracy based on normalized similarity between trees.

Utilization of Chinese tallow tree and bagasse for medium density fiberboard

Treesearch

Sangyeob Lee; Todd F. Shupe; Chung Y. Hse

2004-01-01

The objective of this research was to investigate various adhesive systems and determine the best composite formulation for selected mechanical and physical properties of medium density fiberboard (MDF) made from wood and bagasse fibers. This study investigated opportunities ofbiomass utilization for natural fiber-based composites from agricultural (bagasse) and...

The Inference of Gene Trees with Species Trees

PubMed Central

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

2015-01-01

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

Heterapoderopsis bicallosicollis (Coleoptera: Attelabidae): a potential biological control agent for Triadica sebifera.

PubMed

Wang, Yi; Ding, Jianqing; Wheeler, Gregory S; Purcell, Matthew F; Zhang, Guoan

2009-08-01

Native to China, Chinese tallow, Triadica sebifera L. Small (Euphorbiaceae), is an invasive plant in the southeastern United States. The leaf-rolling weevil, Heterapoderopsis bicallosicollis Voss, is a common herbivore attacking this plant in China. To evaluate its potential as a biological control agent of T. sebifera, biology and host specificity of this weevil were studied in China. H. bicallosicollis occurs over a wide, native, geographic range and its immatures successfully develop at 15-35 degrees C, indicating its physiological potential to establish and persist throughout the range of climatic conditions where the target plant grows in the United States. Adults make feeding holes on leaves. Before oviposition, the female makes a sealed leaf roll called a nidus and then lays one to two eggs inside. Eggs, larvae, and pupae develop within nidi, and larvae survive only when they develop inside the nidi. This requirement makes the weevil highly host specific to T. sebifera. In laboratory no-choice tests of 54 species from eight families, adults fed on only 3 plant species, T. sebifera, Sapium chihsinianum S. K. Lee, and Phyllanthus urinaria L. and only oviposited on T. sebifera. These results were confirmed where, in multiple-choice tests, adults only oviposited on T. sebifera. Given that T. sebifera is the only species in the genus Triadica in the United States, the results of this study suggest that H. bicallosicollis is a potential biological control agent of T. sebifera and should be considered to be imported into quarantine in the United States for further tests on native North American species.

ColorTree: a batch customization tool for phylogenic trees

PubMed Central

Chen, Wei-Hua; Lercher, Martin J

2009-01-01

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

ColorTree: a batch customization tool for phylogenic trees.

PubMed

Chen, Wei-Hua; Lercher, Martin J

2009-07-31

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

Tallow amphopolycarboxyglycinate-stabilized silver nanoparticles: new frontiers in development of plant protection products with a broad spectrum of action against phytopathogens

NASA Astrophysics Data System (ADS)

Krutyakov, Yurii A.; Kudrinskiy, Alexey A.; Zherebin, Pavel M.; Yapryntsev, Alexey D.; Pobedinskaya, Marina A.; Elansky, Sergey N.; Denisov, Albert N.; Mikhaylov, Dmitry M.; Lisichkin, Georgii V.

2016-07-01

Sustainable agriculture calls for minimal use of agrochemicals in order to protect the environment. It has caused an increase in the rate of nanoparticles use, in particular silver nanoparticles (AgNPs) due to their safety for mammals, unique biological activity and a broad spectrum of action against fungal and bacterial pathogens. Until now the use of AgNPs dispersions in the agricultural sector has been essentially limited due to many factors decreased their stability (mixing with other pesticides, presence of electrolytes). We present a versatile synthesis of polyampholyte surfactant (tallow amphopolycarboxyglycinate) stabilized AgNPs. We took a close look at unique aggregation behavior (via dynamic light scattering and UV-vis spectroscopy) and biocidal activity of obtained silver colloids. AgNPs are characterized by exclusively high aggregative stability in the presence of coagulating agents NaNO3 and NaSO4 (up to 1 M), during drying/redispergation, and frost/defrost cycles. The dispersion of AgNPs shows high biocidal activity (EC50 is ten times lower than commercial species ones) with respect to Phytophthora infestans and phytopathogenic fungi. This points to the possibility of successful application of silver preparations within agriculture with the goal of partial reduction of the use of toxic and expensive synthetic antibiotics and pesticides.

Tree Colors: Color Schemes for Tree-Structured Data.

PubMed

Tennekes, Martijn; de Jonge, Edwin

2014-12-01

We present a method to map tree structures to colors from the Hue-Chroma-Luminance color model, which is known for its well balanced perceptual properties. The Tree Colors method can be tuned with several parameters, whose effect on the resulting color schemes is discussed in detail. We provide a free and open source implementation with sensible parameter defaults. Categorical data are very common in statistical graphics, and often these categories form a classification tree. We evaluate applying Tree Colors to tree structured data with a survey on a large group of users from a national statistical institute. Our user study suggests that Tree Colors are useful, not only for improving node-link diagrams, but also for unveiling tree structure in non-hierarchical visualizations.

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

PubMed

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

2018-01-01

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

Two Trees: Migrating Fault Trees to Decision Trees for Real Time Fault Detection on International Space Station

NASA Technical Reports Server (NTRS)

Lee, Charles; Alena, Richard L.; Robinson, Peter

2004-01-01

We started from ISS fault trees example to migrate to decision trees, presented a method to convert fault trees to decision trees. The method shows that the visualizations of root cause of fault are easier and the tree manipulating becomes more programmatic via available decision tree programs. The visualization of decision trees for the diagnostic shows a format of straight forward and easy understands. For ISS real time fault diagnostic, the status of the systems could be shown by mining the signals through the trees and see where it stops at. The other advantage to use decision trees is that the trees can learn the fault patterns and predict the future fault from the historic data. The learning is not only on the static data sets but also can be online, through accumulating the real time data sets, the decision trees can gain and store faults patterns in the trees and recognize them when they come.

Comparison of oilseed yields: a preliminary review

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

Duke, J.A.; Bagby, M.O.

It was assumed that for most oilseed crops, 90% of the oil yield might be considered as profit. To compare oil seeds, pertinent portions of the yield and energy paragraphs from a summary published by Dr. Duke for DOE Grant No. 59-2246-1-6-054-0 with Dr. Bagby as ADODR were reproduced. The seed yields ranged from 200 to 14,000 kg/ha, the low one too low to consider and the high one suspiciously high. The yield of 14,000 kg oil per hectare is equivalent to more than 30 barrels of oil per hectare. The energy species included ambrette, tung-oil tree, cashew, wood-oil tree,more » mu-oil tree, peanut, mustard greens; rape, colza; black mustard, turnip, safflower, colocynth, coconut, crambe, African oil palm, soybean, cotton, sunflower, Eastern black walnut, Engligh walnut, meadow foam, flax, macadamia nuts, opium poppy, perilla, almond, castorbean, Chinese tallow tree, sesame, jojoba, yellow mustard, stokes' aster, and Zanzibar oilvine. 1 table. (DP)« less

CartograTree: connecting tree genomes, phenotypes and environment.

PubMed

Vasquez-Gross, Hans A; Yu, John J; Figueroa, Ben; Gessler, Damian D G; Neale, David B; Wegrzyn, Jill L

2013-05-01

Today, researchers spend a tremendous amount of time gathering, formatting, filtering and visualizing data collected from disparate sources. Under the umbrella of forest tree biology, we seek to provide a platform and leverage modern technologies to connect biotic and abiotic data. Our goal is to provide an integrated web-based workspace that connects environmental, genomic and phenotypic data via geo-referenced coordinates. Here, we connect the genomic query web-based workspace, DiversiTree and a novel geographical interface called CartograTree to data housed on the TreeGenes database. To accomplish this goal, we implemented Simple Semantic Web Architecture and Protocol to enable the primary genomics database, TreeGenes, to communicate with semantic web services regardless of platform or back-end technologies. The novelty of CartograTree lies in the interactive workspace that allows for geographical visualization and engagement of high performance computing (HPC) resources. The application provides a unique tool set to facilitate research on the ecology, physiology and evolution of forest tree species. CartograTree can be accessed at: http://dendrome.ucdavis.edu/cartogratree. © 2013 Blackwell Publishing Ltd.

Tree Nut Allergies

MedlinePlus

... Blog Vision Awards Common Allergens Tree Nut Allergy Tree Nut Allergy Learn about tree nut allergy, how ... a Tree Nut Label card . Allergic Reactions to Tree Nuts Tree nuts can cause a severe and ...

Big trees, old trees, and growth factor tables

Treesearch

Kevin T. Smith

2018-01-01

The potential for a tree to reach a great size and to live a long life frequently captures the public's imagination. Sometimes the desire to know the age of an impressively large tree is simple curiosity. For others, the date-of-tree establishment can make a big diff erence for management, particularly for trees at historic sites or those mentioned in property...

TreeNetViz: revealing patterns of networks over tree structures.

PubMed

Gou, Liang; Zhang, Xiaolong Luke

2011-12-01

Network data often contain important attributes from various dimensions such as social affiliations and areas of expertise in a social network. If such attributes exhibit a tree structure, visualizing a compound graph consisting of tree and network structures becomes complicated. How to visually reveal patterns of a network over a tree has not been fully studied. In this paper, we propose a compound graph model, TreeNet, to support visualization and analysis of a network at multiple levels of aggregation over a tree. We also present a visualization design, TreeNetViz, to offer the multiscale and cross-scale exploration and interaction of a TreeNet graph. TreeNetViz uses a Radial, Space-Filling (RSF) visualization to represent the tree structure, a circle layout with novel optimization to show aggregated networks derived from TreeNet, and an edge bundling technique to reduce visual complexity. Our circular layout algorithm reduces both total edge-crossings and edge length and also considers hierarchical structure constraints and edge weight in a TreeNet graph. These experiments illustrate that the algorithm can reduce visual cluttering in TreeNet graphs. Our case study also shows that TreeNetViz has the potential to support the analysis of a compound graph by revealing multiscale and cross-scale network patterns. © 2011 IEEE

[Determination of di (hydrogenated tallow alkyl) dimethyl ammonium compounds in textile auxiliaries by ultra-high performance liquid chromatography-tandem mass spectrometry].

PubMed

Zhu, Feng

2015-01-01

A method has been developed for the determination of di (hydrogenated tallow alkyl) dimethyl ammonium compounds (DHTDMAC) in textile auxiliaries by ultra-high performance liquid chromatography-tandem mass spectrometry. (UPLC-MS/MS). The samples were extracted and diluted with acidified methanol by 5% (v/v) formic acid under ultrasonic assistance. The separation was performed on an Eclipse Plus C18 column (50 mm x 2.1 mm, 1.8 microm) using 0.1% (v/v) formic acid solution and methanol as the mobile phases. Identification and quantification were achieved by UPLC-MS/MS with electrospray ionization (ESI) source in positive ion mode and multiple reaction monitoring (MRM) mode. The results indicated that the calibration curve of DHTDMAC showed good linear relationship between peak area and mass concentration in the range of 10-280 microg/L with the correlation coefficient (r2) of 0.9991. The limit of detection (LOD, S/N=3) and the limit of quantification (LOQ, S/N= 10) of this method were 3 mg/kg and 10 mg/kg, respectively. The average recoveries from three typical textile auxiliary matrices including dispersant, antistatic agent and fabric softener, at three spiked levels were in the range of 97.2%-108.3% with the relative standard deviations (RSDs) of 1.5%-4.6%. The method is sensitive, accurate, simple and effective for the analysis of DHTDMAC in textile auxiliaries.

Technical Tree Climbing.

ERIC Educational Resources Information Center

Jenkins, Peter

Tree climbing offers a safe, inexpensive adventure sport that can be performed almost anywhere. Using standard procedures practiced in tree surgery or rock climbing, almost any tree can be climbed. Tree climbing provides challenge and adventure as well as a vigorous upper-body workout. Tree Climbers International classifies trees using a system…

36 CFR 223.4 - Exchange of trees or portions of trees.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 36 Parks, Forests, and Public Property 2 2011-07-01 2011-07-01 false Exchange of trees or portions of trees. 223.4 Section 223.4 Parks, Forests, and Public Property FOREST SERVICE, DEPARTMENT OF... PRODUCTS General Provisions § 223.4 Exchange of trees or portions of trees. Trees or portions of trees may...

36 CFR 223.4 - Exchange of trees or portions of trees.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 36 Parks, Forests, and Public Property 2 2012-07-01 2012-07-01 false Exchange of trees or portions of trees. 223.4 Section 223.4 Parks, Forests, and Public Property FOREST SERVICE, DEPARTMENT OF... PRODUCTS General Provisions § 223.4 Exchange of trees or portions of trees. Trees or portions of trees may...

36 CFR 223.4 - Exchange of trees or portions of trees.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 36 Parks, Forests, and Public Property 2 2014-07-01 2014-07-01 false Exchange of trees or portions of trees. 223.4 Section 223.4 Parks, Forests, and Public Property FOREST SERVICE, DEPARTMENT OF... PRODUCTS General Provisions § 223.4 Exchange of trees or portions of trees. Trees or portions of trees may...

36 CFR 223.4 - Exchange of trees or portions of trees.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 36 Parks, Forests, and Public Property 2 2013-07-01 2013-07-01 false Exchange of trees or portions of trees. 223.4 Section 223.4 Parks, Forests, and Public Property FOREST SERVICE, DEPARTMENT OF... PRODUCTS General Provisions § 223.4 Exchange of trees or portions of trees. Trees or portions of trees may...

Rate of tree carbon accumulation increases continuously with tree size.

PubMed

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

2014-03-06

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

Rate of tree carbon accumulation increases continuously with tree size

USGS Publications Warehouse

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

2014-01-01

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

Tree species, tree genotypes and tree genotypic diversity levels affect microbe-mediated soil ecosystem functions in a subtropical forest.

PubMed

Purahong, Witoon; Durka, Walter; Fischer, Markus; Dommert, Sven; Schöps, Ricardo; Buscot, François; Wubet, Tesfaye

2016-11-18

Tree species identity and tree genotypes contribute to the shaping of soil microbial communities. However, knowledge about how these two factors influence soil ecosystem functions is still lacking. Furthermore, in forest ecosystems tree genotypes co-occur and interact with each other, thus the effects of tree genotypic diversity on soil ecosystem functions merit attention. Here we investigated the effects of tree species, tree genotypes and genotypic diversity levels, alongside soil physicochemical properties, on the overall and specific soil enzyme activity patterns. Our results indicate that tree species identity, tree genotypes and genotypic diversity level have significant influences on overall and specific soil enzyme activity patterns. These three factors influence soil enzyme patterns partly through effects on soil physicochemical properties and substrate quality. Variance partitioning showed that tree species identity, genotypic diversity level, pH and water content all together explained ~30% variations in the overall patterns of soil enzymes. However, we also found that the responses of soil ecosystem functions to tree genotypes and genotypic diversity are complex, being dependent on tree species identity and controlled by multiple factors. Our study highlights the important of inter- and intra-specific variations in tree species in shaping soil ecosystem functions in a subtropical forest.

Tree species, tree genotypes and tree genotypic diversity levels affect microbe-mediated soil ecosystem functions in a subtropical forest

PubMed Central

Purahong, Witoon; Durka, Walter; Fischer, Markus; Dommert, Sven; Schöps, Ricardo; Buscot, François; Wubet, Tesfaye

2016-01-01

Tree species identity and tree genotypes contribute to the shaping of soil microbial communities. However, knowledge about how these two factors influence soil ecosystem functions is still lacking. Furthermore, in forest ecosystems tree genotypes co-occur and interact with each other, thus the effects of tree genotypic diversity on soil ecosystem functions merit attention. Here we investigated the effects of tree species, tree genotypes and genotypic diversity levels, alongside soil physicochemical properties, on the overall and specific soil enzyme activity patterns. Our results indicate that tree species identity, tree genotypes and genotypic diversity level have significant influences on overall and specific soil enzyme activity patterns. These three factors influence soil enzyme patterns partly through effects on soil physicochemical properties and substrate quality. Variance partitioning showed that tree species identity, genotypic diversity level, pH and water content all together explained ~30% variations in the overall patterns of soil enzymes. However, we also found that the responses of soil ecosystem functions to tree genotypes and genotypic diversity are complex, being dependent on tree species identity and controlled by multiple factors. Our study highlights the important of inter- and intra-specific variations in tree species in shaping soil ecosystem functions in a subtropical forest. PMID:27857198

TreeVector: scalable, interactive, phylogenetic trees for the web.

PubMed

Pethica, Ralph; Barker, Gary; Kovacs, Tim; Gough, Julian

2010-01-28

Phylogenetic trees are complex data forms that need to be graphically displayed to be human-readable. Traditional techniques of plotting phylogenetic trees focus on rendering a single static image, but increases in the production of biological data and large-scale analyses demand scalable, browsable, and interactive trees. We introduce TreeVector, a Scalable Vector Graphics-and Java-based method that allows trees to be integrated and viewed seamlessly in standard web browsers with no extra software required, and can be modified and linked using standard web technologies. There are now many bioinformatics servers and databases with a range of dynamic processes and updates to cope with the increasing volume of data. TreeVector is designed as a framework to integrate with these processes and produce user-customized phylogenies automatically. We also address the strengths of phylogenetic trees as part of a linked-in browsing process rather than an end graphic for print. TreeVector is fast and easy to use and is available to download precompiled, but is also open source. It can also be run from the web server listed below or the user's own web server. It has already been deployed on two recognized and widely used database Web sites.

IcyTree: rapid browser-based visualization for phylogenetic trees and networks

PubMed Central

2017-01-01

Abstract Summary: IcyTree is an easy-to-use application which can be used to visualize a wide variety of phylogenetic trees and networks. While numerous phylogenetic tree viewers exist already, IcyTree distinguishes itself by being a purely online tool, having a responsive user interface, supporting phylogenetic networks (ancestral recombination graphs in particular), and efficiently drawing trees that include information such as ancestral locations or trait values. IcyTree also provides intuitive panning and zooming utilities that make exploring large phylogenetic trees of many thousands of taxa feasible. Availability and Implementation: IcyTree is a web application and can be accessed directly at http://tgvaughan.github.com/icytree. Currently supported web browsers include Mozilla Firefox and Google Chrome. IcyTree is written entirely in client-side JavaScript (no plugin required) and, once loaded, does not require network access to run. IcyTree is free software, and the source code is made available at http://github.com/tgvaughan/icytree under version 3 of the GNU General Public License. Contact: tgvaughan@gmail.com PMID:28407035

IcyTree: rapid browser-based visualization for phylogenetic trees and networks.

PubMed

Vaughan, Timothy G

2017-08-01

IcyTree is an easy-to-use application which can be used to visualize a wide variety of phylogenetic trees and networks. While numerous phylogenetic tree viewers exist already, IcyTree distinguishes itself by being a purely online tool, having a responsive user interface, supporting phylogenetic networks (ancestral recombination graphs in particular), and efficiently drawing trees that include information such as ancestral locations or trait values. IcyTree also provides intuitive panning and zooming utilities that make exploring large phylogenetic trees of many thousands of taxa feasible. IcyTree is a web application and can be accessed directly at http://tgvaughan.github.com/icytree . Currently supported web browsers include Mozilla Firefox and Google Chrome. IcyTree is written entirely in client-side JavaScript (no plugin required) and, once loaded, does not require network access to run. IcyTree is free software, and the source code is made available at http://github.com/tgvaughan/icytree under version 3 of the GNU General Public License. tgvaughan@gmail.com. © The Author(s) 2017. Published by Oxford University Press.

Exact solutions for species tree inference from discordant gene trees.

PubMed

Chang, Wen-Chieh; Górecki, Paweł; Eulenstein, Oliver

2013-10-01

Phylogenetic analysis has to overcome the grant challenge of inferring accurate species trees from evolutionary histories of gene families (gene trees) that are discordant with the species tree along whose branches they have evolved. Two well studied approaches to cope with this challenge are to solve either biologically informed gene tree parsimony (GTP) problems under gene duplication, gene loss, and deep coalescence, or the classic RF supertree problem that does not rely on any biological model. Despite the potential of these problems to infer credible species trees, they are NP-hard. Therefore, these problems are addressed by heuristics that typically lack any provable accuracy and precision. We describe fast dynamic programming algorithms that solve the GTP problems and the RF supertree problem exactly, and demonstrate that our algorithms can solve instances with data sets consisting of as many as 22 taxa. Extensions of our algorithms can also report the number of all optimal species trees, as well as the trees themselves. To better asses the quality of the resulting species trees that best fit the given gene trees, we also compute the worst case species trees, their numbers, and optimization score for each of the computational problems. Finally, we demonstrate the performance of our exact algorithms using empirical and simulated data sets, and analyze the quality of heuristic solutions for the studied problems by contrasting them with our exact solutions.

TreeScaper: Visualizing and Extracting Phylogenetic Signal from Sets of Trees.

PubMed

Huang, Wen; Zhou, Guifang; Marchand, Melissa; Ash, Jeremy R; Morris, David; Van Dooren, Paul; Brown, Jeremy M; Gallivan, Kyle A; Wilgenbusch, Jim C

2016-12-01

Modern phylogenomic analyses often result in large collections of phylogenetic trees representing uncertainty in individual gene trees, variation across genes, or both. Extracting phylogenetic signal from these tree sets can be challenging, as they are difficult to visualize, explore, and quantify. To overcome some of these challenges, we have developed TreeScaper, an application for tree set visualization as well as the identification of distinct phylogenetic signals. GUI and command-line versions of TreeScaper and a manual with tutorials can be downloaded from https://github.com/whuang08/TreeScaper/releases TreeScaper is distributed under the GNU General Public License. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

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...

Tree-space statistics and approximations for large-scale analysis of anatomical trees.

PubMed

Feragen, Aasa; Owen, Megan; Petersen, Jens; Wille, Mathilde M W; Thomsen, Laura H; Dirksen, Asger; de Bruijne, Marleen

2013-01-01

Statistical analysis of anatomical trees is hard to perform due to differences in the topological structure of the trees. In this paper we define statistical properties of leaf-labeled anatomical trees with geometric edge attributes by considering the anatomical trees as points in the geometric space of leaf-labeled trees. This tree-space is a geodesic metric space where any two trees are connected by a unique shortest path, which corresponds to a tree deformation. However, tree-space is not a manifold, and the usual strategy of performing statistical analysis in a tangent space and projecting onto tree-space is not available. Using tree-space and its shortest paths, a variety of statistical properties, such as mean, principal component, hypothesis testing and linear discriminant analysis can be defined. For some of these properties it is still an open problem how to compute them; others (like the mean) can be computed, but efficient alternatives are helpful in speeding up algorithms that use means iteratively, like hypothesis testing. In this paper, we take advantage of a very large dataset (N = 8016) to obtain computable approximations, under the assumption that the data trees parametrize the relevant parts of tree-space well. Using the developed approximate statistics, we illustrate how the structure and geometry of airway trees vary across a population and show that airway trees with Chronic Obstructive Pulmonary Disease come from a different distribution in tree-space than healthy ones. Software is available from http://image.diku.dk/aasa/software.php.

Audubon Tree Study Program.

ERIC Educational Resources Information Center

National Audubon Society, New York, NY.

Included are an illustrated student reader, "The Story of Trees," a leaders' guide, and a large tree chart with 37 colored pictures. The student reader reviews several aspects of trees: a definition of a tree; where and how trees grow; flowers, pollination and seed production; how trees make their food; how to recognize trees; seasonal changes;…

Relative Suffix Trees.

PubMed

Farruggia, Andrea; Gagie, Travis; Navarro, Gonzalo; Puglisi, Simon J; Sirén, Jouni

2018-05-01

Suffix trees are one of the most versatile data structures in stringology, with many applications in bioinformatics. Their main drawback is their size, which can be tens of times larger than the input sequence. Much effort has been put into reducing the space usage, leading ultimately to compressed suffix trees. These compressed data structures can efficiently simulate the suffix tree, while using space proportional to a compressed representation of the sequence. In this work, we take a new approach to compressed suffix trees for repetitive sequence collections, such as collections of individual genomes. We compress the suffix trees of individual sequences relative to the suffix tree of a reference sequence. These relative data structures provide competitive time/space trade-offs, being almost as small as the smallest compressed suffix trees for repetitive collections, and competitive in time with the largest and fastest compressed suffix trees.

Relative Suffix Trees

PubMed Central

Farruggia, Andrea; Gagie, Travis; Navarro, Gonzalo; Puglisi, Simon J; Sirén, Jouni

2018-01-01

Abstract Suffix trees are one of the most versatile data structures in stringology, with many applications in bioinformatics. Their main drawback is their size, which can be tens of times larger than the input sequence. Much effort has been put into reducing the space usage, leading ultimately to compressed suffix trees. These compressed data structures can efficiently simulate the suffix tree, while using space proportional to a compressed representation of the sequence. In this work, we take a new approach to compressed suffix trees for repetitive sequence collections, such as collections of individual genomes. We compress the suffix trees of individual sequences relative to the suffix tree of a reference sequence. These relative data structures provide competitive time/space trade-offs, being almost as small as the smallest compressed suffix trees for repetitive collections, and competitive in time with the largest and fastest compressed suffix trees. PMID:29795706

Steiner trees and spanning trees in six-pin soap films

NASA Astrophysics Data System (ADS)

Dutta, Prasun; Khastgir, S. Pratik; Roy, Anushree

2010-02-01

The problem of finding minimum (local as well as absolute) path lengths joining given points (or terminals) on a plane is known as the Steiner problem. The Steiner problem arises in finding the minimum total road length joining several towns and cities. We study the Steiner tree problem using six-pin soap films. Experimentally, we observe spanning trees as well as Steiner trees partly by varying the pin diameter. We propose a possibly exact expression for the length of a spanning tree or a Steiner tree, which fails mysteriously in certain cases.

Fault-Tree Compiler

NASA Technical Reports Server (NTRS)

Butler, Ricky W.; Boerschlein, David P.

1993-01-01

Fault-Tree Compiler (FTC) program, is software tool used to calculate probability of top event in fault tree. Gates of five different types allowed in fault tree: AND, OR, EXCLUSIVE OR, INVERT, and M OF N. High-level input language easy to understand and use. In addition, program supports hierarchical fault-tree definition feature, which simplifies tree-description process and reduces execution time. Set of programs created forming basis for reliability-analysis workstation: SURE, ASSIST, PAWS/STEM, and FTC fault-tree tool (LAR-14586). Written in PASCAL, ANSI-compliant C language, and FORTRAN 77. Other versions available upon request.

Why do trees die? Characterizing the drivers of background tree mortality

USGS Publications Warehouse

Das, Adrian J.; Stephenson, Nathan L.; Davis, Kristin P.

2016-01-01

The drivers of background tree mortality rates—the typical low rates of tree mortality found in forests in the absence of acute stresses like drought—are central to our understanding of forest dynamics, the effects of ongoing environmental changes on forests, and the causes and consequences of geographical gradients in the nature and strength of biotic interactions. To shed light on factors contributing to background tree mortality, we analyzed detailed pathological data from 200,668 tree-years of observation and 3,729 individual tree deaths, recorded over a 13-yr period in a network of old-growth forest plots in California's Sierra Nevada mountain range. We found that: (1) Biotic mortality factors (mostly insects and pathogens) dominated (58%), particularly in larger trees (86%). Bark beetles were the most prevalent (40%), even though there were no outbreaks during the study period; in contrast, the contribution of defoliators was negligible. (2) Relative occurrences of broad classes of mortality factors (biotic, 58%; suppression, 51%; and mechanical, 25%) are similar among tree taxa, but may vary with tree size and growth rate. (3) We found little evidence of distinct groups of mortality factors that predictably occur together on trees. Our results have at least three sets of implications. First, rather than being driven by abiotic factors such as lightning or windstorms, the “ambient” or “random” background mortality that many forest models presume to be independent of tree growth rate is instead dominated by biotic agents of tree mortality, with potentially critical implications for forecasting future mortality. Mechanistic models of background mortality, even for healthy, rapidly growing trees, must therefore include the insects and pathogens that kill trees. Second, the biotic agents of tree mortality, instead of occurring in a few predictable combinations, may generally act opportunistically and with a relatively large degree of independence from

Tree Classification Software

NASA Technical Reports Server (NTRS)

Buntine, Wray

1993-01-01

This paper introduces the IND Tree Package to prospective users. IND does supervised learning using classification trees. This learning task is a basic tool used in the development of diagnosis, monitoring and expert systems. The IND Tree Package was developed as part of a NASA project to semi-automate the development of data analysis and modelling algorithms using artificial intelligence techniques. The IND Tree Package integrates features from CART and C4 with newer Bayesian and minimum encoding methods for growing classification trees and graphs. The IND Tree Package also provides an experimental control suite on top. The newer features give improved probability estimates often required in diagnostic and screening tasks. The package comes with a manual, Unix 'man' entries, and a guide to tree methods and research. The IND Tree Package is implemented in C under Unix and was beta-tested at university and commercial research laboratories in the United States.

DupTree: a program for large-scale phylogenetic analyses using gene tree parsimony.

PubMed

Wehe, André; Bansal, Mukul S; Burleigh, J Gordon; Eulenstein, Oliver

2008-07-01

DupTree is a new software program for inferring rooted species trees from collections of gene trees using the gene tree parsimony approach. The program implements a novel algorithm that significantly improves upon the run time of standard search heuristics for gene tree parsimony, and enables the first truly genome-scale phylogenetic analyses. In addition, DupTree allows users to examine alternate rootings and to weight the reconciliation costs for gene trees. DupTree is an open source project written in C++. DupTree for Mac OS X, Windows, and Linux along with a sample dataset and an on-line manual are available at http://genome.cs.iastate.edu/CBL/DupTree

Liana competition with tropical trees varies seasonally but not with tree species identity.

PubMed

Leonor, Alvarez-Cansino; Schnitzer, Stefan A; Reid, Joseph P; Powers, Jennifer S

2015-01-01

Lianas in tropical forests compete intensely with trees for above- and belowground resources and limit tree growth and regeneration. Liana competition with adult canopy trees may be particularly strong, and, if lianas compete more intensely with some tree species than others, they may influence tree species composition. We performed the first systematic, large-scale liana removal experiment to assess the competitive effects of lianas on multiple tropical tree species by measuring sap velocity and growth in a lowland tropical forest in Panama. Tree sap velocity increased 60% soon after liana removal compared to control trees, and tree diameter growth increased 25% after one year. Although tree species varied in their response to lianas, this variation was not significant, suggesting that lianas competed similarly with all tree species examined. The effect of lianas on tree sap velocity was particularly strong during the dry season, when soil moisture was low, suggesting that lianas compete intensely with trees for water. Under the predicted global change scenario of increased temperature and drought intensity, competition from lianas may become more prevalent in seasonal tropical forests, which, according to our data, should have a negative effect on most tropical tree species.

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

PubMed

Fouquier, Jennifer; Rideout, Jai Ram; Bolyen, Evan; Chase, John; Shiffer, Arron; McDonald, Daniel; Knight, Rob; Caporaso, J Gregory; Kelley, Scott T

2016-02-24

Fungi play critical roles in many ecosystems, cause serious diseases in plants and animals, and pose significant threats to human health and structural integrity problems in built environments. While most fungal diversity remains unknown, the development of PCR primers for the internal transcribed spacer (ITS) combined with next-generation sequencing has substantially improved our ability to profile fungal microbial diversity. Although the high sequence variability in the ITS region facilitates more accurate species identification, it also makes multiple sequence alignment and phylogenetic analysis unreliable across evolutionarily distant fungi because the sequences are hard to align accurately. To address this issue, we created ghost-tree, a bioinformatics tool that integrates sequence data from two genetic markers into a single phylogenetic tree that can be used for diversity analyses. Our approach starts with a "foundation" phylogeny based on one genetic marker whose sequences can be aligned across organisms spanning divergent taxonomic groups (e.g., fungal families). Then, "extension" phylogenies are built for more closely related organisms (e.g., fungal species or strains) using a second more rapidly evolving genetic marker. These smaller phylogenies are then grafted onto the foundation tree by mapping taxonomic names such that each corresponding foundation-tree tip would branch into its new "extension tree" child. We applied ghost-tree to graft fungal extension phylogenies derived from ITS sequences onto a foundation phylogeny derived from fungal 18S sequences. Our analysis of simulated and real fungal ITS data sets found that phylogenetic distances between fungal communities computed using ghost-tree phylogenies explained significantly more variance than non-phylogenetic distances. The phylogenetic metrics also improved our ability to distinguish small differences (effect sizes) between microbial communities, though results were similar to non

Trees are good, but…

Treesearch

E.G. McPherson; F. Ferrini

2010-01-01

We know that “trees are good,” and most people believe this to be true. But if this is so, why are so many trees neglected, and so many tree wells empty? An individual’s attitude toward trees may result from their firsthand encounters with specific trees. Understanding how attitudes about trees are shaped, particularly aversion to trees, is critical to the business of...

Cavity tree selection by red-cockaded woodpeckers in relation to tree age

Treesearch

D. Craig Rudolph; Richard N. Conner

1991-01-01

We aged over 1350 Red-cockaded Woodpecker (Picoides borealis) cavity trees and a comparable number of randomly selected trees. Resulting data strongly support the hypothesis that Red-cockaded Woodpeckers preferentially select older trees. Ages of recently initiated cavity trees in the Texas study areas generally were similar to those of cavity trees...

Why do trees die? Characterizing the drivers of background tree mortality.

PubMed

Das, Adrian J; Stephenson, Nathan L; Davis, Kristin P

2016-10-01

The drivers of background tree mortality rates-the typical low rates of tree mortality found in forests in the absence of acute stresses like drought-are central to our understanding of forest dynamics, the effects of ongoing environmental changes on forests, and the causes and consequences of geographical gradients in the nature and strength of biotic interactions. To shed light on factors contributing to background tree mortality, we analyzed detailed pathological data from 200,668 tree-years of observation and 3,729 individual tree deaths, recorded over a 13-yr period in a network of old-growth forest plots in California's Sierra Nevada mountain range. We found that: (1) Biotic mortality factors (mostly insects and pathogens) dominated (58%), particularly in larger trees (86%). Bark beetles were the most prevalent (40%), even though there were no outbreaks during the study period; in contrast, the contribution of defoliators was negligible. (2) Relative occurrences of broad classes of mortality factors (biotic, 58%; suppression, 51%; and mechanical, 25%) are similar among tree taxa, but may vary with tree size and growth rate. (3) We found little evidence of distinct groups of mortality factors that predictably occur together on trees. Our results have at least three sets of implications. First, rather than being driven by abiotic factors such as lightning or windstorms, the "ambient" or "random" background mortality that many forest models presume to be independent of tree growth rate is instead dominated by biotic agents of tree mortality, with potentially critical implications for forecasting future mortality. Mechanistic models of background mortality, even for healthy, rapidly growing trees, must therefore include the insects and pathogens that kill trees. Second, the biotic agents of tree mortality, instead of occurring in a few predictable combinations, may generally act opportunistically and with a relatively large degree of independence from one another

Trees in the Landscape.

ERIC Educational Resources Information Center

Webb, Richard; Forbatha, Ann

1982-01-01

Strategies for using trees in classroom instruction are provided. Includes: (1) activities (such as tree identification, mapping, measuring tree height/width); (2) list of asthetic, architectural, engineering, climate, and wildlife functions of trees; (3) tree discussion questions; and (4) references. (JN)

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

PubMed Central

2013-01-01

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

Looking for trees in the forest: summary tree from posterior samples.

PubMed

Heled, Joseph; Bouckaert, Remco R

2013-10-04

Bayesian phylogenetic analysis generates a set of trees which are often condensed into a single tree representing the whole set. Many methods exist for selecting a representative topology for a set of unrooted trees, few exist for assigning branch lengths to a fixed topology, and even fewer for simultaneously setting the topology and branch lengths. However, there is very little research into locating a good representative for a set of rooted time trees like the ones obtained from a BEAST analysis. We empirically compare new and known methods for generating a summary tree. Some new methods are motivated by mathematical constructions such as tree metrics, while the rest employ tree concepts which work well in practice. These use more of the posterior than existing methods, which discard information not directly mapped to the chosen topology. Using results from a large number of simulations we assess the quality of a summary tree, measuring (a) how well it explains the sequence data under the model and (b) how close it is to the "truth", i.e to the tree used to generate the sequences. Our simulations indicate that no single method is "best". Methods producing good divergence time estimates have poor branch lengths and lower model fit, and vice versa. Using the results presented here, a user can choose the appropriate method based on the purpose of the summary tree.

Trees

ERIC Educational Resources Information Center

Al-Khaja, Nawal

2007-01-01

This is a thematic lesson plan for young learners about palm trees and the importance of taking care of them. The two part lesson teaches listening, reading and speaking skills. The lesson includes parts of a tree; the modal auxiliary, can; dialogues and a role play activity.

Transpiration and whole-tree conductance in ponderosa pine trees of different heights.

PubMed

Ryan, M G; Bond, B J; Law, B E; Hubbard, R M; Woodruff, D; Cienciala, E; Kucera, J

2000-09-01

Changes in leaf physiology with tree age and size could alter forest growth, water yield, and carbon fluxes. We measured tree water flux (Q) for 14 ponderosa pine trees in two size classes (12 m tall and ∼40 years old, and 36 m tall and ∼ 290 years old) to determine if transpiration (E) and whole-tree conductance (g t ) differed between the two sizes of trees. For both size classes, E was approximately equal to Q measured 2 m above the ground: Q was most highly correlated with current, not lagged, water vapor pressure deficit, and night Q was <12% of total daily flux. E for days 165-195 and 240-260 averaged 0.97 mmol m -2 (leaf area, projected) s -1 for the 12-m trees and 0.57 mmol m -2 (leaf area) s -1 for the 36-m trees. When photosynthetically active radiation (I P ) exceeded the light saturation for photosynthesis in ponderosa pine (900 µmol m -2 (ground) s -1 ), differences in E were more pronounced: 2.4 mmol m -2 (leaf area) s -1 for the 12-m trees and 1.2 mmol m -2 s -1 for the 36-m trees, yielding g t of 140 mmol m -2 (leaf area) s -1 for the 12-m trees and 72 mmol m -2 s -1 for the 36-m trees. Extrapolated to forests with leaf area index =1, the 36-m trees would transpire 117 mm between 1 June and 31 August compared to 170 mm for the 12-m trees, a difference of 15% of average annual precipitation. Lower g t in the taller trees also likely lowers photosynthesis during the growing season.

Minimum variance rooting of phylogenetic trees and implications for species tree reconstruction.

PubMed

Mai, Uyen; Sayyari, Erfan; Mirarab, Siavash

2017-01-01

Phylogenetic trees inferred using commonly-used models of sequence evolution are unrooted, but the root position matters both for interpretation and downstream applications. This issue has been long recognized; however, whether the potential for discordance between the species tree and gene trees impacts methods of rooting a phylogenetic tree has not been extensively studied. In this paper, we introduce a new method of rooting a tree based on its branch length distribution; our method, which minimizes the variance of root to tip distances, is inspired by the traditional midpoint rerooting and is justified when deviations from the strict molecular clock are random. Like midpoint rerooting, the method can be implemented in a linear time algorithm. In extensive simulations that consider discordance between gene trees and the species tree, we show that the new method is more accurate than midpoint rerooting, but its relative accuracy compared to using outgroups to root gene trees depends on the size of the dataset and levels of deviations from the strict clock. We show high levels of error for all methods of rooting estimated gene trees due to factors that include effects of gene tree discordance, deviations from the clock, and gene tree estimation error. Our simulations, however, did not reveal significant differences between two equivalent methods for species tree estimation that use rooted and unrooted input, namely, STAR and NJst. Nevertheless, our results point to limitations of existing scalable rooting methods.

Minimum variance rooting of phylogenetic trees and implications for species tree reconstruction

PubMed Central

Sayyari, Erfan; Mirarab, Siavash

2017-01-01

Phylogenetic trees inferred using commonly-used models of sequence evolution are unrooted, but the root position matters both for interpretation and downstream applications. This issue has been long recognized; however, whether the potential for discordance between the species tree and gene trees impacts methods of rooting a phylogenetic tree has not been extensively studied. In this paper, we introduce a new method of rooting a tree based on its branch length distribution; our method, which minimizes the variance of root to tip distances, is inspired by the traditional midpoint rerooting and is justified when deviations from the strict molecular clock are random. Like midpoint rerooting, the method can be implemented in a linear time algorithm. In extensive simulations that consider discordance between gene trees and the species tree, we show that the new method is more accurate than midpoint rerooting, but its relative accuracy compared to using outgroups to root gene trees depends on the size of the dataset and levels of deviations from the strict clock. We show high levels of error for all methods of rooting estimated gene trees due to factors that include effects of gene tree discordance, deviations from the clock, and gene tree estimation error. Our simulations, however, did not reveal significant differences between two equivalent methods for species tree estimation that use rooted and unrooted input, namely, STAR and NJst. Nevertheless, our results point to limitations of existing scalable rooting methods. PMID:28800608

Looking for trees in the forest: summary tree from posterior samples

PubMed Central

2013-01-01

Background Bayesian phylogenetic analysis generates a set of trees which are often condensed into a single tree representing the whole set. Many methods exist for selecting a representative topology for a set of unrooted trees, few exist for assigning branch lengths to a fixed topology, and even fewer for simultaneously setting the topology and branch lengths. However, there is very little research into locating a good representative for a set of rooted time trees like the ones obtained from a BEAST analysis. Results We empirically compare new and known methods for generating a summary tree. Some new methods are motivated by mathematical constructions such as tree metrics, while the rest employ tree concepts which work well in practice. These use more of the posterior than existing methods, which discard information not directly mapped to the chosen topology. Using results from a large number of simulations we assess the quality of a summary tree, measuring (a) how well it explains the sequence data under the model and (b) how close it is to the “truth”, i.e to the tree used to generate the sequences. Conclusions Our simulations indicate that no single method is “best”. Methods producing good divergence time estimates have poor branch lengths and lower model fit, and vice versa. Using the results presented here, a user can choose the appropriate method based on the purpose of the summary tree. PMID:24093883

Tree diversity in relation to tree height: alternative perspectives.

PubMed

Givnish, Thomas J

2017-03-01

Marks et al. (Ecol. Lett., 19, 2016, 743-751) show that tree diversity increases with tree height in North America and argue it reflects habitat 'suitability'. This finding conflicts with classical results, lacks controls for covariates of tree height, and can be explained alternatively using the modified Janzen-Connell effect and regional variance in habitats. © 2017 John Wiley & Sons Ltd/CNRS.

TreePlus: interactive exploration of networks with enhanced tree layouts.

PubMed

Lee, Bongshin; Parr, Cynthia S; Plaisant, Catherine; Bederson, Benjamin B; Veksler, Vladislav D; Gray, Wayne D; Kotfila, Christopher

2006-01-01

Despite extensive research, it is still difficult to produce effective interactive layouts for large graphs. Dense layout and occlusion make food webs, ontologies, and social networks difficult to understand and interact with. We propose a new interactive Visual Analytics component called TreePlus that is based on a tree-style layout. TreePlus reveals the missing graph structure with visualization and interaction while maintaining good readability. To support exploration of the local structure of the graph and gathering of information from the extensive reading of labels, we use a guiding metaphor of "Plant a seed and watch it grow." It allows users to start with a node and expand the graph as needed, which complements the classic overview techniques that can be effective at (but often limited to) revealing clusters. We describe our design goals, describe the interface, and report on a controlled user study with 28 participants comparing TreePlus with a traditional graph interface for six tasks. In general, the advantage of TreePlus over the traditional interface increased as the density of the displayed data increased. Participants also reported higher levels of confidence in their answers with TreePlus and most of them preferred TreePlus.

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.

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....

Urban park tree inventories

Treesearch

Joe R. McBride; David J. Nowak

1989-01-01

A survey of published reports on urban park tree inventories in the United States and the United Kingdom reveal two types of inventories: (1) Tree Location Inventories and (2) Generalized Information Inventories. Tree location inventories permit managers to relocate specific park trees, along with providing individual tree characteristics and condition data. In...

The Tree Worker's Manual.

ERIC Educational Resources Information Center

Smithyman, S. J.

This manual is designed to prepare students for entry-level positions as tree care professionals. Addressed in the individual chapters of the guide are the following topics: the tree service industry; clothing, eqiupment, and tools; tree workers; basic tree anatomy; techniques of pruning; procedures for climbing and working in the tree; aerial…

Simple street tree sampling

Treesearch

David J. Nowak; Jeffrey T. Walton; James Baldwin; Jerry Bond

2015-01-01

Information on street trees is critical for management of this important resource. Sampling of street tree populations provides an efficient means to obtain street tree population information. Long-term repeat measures of street tree samples supply additional information on street tree changes and can be used to report damages from catastrophic events. Analyses of...

Folding Automaton for Trees

NASA Astrophysics Data System (ADS)

Subashini, N.; Thiagarajan, K.

2018-04-01

In this paper we observed the definition of folding technique in graph theory and we derived the corresponding automaton for trees. Also derived some propositions on symmetrical structure tree, non-symmetrical structure tree, point symmetrical structure tree, edge symmetrical structure tree along with finite number of points. This approach provides to derive one edge after n’ number of foldings.

Relating phylogenetic trees to transmission trees of infectious disease outbreaks.

PubMed

Ypma, Rolf J F; van Ballegooijen, W Marijn; Wallinga, Jacco

2013-11-01

Transmission events are the fundamental building blocks of the dynamics of any infectious disease. Much about the epidemiology of a disease can be learned when these individual transmission events are known or can be estimated. Such estimations are difficult and generally feasible only when detailed epidemiological data are available. The genealogy estimated from genetic sequences of sampled pathogens is another rich source of information on transmission history. Optimal inference of transmission events calls for the combination of genetic data and epidemiological data into one joint analysis. A key difficulty is that the transmission tree, which describes the transmission events between infected hosts, differs from the phylogenetic tree, which describes the ancestral relationships between pathogens sampled from these hosts. The trees differ both in timing of the internal nodes and in topology. These differences become more pronounced when a higher fraction of infected hosts is sampled. We show how the phylogenetic tree of sampled pathogens is related to the transmission tree of an outbreak of an infectious disease, by the within-host dynamics of pathogens. We provide a statistical framework to infer key epidemiological and mutational parameters by simultaneously estimating the phylogenetic tree and the transmission tree. We test the approach using simulations and illustrate its use on an outbreak of foot-and-mouth disease. The approach unifies existing methods in the emerging field of phylodynamics with transmission tree reconstruction methods that are used in infectious disease epidemiology.

Decision-Tree Program

NASA Technical Reports Server (NTRS)

Buntine, Wray

1994-01-01

IND computer program introduces Bayesian and Markov/maximum-likelihood (MML) methods and more-sophisticated methods of searching in growing trees. Produces more-accurate class-probability estimates important in applications like diagnosis. Provides range of features and styles with convenience for casual user, fine-tuning for advanced user or for those interested in research. Consists of four basic kinds of routines: data-manipulation, tree-generation, tree-testing, and tree-display. Written in C language.

Tree-growth analyses to estimate tree species' drought tolerance.

PubMed

Eilmann, Britta; Rigling, Andreas

2012-02-01

Climate change is challenging forestry management and practices. Among other things, tree species with the ability to cope with more extreme climate conditions have to be identified. However, while environmental factors may severely limit tree growth or even cause tree death, assessing a tree species' potential for surviving future aggravated environmental conditions is rather demanding. The aim of this study was to find a tree-ring-based method suitable for identifying very drought-tolerant species, particularly potential substitute species for Scots pine (Pinus sylvestris L.) in Valais. In this inner-Alpine valley, Scots pine used to be the dominating species for dry forests, but today it suffers from high drought-induced mortality. We investigate the growth response of two native tree species, Scots pine and European larch (Larix decidua Mill.), and two non-native species, black pine (Pinus nigra Arnold) and Douglas fir (Pseudotsuga menziesii Mirb. var. menziesii), to drought. This involved analysing how the radial increment of these species responded to increasing water shortage (abandonment of irrigation) and to increasingly frequent drought years. Black pine and Douglas fir are able to cope with drought better than Scots pine and larch, as they show relatively high radial growth even after irrigation has been stopped and a plastic growth response to drought years. European larch does not seem to be able to cope with these dry conditions as it lacks the ability to recover from drought years. The analysis of trees' short-term response to extreme climate events seems to be the most promising and suitable method for detecting how tolerant a tree species is towards drought. However, combining all the methods used in this study provides a complete picture of how water shortage could limit species.

Community Tree Planting Guide

Treesearch

Katie Himanga; Douglas Jones; Jean Miller; Janette Monear; Gail Steinman; Katherine Widin

2001-01-01

Tree Trust has been helping people plant trees in their communities since 1976. Our goal is to educate people about the importance of trees in their community and guide them through the process of successful tree-planting projects. Franklin Delano Roosevelt once said ?to exist as a nation, to prosper as a state, and to live as a people, we must have trees?....

Are trees long-lived?

Treesearch

Kevin T. Smith

2009-01-01

Trees and tree care can capture the best of people's motivations and intentions. Trees are living memorials that help communities heal at sites of national tragedy, such as Oklahoma City and the World Trade Center. We mark the places of important historical events by the trees that grew nearby even if the original tree, such as the Charter Oak in Connecticut or...

There's Life in Hazard Trees

Treesearch

Mary Torsello; Toni McLellan

The goals of hazard tree management programs are to maximize public safety and maintain a healthy sustainable tree resource. Although hazard tree management frequently targets removal of trees or parts of trees that attract wildlife, it can take into account a diversity of tree values. With just a little extra planning, hazard tree management can be highly beneficial...

Tree nut allergens.

PubMed

Geiselhart, Sabine; Hoffmann-Sommergruber, Karin; Bublin, Merima

2018-04-18

Tree nuts are considered as part of a healthy diet due to their high nutritional quality. However, they are also a potent source of allergenic proteins inducing IgE mediated hypersensitivity often causing serious, life-threatening reactions. The reported prevalence of tree nut allergy is up to 4.9% worldwide. The general term "tree nuts" comprises a number of nuts, seeds, and drupes, derived from trees from different botanical families. For hazelnut and walnut several allergens have been identified which are already partly applied in component resolved diagnosis, while for other tree nuts such as macadamia, coconut, and Brazil nut only individual allergens were identified and data on additional allergenic proteins are missing. This review summarizes the current knowledge on tree nut allergens and describes their physicochemical and immunological characterization and clinical relevance. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

National Christmas Tree Association > Education > White House Tree

Science.gov Websites

Vander Velden, owners of Whispering Pines Tree Farm in Octonto, Wisconsin. The tree, a 19 foot Douglas Visitors Office and Jim Adams with the National Park Service. This 19 foot Balsam fir will be displayed in

TreeRipper web application: towards a fully automated optical tree recognition software.

PubMed

Hughes, Joseph

2011-05-20

Relationships between species, genes and genomes have been printed as trees for over a century. Whilst this may have been the best format for exchanging and sharing phylogenetic hypotheses during the 20th century, the worldwide web now provides faster and automated ways of transferring and sharing phylogenetic knowledge. However, novel software is needed to defrost these published phylogenies for the 21st century. TreeRipper is a simple website for the fully-automated recognition of multifurcating phylogenetic trees (http://linnaeus.zoology.gla.ac.uk/~jhughes/treeripper/). The program accepts a range of input image formats (PNG, JPG/JPEG or GIF). The underlying command line c++ program follows a number of cleaning steps to detect lines, remove node labels, patch-up broken lines and corners and detect line edges. The edge contour is then determined to detect the branch length, tip label positions and the topology of the tree. Optical Character Recognition (OCR) is used to convert the tip labels into text with the freely available tesseract-ocr software. 32% of images meeting the prerequisites for TreeRipper were successfully recognised, the largest tree had 115 leaves. Despite the diversity of ways phylogenies have been illustrated making the design of a fully automated tree recognition software difficult, TreeRipper is a step towards automating the digitization of past phylogenies. We also provide a dataset of 100 tree images and associated tree files for training and/or benchmarking future software. TreeRipper is an open source project licensed under the GNU General Public Licence v3.

On Determining if Tree-based Networks Contain Fixed Trees.

PubMed

Anaya, Maria; Anipchenko-Ulaj, Olga; Ashfaq, Aisha; Chiu, Joyce; Kaiser, Mahedi; Ohsawa, Max Shoji; Owen, Megan; Pavlechko, Ella; St John, Katherine; Suleria, Shivam; Thompson, Keith; Yap, Corrine

2016-05-01

We address an open question of Francis and Steel about phylogenetic networks and trees. They give a polynomial time algorithm to decide if a phylogenetic network, N, is tree-based and pose the problem: given a fixed tree T and network N, is N based on T? We show that it is [Formula: see text]-hard to decide, by reduction from 3-Dimensional Matching (3DM) and further that the problem is fixed-parameter tractable.

Tree leaf trade-offs are stronger for sub-canopy trees: leaf traits reveal little about growth rates in canopy trees.

PubMed

Wills, Jarrah; Herbohn, John; Hu, Jing; Sohel, Shawkat; Baynes, Jack; Firn, Jennifer

2018-06-01

Can morphological plant functional traits predict demographic rates (e.g., growth) within plant communities as diverse as tropical forests? This is one of the most important next-step questions in trait-based ecology and particularly for global reforestation efforts. Due to the diversity of tropical tree species and their longevity, it is difficult to predict their performance prior to reforestation efforts. In this study, we investigate if simple leaf traits are predictors of the more complex ecological process of plant growth in regenerating selectively logged natural forest within the Wet Tropics (WTs) bioregion of Australia. This study used a rich historical data set to quantify tree growth within plots located at Danbulla National Park and State Forest on the Atherton Tableland. Leaf traits were collected from trees that have exhibited fast or slow growth over the last ~50 yr of measurement. Leaf traits were found to be poor predictors of tree growth for trees that have entered the canopy; however, for sub-canopy trees, leaf traits had a stronger association with growth rates. Leaf phosphorus concentrations were the strongest predictor of Periodic Annual Increment (PAI) for trees growing within the sub-canopy, with trees with higher leaf phosphorus levels showing a higher PAI. Sub-canopy tree leaves also exhibited stronger trade-offs between leaf traits and adhere to theoretical predictions more so than for canopy trees. We suggest that, in order for leaf traits to be more applicable to reforestation, size dependence of traits and growth relationships need to be more carefully considered, particularly when reforestation practitioners assign mean trait values to tropical tree species from multiple canopy strata. © 2018 by the Ecological Society of America.

Whole-tree distribution and temporal variation of non-structural carbohydrates in broadleaf evergreen trees.

PubMed

Smith, Merryn G; Miller, Rebecca E; Arndt, Stefan K; Kasel, Sabine; Bennett, Lauren T

2018-04-01

Non-structural carbohydrates (NSCs) form a fundamental yet poorly quantified carbon pool in trees. Studies of NSC seasonality in forest trees have seldom measured whole-tree NSC stocks and allocation among organs, and are not representative of all tree functional types. Non-structural carbohydrate research has primarily focussed on broadleaf deciduous and coniferous evergreen trees with distinct growing seasons, while broadleaf evergreen trees remain under-studied despite their different growth phenology. We measured whole-tree NSC allocation and temporal variation in Eucalyptus obliqua L'Hér., a broadleaf evergreen tree species typically occurring in mixed-age temperate forests, which has year-round growth and the capacity to resprout after fire. Our overarching objective was to improve the empirical basis for understanding the functional importance of NSC allocation and stock changes at the tree- and organ-level in this tree functional type. Starch was the principal storage carbohydrate and was primarily stored in the stem and roots of young (14-year-old) trees rather than the lignotuber, which did not appear to be a specialized starch storage organ. Whole-tree NSC stocks were depleted during spring and summer due to significant decreases in starch mass in the roots and stem, seemingly to support root and crown growth but potentially exacerbated by water stress in summer. Seasonality of stem NSCs differed between young and mature trees, and was not synchronized with stem basal area increments in mature trees. Our results suggest that the relative magnitude of seasonal NSC stock changes could vary with tree growth stage, and that the main drivers of NSC fluctuations in broadleaf evergreen trees in temperate biomes could be periodic disturbances such as summer drought and fire, rather than growth phenology. These results have implications for understanding post-fire tree recovery via resprouting, and for incorporating NSC pools into carbon models of mixed

SILVA tree viewer: interactive web browsing of the SILVA phylogenetic guide trees.

PubMed

Beccati, Alan; Gerken, Jan; Quast, Christian; Yilmaz, Pelin; Glöckner, Frank Oliver

2017-09-30

Phylogenetic trees are an important tool to study the evolutionary relationships among organisms. The huge amount of available taxa poses difficulties in their interactive visualization. This hampers the interaction with the users to provide feedback for the further improvement of the taxonomic framework. The SILVA Tree Viewer is a web application designed for visualizing large phylogenetic trees without requiring the download of any software tool or data files. The SILVA Tree Viewer is based on Web Geographic Information Systems (Web-GIS) technology with a PostgreSQL backend. It enables zoom and pan functionalities similar to Google Maps. The SILVA Tree Viewer enables access to two phylogenetic (guide) trees provided by the SILVA database: the SSU Ref NR99 inferred from high-quality, full-length small subunit sequences, clustered at 99% sequence identity and the LSU Ref inferred from high-quality, full-length large subunit sequences. The Tree Viewer provides tree navigation, search and browse tools as well as an interactive feedback system to collect any kinds of requests ranging from taxonomy to data curation and improving the tool itself.

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

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

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

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

Polyoxyethylene Tallow Amine, a Glyphosate Formulation Adjuvant: Soil Adsorption Characteristics, Degradation Profile, and Occurrence on Selected Soils from Agricultural Fields in Iowa, Illinois, Indiana, Kansas, Mississippi, and Missouri.

PubMed

Tush, Daniel; Meyer, Michael T

2016-06-07

Polyoxyethylene tallow amine (POEA) is an inert ingredient added to formulations of glyphosate, the most widely applied agricultural herbicide. POEA has been shown to have toxic effects to some aquatic organisms making the potential transport of POEA from the application site into the environment an important concern. This study characterized the adsorption of POEA to soils and assessed its occurrence and homologue distribution in agricultural soils from six states. Adsorption experiments of POEA to selected soils showed that POEA adsorbed much stronger than glyphosate; calcium chloride increased the binding of POEA; and the binding of POEA was stronger in low pH conditions. POEA was detected on a soil sample from an agricultural field near Lawrence, Kansas, but with a loss of homologues that contain alkenes. POEA was also detected on soil samples collected between February and early March from corn and soybean fields from ten different sites in five other states (Iowa, Illinois, Indiana, Missouri, Mississippi). This is the first study to characterize the adsorption of POEA to soil, the potential widespread occurrence of POEA on agricultural soils, and the persistence of the POEA homologues on agricultural soils into the following growing season.

Polyoxyethylene tallow amine, a glyphosate formulation adjuvant: Soil adsorption characteristics, degradation profile, and occurrence on selected soils from agricultural fields in Iowa, Illinois, Indiana, Kansas, Mississippi, and Missouri

USGS Publications Warehouse

Tush, Daniel L.; Meyer, Michael T.

2016-01-01

Polyoxyethylene tallow amine (POEA) is an inert ingredient added to formulations of glyphosate, the most widely applied agricultural herbicide. POEA has been shown to have toxic effects to some aquatic organisms making the potential transport of POEA from the application site into the environment an important concern. This study characterized the adsorption of POEA to soils and assessed its occurrence and homologue distribution in agricultural soils from six states. Adsorption experiments of POEA to selected soils showed that POEA adsorbed much stronger than glyphosate; calcium chloride increased the binding of POEA; and the binding of POEA was stronger in low pH conditions. POEA was detected on a soil sample from an agricultural field near Lawrence, Kansas, but with a loss of homologues that contain alkenes. POEA was also detected on soil samples collected between February and early March from corn and soybean fields from ten different sites in five other states (Iowa, Illinois, Indiana, Missouri, Mississippi). This is the first study to characterize the adsorption of POEA to soil, the potential widespread occurrence of POEA on agricultural soils, and the persistence of the POEA homologues on agricultural soils into the following growing season.

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.

77 FR 66832 - Notice of Receipt of Pesticide Products; Registration Applications To Register New Uses

Federal Register 2010, 2011, 2012, 2013, 2014

2012-11-07

..., tallow wood, tea oil plant, and vernonia). Contact: Bethany Benbow, (703) 347-8072, email address: benbow... seed, rose hip, sesame, Stokes aster, sweet rocket, tallow wood, tea oil plant, and vernonia). Contact...

Whole-tree canopy enclosures: why cage a tree?

Treesearch

Jerome F. Grant; Abdul Hakeem; Paris L. Lambdin; Gregory J. Wiggins; Rusty J. Rhea

2011-01-01

The use of whole-tree canopy enclosures (i.e., cages) is not a typical approach to assessing biological parameters and interactions in a forest setting. However, the successful application of this technology may enable researchers to better understand certain types of tree/organismal interactions.

Growth of a Pine Tree

ERIC Educational Resources Information Center

Rollinson, Susan Wells

2012-01-01

The growth of a pine tree is examined by preparing "tree cookies" (cross-sectional disks) between whorls of branches. The use of Christmas trees allows the tree cookies to be obtained with inexpensive, commonly available tools. Students use the tree cookies to investigate the annual growth of the tree and how it corresponds to the number of whorls…

Trees in the city: valuing street trees in Portland, Oregon

Treesearch

G.H. Donovan; D.T. Butry

2010-01-01

We use a hedonic price model to simultaneously estimate the effects of street trees on the sales price and the time-on-market (TOM) of houses in Portland. Oregon. On average, street trees add $8,870 to sales price and reduce TOM by 1.7 days. In addition, we found that the benefits of street trees spill over to neighboring houses. Because the provision and maintenance...

Urban tree growth modeling

Treesearch

E. Gregory McPherson; Paula J. Peper

2012-01-01

This paper describes three long-term tree growth studies conducted to evaluate tree performance because repeated measurements of the same trees produce critical data for growth model calibration and validation. Several empirical and process-based approaches to modeling tree growth are reviewed. Modeling is more advanced in the fields of forestry and...

Decoding tree DNA

Treesearch

M. Thompson Conkle

1986-01-01

Check the laboratory reports after your next physical. You'll find information on a number of biochemical processes. Procedures like those used in the medical sciences are yielding valuable information about genetic differences among trees and tree pests. New procedures that provide ways to isolate and move genes are advancing progress in tree improvement. These...

Benefit-based tree valuation

Treesearch

E.G. McPherson

2007-01-01

Benefit-based tree valuation provides alternative estimates of the fair and reasonable value of trees while illustrating the relative contribution of different benefit types. This study compared estimates of tree value obtained using cost- and benefit-based approaches. The cost-based approach used the Council of Landscape and Tree Appraisers trunk formula method, and...

Totally Tree-mendous Activities: Projects To Discover the Beauty and Benefits of Trees.

ERIC Educational Resources Information Center

Hollister, Sarah

This teacher's guide supplies information and hands-on activities to teach about trees from several disciplines. Activities are grouped into six areas that cover botany, social studies, arts and literature (aesthetics), and trees as a resource. Sections include: (1) Tree Identification, which defines trees and leaves and presents activities that…

Winter Birch Trees

ERIC Educational Resources Information Center

Sweeney, Debra; Rounds, Judy

2011-01-01

Trees are great inspiration for artists. Many art teachers find themselves inspired and maybe somewhat obsessed with the natural beauty and elegance of the lofty tree, and how it changes through the seasons. One such tree that grows in several regions and always looks magnificent, regardless of the time of year, is the birch. In this article, the…

36 CFR 223.4 - Exchange of trees or portions of trees.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 36 Parks, Forests, and Public Property 2 2010-07-01 2010-07-01 false Exchange of trees or portions of trees. 223.4 Section 223.4 Parks, Forests, and Public Property FOREST SERVICE, DEPARTMENT OF AGRICULTURE SALE AND DISPOSAL OF NATIONAL FOREST SYSTEM TIMBER General Provisions § 223.4 Exchange of trees or...

How many trees are enough? Tree death and the urban canopy

Treesearch

Lara A. Roman

2014-01-01

Massive city tree planting campaigns have invigorated the urban forestry movement, and engaged politicians, planners, and the public in urban greening. Million tree initiatives have been launched in Los Angeles, CA; Denver, CO; New York City, NY; Philadelphia, PA, and other cities. Sacramento, CA even has a five million tree program. These...

Keeping trees as assets

Treesearch

Kevin T. Smith

2009-01-01

Landscape trees have real value and contribute to making livable communities. Making the most of that value requires providing trees with the proper care and attention. As potentially large and long-lived organisms, trees benefit from commitment to regular care that respects the natural tree system. This system captures, transforms, and uses energy to survive, grow,...

Conspecific plasticity and invasion: invasive populations of Chinese tallow (Triadica sebifera) have performance advantage over native populations only in low soil salinity.

PubMed

Chen, Leiyi; Tiu, Candice J; Peng, Shaolin; Siemann, Evan

2013-01-01

Global climate change may increase biological invasions in part because invasive species may have greater phenotypic plasticity than native species. This may be especially important for abiotic stresses such as salt inundation related to increased hurricane activity or sea level rise. If invasive species indeed have greater plasticity, this may reflect genetic differences between populations in the native and introduced ranges. Here, we examined plasticity of functional and fitness-related traits of Chinese tallow (Triadica sebifera) populations from the introduced and native ranges that were grown along a gradient of soil salinity (control: 0 ppt; Low: 5 ppt; Medium: 10 ppt; High: 15 ppt) in a greenhouse. We used both norm reaction and plasticity index (PIv) to estimate the conspecific phenotypic plasticity variation between invasive and native populations. Overall, invasive populations had higher phenotypic plasticity of height growth rate (HGR), aboveground biomass, stem biomass and specific leaf area (SLA). The plasticity Index (PIv) of height growth rate (HGR) and SLA each were higher for plants from invasive populations. Absolute performance was always comparable or greater for plants from invasive populations versus native populations with the greatest differences at low stress levels. Our results were consistent with the "Master-of-some" pattern for invasive plants in which the fitness of introduced populations was greater in more benign conditions. This suggests that the greater conspecific phenotypic plasticity of invasive populations compared to native populations may increase invasion success in benign conditions but would not provide a potential interspecific competitive advantage in higher salinity soils that may occur with global climate change in coastal areas.

A native plant competitor mediates the impact of above- and belowground damage on an invasive tree.

PubMed

Carrillo, Juli; Siemann, Evan

2016-10-01

Plant competition may mediate the impacts of herbivory on invasive plant species through effects on plant growth and defense. This may predictably depend on whether herbivory occurs above or below ground and on relative plant competitive ability. We simulated the potential impact of above- or belowground damage by biocontrol agents on the growth of a woody invader (Chinese tallow tree, Triadica sebifera) through artificial herbivory, with or without competition with a native grass, little bluestem (Schizachyrium scoparium). We measured two defense responses of Triadica through quantifying constitutive and induced extrafloral nectar production and tolerance of above- and belowground damage (root and shoot biomass regrowth). We examined genetic variation in plant growth and defense across native (China) and invasive (United States) Triadica populations. Without competition, aboveground damage had a greater impact than belowground damage on Triadica performance, whereas with competition and above- and belowground damage impacted Triadica similarly. Whole plant tolerance to damage below ground was negatively associated with tolerance to grass competitors indicating tradeoffs in the ability to tolerate herbivory vs. compete. Competition reduced investment in defensive extrafloral nectar (EFN) production. Aboveground damage inhibited rather than induced EFN production while belowground plant damage did not impact aboveground nectar production. We found some support for the evolution of increased competitive ability hypothesis for invasive plants as United States plants were larger than native China plants and were more plastic in their response to biotic stressors than China plants (they altered their root to shoot ratios dependent on herbivory and competition treatments). Our results indicate that habitat type and the presence of competitors may be a larger determinant of herbivory impact than feeding mode and suggest that integrated pest management strategies including

Fault-Tree Compiler Program

NASA Technical Reports Server (NTRS)

Butler, Ricky W.; Martensen, Anna L.

1992-01-01

FTC, Fault-Tree Compiler program, is reliability-analysis software tool used to calculate probability of top event of fault tree. Five different types of gates allowed in fault tree: AND, OR, EXCLUSIVE OR, INVERT, and M OF N. High-level input language of FTC easy to understand and use. Program supports hierarchical fault-tree-definition feature simplifying process of description of tree and reduces execution time. Solution technique implemented in FORTRAN, and user interface in Pascal. Written to run on DEC VAX computer operating under VMS operating system.

The Needs of Trees

ERIC Educational Resources Information Center

Boyd, Amy E.; Cooper, Jim

2004-01-01

Tree rings can be used not only to look at plant growth, but also to make connections between plant growth and resource availability. In this lesson, students in 2nd-4th grades use role-play to become familiar with basic requirements of trees and how availability of those resources is related to tree ring sizes and tree growth. These concepts can…

Monitoring Million Trees LA: Tree performance during the early years and future benefits

Treesearch

E. Gregory McPherson

2014-01-01

Million Trees LA (MTLA) is one of several large-scale mayoral tree planting initiatives striving to create more livable cities through urban forestry. This study combined field sampling of tree survival and growth with numerical modeling of future benefits to assess performance of MTLA plantings. From 2006 to 2010 MTLA planted a diverse mix of 91,786 trees....

The ghosts of trees past: savanna trees create enduring legacies in plant species composition.

PubMed

Stahlheber, Karen A; Crispin, Kimberly L; Anton, Cassidy; D'Antonio, Carla M

2015-09-01

Isolated trees in savannas worldwide are known to modify their local environment and interact directly with neighboring plants. Less is known about how related tree species differ in their impacts on surrounding communities, how the effects of trees vary between years, and how composition might change following loss of the tree. To address these knowledge gaps, we explored the following questions: How do savanna trees influence the surrounding composition of herbaceous plants? Is the influence of trees consistent across different species and years? How does this change following the death of the tree? We surveyed herbaceous species composition and environmental attributes surrounding living and dead evergreen and deciduous Quercus trees in California (USA) savannas across several years that differed in their total precipitation. Oak trees of all species created distinct, homogenous understory communities dominated by exotic grasses across several sites. The composition of the low-diversity understory communities showed less interannual variation than open grassland, despite a two-fold difference in precipitation between the driest and wettest year. Vegetation composition was correlated with variation in soil properties, which were strongly affected by trees. Oaks also influenced the communities beyond the edge of the crown, but this depended on site and oak species. Low-diversity understory communities persisted up to 43 years following the death of the tree. A gradual decline in the effect of trees on the physical, environment following death did not result in vegetation becoming more similar to open grassland over time. The presence of long-lasting legacies of past tree crowns highlights the difficulty of assigning control of the current distribution of herbaceous species in grassland to their contemporary environment.

Characterizing the phylogenetic tree-search problem.

PubMed

Money, Daniel; Whelan, Simon

2012-03-01

Phylogenetic trees are important in many areas of biological research, ranging from systematic studies to the methods used for genome annotation. Finding the best scoring tree under any optimality criterion is an NP-hard problem, which necessitates the use of heuristics for tree-search. Although tree-search plays a major role in obtaining a tree estimate, there remains a limited understanding of its characteristics and how the elements of the statistical inferential procedure interact with the algorithms used. This study begins to answer some of these questions through a detailed examination of maximum likelihood tree-search on a wide range of real genome-scale data sets. We examine all 10,395 trees for each of the 106 genes of an eight-taxa yeast phylogenomic data set, then apply different tree-search algorithms to investigate their performance. We extend our findings by examining two larger genome-scale data sets and a large disparate data set that has been previously used to benchmark the performance of tree-search programs. We identify several broad trends occurring during tree-search that provide an insight into the performance of heuristics and may, in the future, aid their development. These trends include a tendency for the true maximum likelihood (best) tree to also be the shortest tree in terms of branch lengths, a weak tendency for tree-search to recover the best tree, and a tendency for tree-search to encounter fewer local optima in genes that have a high information content. When examining current heuristics for tree-search, we find that nearest-neighbor-interchange performs poorly, and frequently finds trees that are significantly different from the best tree. In contrast, subtree-pruning-and-regrafting tends to perform well, nearly always finding trees that are not significantly different to the best tree. Finally, we demonstrate that the precise implementation of a tree-search strategy, including when and where parameters are optimized, can change

Effect of the inclusion time of dietary saturated and unsaturated fats before slaughter on the accumulation and composition of abdominal fat in female broiler chickens.

PubMed

Sanz, M; Lopez-Bote, C J; Flores, A; Carmona, J M

2000-09-01

The aim of this experiment was to assess the effects of four different feeding programs designed to include tallow, a saturated fat at 0, 8, 12, and 28 d prior to slaughter on female broiler performance and the deposition, fatty acid profile, and melting point of abdominal fat. The following treatment groups were established according to dietary inclusion--from 21 to 49 d of age--of: sunflower oil (SUN), sunflower oil followed by tallow during the last 8 d (SUN + 8TALL), sunflower oil followed by tallow during the last 12 d (SUN + 12TALL), and tallow (TALL). The diets were designed to be isoenergetic and isonitrogenous. Abdominal fat deposition increased linearly with increasing number of days in which birds were fed the tallow-enriched diet. However, linear and quadratic response patterns were found between days before slaughter in which the birds were fed the tallow-enriched diet and abdominal fat melting points. This result suggested an exponential response in which 85% of the maximum level was already attained when the dietary fat type changed from an unsaturated to a saturated condition during the last 8 d of the feeding period. The use of an unsaturated fat source during the first stages of growth, and the substitution of a saturated fat for a few days before slaughter, may offer the advantage of lower abdominal fat deposition and an acceptable fat fluidity compared with the use of a saturated fat source during the whole growing and finishing period.

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

Lynch, G.L.; Berger, L.L.; Fahey, G.C. Jr.

Ruminant nitrogen utilization of soybean meal treated with (1) 70% ethanol at 23 or 78/sup 0/C, (2) 10% coconut oil or tallow, or (3) a combination of 70% ethanol at 78/sup 0/C and coconut oil or tallow was evaluated. Nitrogen solubility was lowest for soybean meal treated with ethanol at 78/sup 0/C, ethanol plus coconut oil and ethanol plus tallow. In situ nitrogen disappearance was lowest for soybean meal treated with ethanol at 78/sup 0/C, ethanol plus coconut oil, and ethanol plus tallow. Rates of nitrogen disappearance between 3 and 12 h were lowest for soybean meal treated with ethanolmore » at 78/sup 0/C, ethanol plus coconut oil, and ethanol plus tallow. Nitrogen retained by lambs was greater for lambs fed soybean meal treated with ethanol at 78/sup 0/C than for those fed untreated soybean meal. Ruminal ammonia 4 h post feeding was lowest for lambs fed soybean meal treated with ethanol at 78/sup 0/C, ethanol plus coconut oil, and coconut oil. These data indicate that the 78/sup 0/C ethanol treatment improved nitrogen utilization.« less

Barking up the wrong tree: injuries due to falls from trees in Solomon Islands.

PubMed

Negin, Joel; Vizintin, Pavle; Houasia, Patrick; Martiniuk, Alexandra L C

2014-12-11

To investigate tree-related injuries in Solomon Islands by the types of trees involved, who is affected and the types of injuries caused. Descriptive case series of all cases of injuries related to trees presenting to the National Referral Hospital in Honiara from 1994 to 2011. Data were collected by the attending clinician using a Trauma Epidemiology form, which provides information on age, sex, cause of injury and type of fracture. Number of injuries by tree type, sex and age. Of the 7651 injuries in the database, 1107 (14%) were caused by falls from trees. Falls from coconut trees led to the highest number of injuries, followed by falls from mango, guava, apple and nut trees. Overall, 85% of injuries occurred in individuals aged < 20 years. For injuries involving guava trees, 77% of patients were aged < 10 years, compared with 46% for the five most commonly involved tree types. Overall, 71% of injuries occurred among males. Of all injuries, 92% were fractures, 3% were dislocations and 5% were non-fracture, non-dislocation injuries. The arm (including wrist, elbow and hand) was the most common location of injury across all tree types. Distal radius fractures in the forearm were particularly common, as were ulna fractures. While mangos and guavas are undeniably delicious, the quest for their flesh can be hazardous. Children will always climb trees, but the search for food among children in lower-income settings may lead to higher rates of injury.

High-Frequency Measurements of Tree Methane Fluxes Indicate a Primary Souce Inside Tree Tissue

NASA Astrophysics Data System (ADS)

Brewer, P.; Megonigal, P.

2017-12-01

Methane emissions from the boles and shoots of living upland trees is a recent discovery with significant implications for methane budgets. Forest soil methane uptake is the greatest terrestrial methane sink, but studies have shown this may be partially for fully offset by tree methane sources. However, our ability to quantify the tree source has been hampered because the ultimate biological source(s) of methane is unclear. We measured methane fluxes from two species of living tree boles in an Eastern North American deciduous forest over 100 consecutive days. Our two hour sampling intervals allowed us to characterize diurnal patterns and seasonal dynamics. We observed wide intraspecific differences in average flux rates and diurnal dynamics, even between adjacent individuals. This and other properties of the fluxes indicates the primary methane source is likely within the tree tissues, not in soil or groundwater. Emissions of methane from trees offset approximately 10% of soil uptake on average, but at times tree fluxes were much higher. Preliminary analyses indicate the highest rates are related to tree life history, tree growth, temperature, ground-water depth, and soil moisture.

Diameter-Constrained Steiner Tree

NASA Astrophysics Data System (ADS)

Ding, Wei; Lin, Guohui; Xue, Guoliang

Given an edge-weighted undirected graph G = (V,E,c,w), where each edge e ∈ E has a cost c(e) and a weight w(e), a set S ⊆ V of terminals and a positive constant D 0, we seek a minimum cost Steiner tree where all terminals appear as leaves and its diameter is bounded by D 0. Note that the diameter of a tree represents the maximum weight of path connecting two different leaves in the tree. Such problem is called the minimum cost diameter-constrained Steiner tree problem. This problem is NP-hard even when the topology of Steiner tree is fixed. In present paper we focus on this restricted version and present a fully polynomial time approximation scheme (FPTAS) for computing a minimum cost diameter-constrained Steiner tree under a fixed topology.

Heavy Metal Bioaccumulation Capability of Woody Plants in Mine wasteland of Karst Areas

NASA Astrophysics Data System (ADS)

Xiuru, Wang; Zhongliang, Huang; Xuan, Zhang; Zijian, Wu

2017-04-01

The bioaccumulation capability and transfer characteristics of Pb, Zn, Cu and Cd in soil and 6 different woody plants collected from a typical lead-zinc mine wasteland of Karst area, Hunan province were investigated, including Cunninghamia lanceolata(Lamb.) Hook., Swida wilsoniana (Wanger.), Koelreuteria paniculata, Paulownia., Cinnamomum camphora (L.) Presl., and Sapium sebiferum (L.) Roxb. The results showed that the 6 plants could adapt to the heavy metal polluted environment, and there was a positive correlation between the heavy metal content in plants and soil.Swida wilsoniana (Wanger.) and Sapium sebiferum (L.) Roxb. had the largest Pb bioaccumulation factor of 0.03; Paulownia. had the highest Zn bioaccumulation factor of 0.37; the largest Pb transfer factor of 1.31 were found in Koelreuteria paniculata; and Zn transfer factor of Paulownia. reached 1.45. These 4 woody plants are suitable for phytoremediation of mine wasteland of Karst areas.

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.

A Metric on Phylogenetic Tree Shapes.

PubMed

Colijn, C; Plazzotta, G

2018-01-01

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

A Metric on Phylogenetic Tree Shapes

PubMed Central

Plazzotta, G.

2018-01-01

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

Visualizing phylogenetic tree landscapes.

PubMed

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

2017-02-02

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

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

Treesearch

Thomas B. Lynch; Robert F. Wittwer

2002-01-01

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

TreeShrink: fast and accurate detection of outlier long branches in collections of phylogenetic trees.

PubMed

Mai, Uyen; Mirarab, Siavash

2018-05-08

Sequence data used in reconstructing phylogenetic trees may include various sources of error. Typically errors are detected at the sequence level, but when missed, the erroneous sequences often appear as unexpectedly long branches in the inferred phylogeny. We propose an automatic method to detect such errors. We build a phylogeny including all the data then detect sequences that artificially inflate the tree diameter. We formulate an optimization problem, called the k-shrink problem, that seeks to find k leaves that could be removed to maximally reduce the tree diameter. We present an algorithm to find the exact solution for this problem in polynomial time. We then use several statistical tests to find outlier species that have an unexpectedly high impact on the tree diameter. These tests can use a single tree or a set of related gene trees and can also adjust to species-specific patterns of branch length. The resulting method is called TreeShrink. We test our method on six phylogenomic biological datasets and an HIV dataset and show that the method successfully detects and removes long branches. TreeShrink removes sequences more conservatively than rogue taxon removal and often reduces gene tree discordance more than rogue taxon removal once the amount of filtering is controlled. TreeShrink is an effective method for detecting sequences that lead to unrealistically long branch lengths in phylogenetic trees. The tool is publicly available at https://github.com/uym2/TreeShrink .

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

PubMed

Letunic, Ivica; Bork, Peer

2011-07-01

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

Tree Rings: Timekeepers of the Past.

ERIC Educational Resources Information Center

Phipps, R. L.; McGowan, J.

One of a series of general interest publications on science issues, this booklet describes the uses of tree rings in historical and biological recordkeeping. Separate sections cover the following topics: dating of tree rings, dating with tree rings, tree ring formation, tree ring identification, sample collections, tree ring cross dating, tree…

Talking Trees

ERIC Educational Resources Information Center

Tolman, Marvin

2005-01-01

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

Tree Amigos.

ERIC Educational Resources Information Center

Center for Environmental Study, Grand Rapids, MI.

Tree Amigos is a special cross-cultural program that uses trees as a common bond to bring the people of the Americas together in unique partnerships to preserve and protect the shared global environment. It is a tangible program that embodies the philosophy that individuals, acting together, can make a difference. This resource book contains…

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

Phylogenetic trees in bioinformatics

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

Burr, Tom L

2008-01-01

Genetic data is often used to infer evolutionary relationships among a collection of viruses, bacteria, animal or plant species, or other operational taxonomic units (OTU). A phylogenetic tree depicts such relationships and provides a visual representation of the estimated branching order of the OTUs. Tree estimation is unique for several reasons, including: the types of data used to represent each OTU; the use ofprobabilistic nucleotide substitution models; the inference goals involving both tree topology and branch length, and the huge number of possible trees for a given sample of a very modest number of OTUs, which implies that fmding themore » best tree(s) to describe the genetic data for each OTU is computationally demanding. Bioinformatics is too large a field to review here. We focus on that aspect of bioinformatics that includes study of similarities in genetic data from multiple OTUs. Although research questions are diverse, a common underlying challenge is to estimate the evolutionary history of the OTUs. Therefore, this paper reviews the role of phylogenetic tree estimation in bioinformatics, available methods and software, and identifies areas for additional research and development.« less

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…

Surface storage of rainfall in tree crowns: not all trees are equal

Treesearch

E. Gregory McPherson; Q. Xiao; Natalie van Doorn; P. Peper; E. Teach

2017-01-01

Urban forests can be an effective strategy for managing stormwater. The soil that supports tree growth acts like a reservoir that reduces runoff. The tree crown intercepts rainfall on leaves and stems and its evaporation reduces water reaching the ground below. Until now surface storage capacities have been studied only for forest trees. Based on forest research, green...

The limits to tree height.

PubMed

Koch, George W; Sillett, Stephen C; Jennings, Gregory M; Davis, Stephen D

2004-04-22

Trees grow tall where resources are abundant, stresses are minor, and competition for light places a premium on height growth. The height to which trees can grow and the biophysical determinants of maximum height are poorly understood. Some models predict heights of up to 120 m in the absence of mechanical damage, but there are historical accounts of taller trees. Current hypotheses of height limitation focus on increasing water transport constraints in taller trees and the resulting reductions in leaf photosynthesis. We studied redwoods (Sequoia sempervirens), including the tallest known tree on Earth (112.7 m), in wet temperate forests of northern California. Our regression analyses of height gradients in leaf functional characteristics estimate a maximum tree height of 122-130 m barring mechanical damage, similar to the tallest recorded trees of the past. As trees grow taller, increasing leaf water stress due to gravity and path length resistance may ultimately limit leaf expansion and photosynthesis for further height growth, even with ample soil moisture.

Factors affecting the concordance between orthologous gene trees and species tree in bacteria.

PubMed

Castillo-Ramírez, Santiago; González, Víctor

2008-10-30

As originally defined, orthologous genes implied a reflection of the history of the species. In recent years, many studies have examined the concordance between orthologous gene trees and species trees in bacteria. These studies have produced contradictory results that may have been influenced by orthologous gene misidentification and artefactual phylogenetic reconstructions. Here, using a method that allows the detection and exclusion of false positives during identification of orthologous genes, we address the question of whether putative orthologous genes within bacteria really reflect the history of the species. We identified a set of 370 orthologous genes from the bacterial order Rhizobiales. Although manifesting strong vertical signal, almost every orthologous gene had a distinct phylogeny, and the most common topology among the orthologous gene trees did not correspond with the best estimate of the species tree. However, each orthologous gene tree shared an average of 70% of its bipartitions with the best estimate of the species tree. Stochastic error related to gene size affected the concordance between the best estimated of the species tree and the orthologous gene trees, although this effect was weak and distributed unevenly among the functional categories. The nodes showing the greatest discordance were those defined by the shortest internal branches in the best estimated of the species tree. Moreover, a clear bias was evident with respect to the function of the orthologous genes, and the degree of divergence among the orthologous genes appeared to be related to their functional classification. Orthologous genes do not reflect the history of the species when taken as individual markers, but they do when taken as a whole. Stochastic error affected the concordance of orthologous genes with the species tree, albeit weakly. We conclude that two important biological causes of discordance among orthologous genes are incomplete lineage sorting and functional

The fault-tree compiler

NASA Technical Reports Server (NTRS)

Martensen, Anna L.; Butler, Ricky W.

1987-01-01

The Fault Tree Compiler Program is a new reliability tool used to predict the top event probability for a fault tree. Five different gate types are allowed in the fault tree: AND, OR, EXCLUSIVE OR, INVERT, and M OF N gates. The high level input language is easy to understand and use when describing the system tree. In addition, the use of the hierarchical fault tree capability can simplify the tree description and decrease program execution time. The current solution technique provides an answer precise (within the limits of double precision floating point arithmetic) to the five digits in the answer. The user may vary one failure rate or failure probability over a range of values and plot the results for sensitivity analyses. The solution technique is implemented in FORTRAN; the remaining program code is implemented in Pascal. The program is written to run on a Digital Corporation VAX with the VMS operation system.

Stand conditions and tree characteristics affect quality of longleaf pine for red-cockaded woodpecker cavity trees

Treesearch

W.G. Ross; D.L. Kulhavy; R.N. Conner

1997-01-01

We measured resin flow of longleaf (Pinus palustris Mill.) pines in red-cockaded woodpecker (Picoides borealis Vieillot) clusters in the Angelina National Forest in Texas, and the Apalachicola National Forest in Florida. Sample trees were categorized as active cavity trees, inactive cavity trees and control trees. Sample trees were further...

75 FR 51507 - WisdomTree Asset Management, Inc., and WisdomTree Trust; Notice of Application

Federal Register 2010, 2011, 2012, 2013, 2014

2010-08-20

...] WisdomTree Asset Management, Inc., and WisdomTree Trust; Notice of Application August 13, 2010. AGENCY... subadvisory agreements without shareholder approval. Applicants: WisdomTree Asset Management, Inc (``WTAM'' or ``Adviser'') and WisdomTree Trust (``Trust''). Filing Dates: The application was filed on December 23, 2009...

Conspecific Plasticity and Invasion: Invasive Populations of Chinese Tallow (Triadica sebifera) Have Performance Advantage over Native Populations Only in Low Soil Salinity

PubMed Central

Chen, Leiyi; Tiu, Candice J.; Peng, Shaolin; Siemann, Evan

2013-01-01

Global climate change may increase biological invasions in part because invasive species may have greater phenotypic plasticity than native species. This may be especially important for abiotic stresses such as salt inundation related to increased hurricane activity or sea level rise. If invasive species indeed have greater plasticity, this may reflect genetic differences between populations in the native and introduced ranges. Here, we examined plasticity of functional and fitness-related traits of Chinese tallow (Triadica sebifera) populations from the introduced and native ranges that were grown along a gradient of soil salinity (control: 0 ppt; Low: 5 ppt; Medium: 10 ppt; High: 15 ppt) in a greenhouse. We used both norm reaction and plasticity index (PIv) to estimate the conspecific phenotypic plasticity variation between invasive and native populations. Overall, invasive populations had higher phenotypic plasticity of height growth rate (HGR), aboveground biomass, stem biomass and specific leaf area (SLA). The plasticity Index (PIv) of height growth rate (HGR) and SLA each were higher for plants from invasive populations. Absolute performance was always comparable or greater for plants from invasive populations versus native populations with the greatest differences at low stress levels. Our results were consistent with the “Master-of-some” pattern for invasive plants in which the fitness of introduced populations was greater in more benign conditions. This suggests that the greater conspecific phenotypic plasticity of invasive populations compared to native populations may increase invasion success in benign conditions but would not provide a potential interspecific competitive advantage in higher salinity soils that may occur with global climate change in coastal areas. PMID:24040366

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

NASA Astrophysics Data System (ADS)

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

2012-04-01

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

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

PubMed

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

2007-04-01

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

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.

New perspectives on the ecology of tree structure and tree communities through terrestrial laser scanning.

PubMed

Malhi, Yadvinder; Jackson, Tobias; Patrick Bentley, Lisa; Lau, Alvaro; Shenkin, Alexander; Herold, Martin; Calders, Kim; Bartholomeus, Harm; Disney, Mathias I

2018-04-06

Terrestrial laser scanning (TLS) opens up the possibility of describing the three-dimensional structures of trees in natural environments with unprecedented detail and accuracy. It is already being extensively applied to describe how ecosystem biomass and structure vary between sites, but can also facilitate major advances in developing and testing mechanistic theories of tree form and forest structure, thereby enabling us to understand why trees and forests have the biomass and three-dimensional structure they do. Here we focus on the ecological challenges and benefits of understanding tree form, and highlight some advances related to capturing and describing tree shape that are becoming possible with the advent of TLS. We present examples of ongoing work that applies, or could potentially apply, new TLS measurements to better understand the constraints on optimization of tree form. Theories of resource distribution networks, such as metabolic scaling theory, can be tested and further refined. TLS can also provide new approaches to the scaling of woody surface area and crown area, and thereby better quantify the metabolism of trees. Finally, we demonstrate how we can develop a more mechanistic understanding of the effects of avoidance of wind risk on tree form and maximum size. Over the next few years, TLS promises to deliver both major empirical and conceptual advances in the quantitative understanding of trees and tree-dominated ecosystems, leading to advances in understanding the ecology of why trees and ecosystems look and grow the way they do.

The Re-Think Tree.

ERIC Educational Resources Information Center

Gear, Jim

1993-01-01

The Re-Think Tree is a simple framework to help individuals assess and improve their behaviors related to environmental issues. The branches of the tree in order of priority are refuse, reduce, re-use, and recycle. Roots of the tree include such things as public opinion, education, and watchdog groups. (KS)

Coalescent-based species tree inference from gene tree topologies under incomplete lineage sorting by maximum likelihood.

PubMed

Wu, Yufeng

2012-03-01

Incomplete lineage sorting can cause incongruence between the phylogenetic history of genes (the gene tree) and that of the species (the species tree), which can complicate the inference of phylogenies. In this article, I present a new coalescent-based algorithm for species tree inference with maximum likelihood. I first describe an improved method for computing the probability of a gene tree topology given a species tree, which is much faster than an existing algorithm by Degnan and Salter (2005). Based on this method, I develop a practical algorithm that takes a set of gene tree topologies and infers species trees with maximum likelihood. This algorithm searches for the best species tree by starting from initial species trees and performing heuristic search to obtain better trees with higher likelihood. This algorithm, called STELLS (which stands for Species Tree InfErence with Likelihood for Lineage Sorting), has been implemented in a program that is downloadable from the author's web page. The simulation results show that the STELLS algorithm is more accurate than an existing maximum likelihood method for many datasets, especially when there is noise in gene trees. I also show that the STELLS algorithm is efficient and can be applied to real biological datasets. © 2011 The Author. Evolution© 2011 The Society for the Study of Evolution.

Effect of dietary fat source on lipoprotein composition and plasma lipid concentrations in pigs.

PubMed

Faidley, T D; Luhman, C M; Galloway, S T; Foley, M K; Beitz, D C

1990-10-01

Most studies of the effects of dietary fat sources on plasma lipid components have used diets with extreme fat compositions; the current study was designed to more nearly mimic human dietary fat intake. Young growing pigs were fed diets containing either 20 or 40% of energy as soy oil, beef tallow or a 50/50 blend of soy oil and tallow. Different dietary fats did not affect concentrations of cholesterol, triacylglycerol or protein in plasma or major lipoprotein fractions. The concentration of phospholipid was less in plasma and in very low density lipoproteins with soy oil feeding than with tallow feeding. The weight percentage of cholesteryl ester in the low density lipoprotein fraction tended to be greater with 40% than with 20% tallow and tended to be less with 40% than with 20% soy oil. Phospholipid as a weight percentage of low density lipoprotein was least in pigs fed soy oil. Tallow feeding increased the percentage of myristic, palmitic, palmitoleic and oleic acids in plasma, relative to both other groups. Soy oil feeding increased the percentage of linoleic and linolenic acids. These moderate diets were not hypercholesterolemic, but they did alter plasma fatty acid composition and phospholipid concentrations in plasma and very low density lipoprotein.

How Trees Can Save Energy.

ERIC Educational Resources Information Center

Fazio, James R., Ed.

1991-01-01

This document might easily have been called "How To Use Trees To Save Energy". It presents the energy saving advantages of landscaping the home and community with trees. The discussion includes: (1) landscaping advice to obtain the benefits of tree shade; (2) the heat island phenomenon in cities; (3) how and where to properly plant trees for…

Minnesota's Forest Trees. Revised.

ERIC Educational Resources Information Center

Miles, William R.; Fuller, Bruce L.

This bulletin describes 46 of the more common trees found in Minnesota's forests and windbreaks. The bulletin contains two tree keys, a summer key and a winter key, to help the reader identify these trees. Besides the two keys, the bulletin includes an introduction, instructions for key use, illustrations of leaf characteristics and twig…

DIF Trees: Using Classification Trees to Detect Differential Item Functioning

ERIC Educational Resources Information Center

Vaughn, Brandon K.; Wang, Qiu

2010-01-01

A nonparametric tree classification procedure is used to detect differential item functioning for items that are dichotomously scored. Classification trees are shown to be an alternative procedure to detect differential item functioning other than the use of traditional Mantel-Haenszel and logistic regression analysis. A nonparametric…

Tree-ring isotopes reveal drought sensitivity in trees killed by spruce beetle outbreaks in south-central Alaska.

PubMed

Csank, Adam Z; Miller, Amy E; Sherriff, Rosemary L; Berg, Edward E; Welker, Jeffrey M

2016-10-01

Increasing temperatures have resulted in reduced growth and increased tree mortality across large areas of western North American forests. We use tree-ring isotope chronologies (δ 13 C and δ 18 O) from live and dead trees from four locations in south-central Alaska, USA, to test whether white spruce trees killed by recent spruce beetle (Dendroctonus rufipennis Kirby) outbreaks showed evidence of drought stress prior to death. Trees that were killed were more sensitive to spring/summer temperature and/or precipitation than trees that survived. At two of our sites, we found greater correlations between the δ 13 C and δ 18 O chronologies and spring/summer temperatures in dead trees than in live trees, suggesting that trees that are more sensitive to temperature-induced drought stress are more likely to be killed. At one site, the difference between δ 13 C in live and dead trees was related to winter/spring precipitation, with dead trees showing stronger correlations between δ 13 C and precipitation, again suggesting increased water stress in dead trees. At all sites where δ 18 O was measured, δ 18 O chronologies showed the greatest difference in climate response between live and dead groups, with δ 18 O in live trees correlating more strongly with late winter precipitation than dead trees. Our results indicate that sites where trees are already sensitive to warm or dry early growing-season conditions experienced the most beetle-kill, which has important implications for forecasting future mortality events in Alaska. © 2016 by the Ecological Society of America.

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.

Multi-level tree analysis of pulmonary artery/vein trees in non-contrast CT images

NASA Astrophysics Data System (ADS)

Gao, Zhiyun; Grout, Randall W.; Hoffman, Eric A.; Saha, Punam K.

2012-02-01

Diseases like pulmonary embolism and pulmonary hypertension are associated with vascular dystrophy. Identifying such pulmonary artery/vein (A/V) tree dystrophy in terms of quantitative measures via CT imaging significantly facilitates early detection of disease or a treatment monitoring process. A tree structure, consisting of nodes and connected arcs, linked to the volumetric representation allows multi-level geometric and volumetric analysis of A/V trees. Here, a new theory and method is presented to generate multi-level A/V tree representation of volumetric data and to compute quantitative measures of A/V tree geometry and topology at various tree hierarchies. The new method is primarily designed on arc skeleton computation followed by a tree construction based topologic and geometric analysis of the skeleton. The method starts with a volumetric A/V representation as input and generates its topologic and multi-level volumetric tree representations long with different multi-level morphometric measures. A new recursive merging and pruning algorithms are introduced to detect bad junctions and noisy branches often associated with digital geometric and topologic analysis. Also, a new notion of shortest axial path is introduced to improve the skeletal arc joining two junctions. The accuracy of the multi-level tree analysis algorithm has been evaluated using computer generated phantoms and pulmonary CT images of a pig vessel cast phantom while the reproducibility of method is evaluated using multi-user A/V separation of in vivo contrast-enhanced CT images of a pig lung at different respiratory volumes.

Depth of soil water uptake by tropical rainforest trees during dry periods: does tree dimension matter?

PubMed

Stahl, Clément; Hérault, Bruno; Rossi, Vivien; Burban, Benoit; Bréchet, Claude; Bonal, Damien

2013-12-01

Though the root biomass of tropical rainforest trees is concentrated in the upper soil layers, soil water uptake by deep roots has been shown to contribute to tree transpiration. A precise evaluation of the relationship between tree dimensions and depth of water uptake would be useful in tree-based modelling approaches designed to anticipate the response of tropical rainforest ecosystems to future changes in environmental conditions. We used an innovative dual-isotope labelling approach (deuterium in surface soil and oxygen at 120-cm depth) coupled with a modelling approach to investigate the role of tree dimensions in soil water uptake in a tropical rainforest exposed to seasonal drought. We studied 65 trees of varying diameter and height and with a wide range of predawn leaf water potential (Ψpd) values. We confirmed that about half of the studied trees relied on soil water below 100-cm depth during dry periods. Ψpd was negatively correlated with depth of water extraction and can be taken as a rough proxy of this depth. Some trees showed considerable plasticity in their depth of water uptake, exhibiting an efficient adaptive strategy for water and nutrient resource acquisition. We did not find a strong relationship between tree dimensions and depth of water uptake. While tall trees preferentially extract water from layers below 100-cm depth, shorter trees show broad variations in mean depth of water uptake. This precludes the use of tree dimensions to parameterize functional models.

Reinforcement Learning Trees

PubMed Central

Zhu, Ruoqing; Zeng, Donglin; Kosorok, Michael R.

2015-01-01

In this paper, we introduce a new type of tree-based method, reinforcement learning trees (RLT), which exhibits significantly improved performance over traditional methods such as random forests (Breiman, 2001) under high-dimensional settings. The innovations are three-fold. First, the new method implements reinforcement learning at each selection of a splitting variable during the tree construction processes. By splitting on the variable that brings the greatest future improvement in later splits, rather than choosing the one with largest marginal effect from the immediate split, the constructed tree utilizes the available samples in a more efficient way. Moreover, such an approach enables linear combination cuts at little extra computational cost. Second, we propose a variable muting procedure that progressively eliminates noise variables during the construction of each individual tree. The muting procedure also takes advantage of reinforcement learning and prevents noise variables from being considered in the search for splitting rules, so that towards terminal nodes, where the sample size is small, the splitting rules are still constructed from only strong variables. Last, we investigate asymptotic properties of the proposed method under basic assumptions and discuss rationale in general settings. PMID:26903687

The Wish Tree Project

ERIC Educational Resources Information Center

Brooks, Sarah DeWitt

2010-01-01

This article describes the author's experience in implementing a Wish Tree project in her school in an effort to bring the school community together with a positive art-making experience during a potentially stressful time. The concept of a wish tree is simple: plant a tree; provide tags and pencils for writing wishes; and encourage everyone to…

Faster Bit-Parallel Algorithms for Unordered Pseudo-tree Matching and Tree Homeomorphism

NASA Astrophysics Data System (ADS)

Kaneta, Yusaku; Arimura, Hiroki

In this paper, we consider the unordered pseudo-tree matching problem, which is a problem of, given two unordered labeled trees P and T, finding all occurrences of P in T via such many-one embeddings that preserve node labels and parent-child relationship. This problem is closely related to tree pattern matching problem for XPath queries with child axis only. If m > w , we present an efficient algorithm that solves the problem in O(nm log(w)/w) time using O(hm/w + mlog(w)/w) space and O(m log(w)) preprocessing on a unit-cost arithmetic RAM model with addition, where m is the number of nodes in P, n is the number of nodes in T, h is the height of T, and w is the word length. We also discuss a modification of our algorithm for the unordered tree homeomorphism problem, which corresponds to a tree pattern matching problem for XPath queries with descendant axis only.

A new species of Tenuipalpus Donnadieu (Acari: Tenuipalpidae) from Brazil, with ontogeny of chaetotaxy

USDA-ARS?s Scientific Manuscript database

Tenuipalpus toropi sp. nov., is described from females, males, deutonymphs, protonymphs and larvae collected on Sapium glandulatum (Vell.) Pax (Euphorbiaceae) from the northwest of the State of São Paulo, Brazil. We include details of the development in idiosomal and leg chaetotaxy for all stages of...

Chem-Is-Tree.

ERIC Educational Resources Information Center

Barry, Dana M.

1997-01-01

Provides details on the chemical composition of trees including a definition of wood. Also includes an activity on anthocyanins as well as a discussion of the resistance of wood to solvents and chemicals. Lists interesting products from trees. (DDR)

Tree Defects: A Photo Guide

Treesearch

Alex L Shigo

1983-01-01

This guide shows, in 110 photos, how discoloration and decay form in trees. An expanded concept of tree decay is given. After wounding, trees form boundaries to resist the spread of pathogens. The boundary-setting defense process is called compartmentalization, and model of the process is CODIT. The expanded concept and the model are used to reexamine many other tree...

The national tree-list layer

Treesearch

Stacy A. Drury; Jason M. Herynk

2011-01-01

The National Tree-List Layer (NTLL) project used LANDFIRE map products to produce the first national tree-list map layer that represents tree populations at stand and regional levels. The NTLL was produced in a short time frame to address the needs of Fire and Aviation Management for a map layer that could be used as input for simulating fire-caused tree mortality...

On the Number of Non-equivalent Ancestral Configurations for Matching Gene Trees and Species Trees.

PubMed

Disanto, Filippo; Rosenberg, Noah A

2017-09-14

An ancestral configuration is one of the combinatorially distinct sets of gene lineages that, for a given gene tree, can reach a given node of a specified species tree. Ancestral configurations have appeared in recursive algebraic computations of the conditional probability that a gene tree topology is produced under the multispecies coalescent model for a given species tree. For matching gene trees and species trees, we study the number of ancestral configurations, considered up to an equivalence relation introduced by Wu (Evolution 66:763-775, 2012) to reduce the complexity of the recursive probability computation. We examine the largest number of non-equivalent ancestral configurations possible for a given tree size n. Whereas the smallest number of non-equivalent ancestral configurations increases polynomially with n, we show that the largest number increases with [Formula: see text], where k is a constant that satisfies [Formula: see text]. Under a uniform distribution on the set of binary labeled trees with a given size n, the mean number of non-equivalent ancestral configurations grows exponentially with n. The results refine an earlier analysis of the number of ancestral configurations considered without applying the equivalence relation, showing that use of the equivalence relation does not alter the exponential nature of the increase with tree size.

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

PubMed Central

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

2016-01-01

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

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

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

Terrestrial apes and phylogenetic trees

PubMed Central

Arsuaga, Juan Luis

2010-01-01

The image that best expresses Darwin’s thinking is the tree of life. However, Darwin’s human evolutionary tree lacked almost everything because only the Neanderthals were known at the time and they were considered one extreme expression of our own species. Darwin believed that the root of the human tree was very deep and in Africa. It was not until 1962 that the root was shown to be much more recent in time and definitively in Africa. On the other hand, some neo-Darwinians believed that our family tree was not a tree, because there were no branches, but, rather, a straight stem. The recent years have witnessed spectacular discoveries in Africa that take us close to the origin of the human tree and in Spain at Atapuerca that help us better understand the origin of the Neanderthals as well as our own species. The final form of the tree, and the number of branches, remains an object of passionate debate. PMID:20445090

Nonbinary Tree-Based Phylogenetic Networks.

PubMed

Jetten, Laura; van Iersel, Leo

2018-01-01

Rooted phylogenetic networks are used to describe evolutionary histories that contain non-treelike evolutionary events such as hybridization and horizontal gene transfer. In some cases, such histories can be described by a phylogenetic base-tree with additional linking arcs, which can, for example, represent gene transfer events. Such phylogenetic networks are called tree-based. Here, we consider two possible generalizations of this concept to nonbinary networks, which we call tree-based and strictly-tree-based nonbinary phylogenetic networks. We give simple graph-theoretic characterizations of tree-based and strictly-tree-based nonbinary phylogenetic networks. Moreover, we show for each of these two classes that it can be decided in polynomial time whether a given network is contained in the class. Our approach also provides a new view on tree-based binary phylogenetic networks. Finally, we discuss two examples of nonbinary phylogenetic networks in biology and show how our results can be applied to them.

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...

Wrist postures and forces in tree planters during three tree unloading conditions.

PubMed

Denbeigh, Kathleen; Slot, Tegan R; Dumas, Geneviève A

2013-01-01

The aims of this study were to investigate wrist postures and forces while operating the shovel during tree planting and to determine if different tree unloading techniques result in variations in wrist postures and forces. Experienced tree planters performed the planting task in a laboratory environment for three conditions: (1) symmetric tree unloading, and asymmetric unloading resulting in (2) right-loaded planting bags and (3) left-loaded planting bags. An optoelectric system and a shovel instrumented with strain gauges captured wrist posture and forces at the wrist, respectively. Wrist extension of up to 45° was observed, and this posture, in combination with varying degrees of wrist deviation, may be a primary risk factor for musculoskeletal pain. Average resultant forces at the wrist were moderately high (>30 N) for each unloading condition, indicating increased risk for the development of repetitive strain injuries such as carpal tunnel syndrome. No significant differences in wrist posture or forces existed between unloading conditions. Wrist pain is a major musculoskeletal complaint among tree planters. This study measured wrist postures and forces at the wrist while operating the shovel during tree planting. The wrist extension observed, in combination with deviation, may be a key risk factor for musculoskeletal pain. Forces at the wrist indicate increased risk for repetitive strain injuries.

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.

Modeling individual tree survial

Treesearch

Quang V. Cao

2016-01-01

Information provided by growth and yield models is the basis for forest managers to make decisions on how to manage their forests. Among different types of growth models, whole-stand models offer predictions at stand level, whereas individual-tree models give detailed information at tree level. The well-known logistic regression is commonly used to predict tree...

Decision trees in epidemiological research.

PubMed

Venkatasubramaniam, Ashwini; Wolfson, Julian; Mitchell, Nathan; Barnes, Timothy; JaKa, Meghan; French, Simone

2017-01-01

In many studies, it is of interest to identify population subgroups that are relatively homogeneous with respect to an outcome. The nature of these subgroups can provide insight into effect mechanisms and suggest targets for tailored interventions. However, identifying relevant subgroups can be challenging with standard statistical methods. We review the literature on decision trees, a family of techniques for partitioning the population, on the basis of covariates, into distinct subgroups who share similar values of an outcome variable. We compare two decision tree methods, the popular Classification and Regression tree (CART) technique and the newer Conditional Inference tree (CTree) technique, assessing their performance in a simulation study and using data from the Box Lunch Study, a randomized controlled trial of a portion size intervention. Both CART and CTree identify homogeneous population subgroups and offer improved prediction accuracy relative to regression-based approaches when subgroups are truly present in the data. An important distinction between CART and CTree is that the latter uses a formal statistical hypothesis testing framework in building decision trees, which simplifies the process of identifying and interpreting the final tree model. We also introduce a novel way to visualize the subgroups defined by decision trees. Our novel graphical visualization provides a more scientifically meaningful characterization of the subgroups identified by decision trees. Decision trees are a useful tool for identifying homogeneous subgroups defined by combinations of individual characteristics. While all decision tree techniques generate subgroups, we advocate the use of the newer CTree technique due to its simplicity and ease of interpretation.

Urban tree database and allometric equations

Treesearch

E. Gregory McPherson; Natalie S. van Doorn; Paula J.  Peper

2016-01-01

Information on urban tree growth underpins models used to calculate the effects of trees on the environment and human well-being. Maximum tree size and other growth data are used by urban forest managers, landscape architects, and planners to select trees most suitable to the amount of growing space, thereby reducing costly future conflicts between trees and...

Non-unique key B-Tree implementation

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

Ries, D.R.

1980-12-23

The B-Trees are an indexed method to allow fast retrieval and order preserving updates to a FRAMIS relation based on a designated set of keys in the relation. A B-Tree access method is being implemented to provide indexed and sequential (in index order) access to FRAMIS relations. The implementation modifies the basic B-Tree structure to correctly allow multiple key values and still maintain the balanced page fill property of B-Trees. The data structures of the B-Tree are presented first, including the FRAMIS solution to the duplicate key value problem. Then the access level routines and utilities are presented. These routinesmore » include the original B-Tree creation; searching the B-Tree; and inserting, deleting, and replacing tuples on the B-Tree. In conclusion, the uses of the B-Tree access structures at the semantic level to enhance the FRAMIS performance are discussed. 10 figures.« less

Common allometric response of open-grown leader shoots to tree height in co-occurring deciduous broadleaved trees

PubMed Central

Miyata, Rie; Kubo, Takuya; Nabeshima, Eri; Kohyama, Takashi S.

2011-01-01

Background and Aims Morphology of crown shoots changes with tree height. The height of forest trees is usually correlated with the light environment and this makes it difficult to separate the effects of tree size and of light conditions on the morphological plasticity of crown shoots. This paper addresses the tree-height dependence of shoot traits under full-light conditions where a tree crown is not shaded by other crowns. Methods Focus is given to relationships between tree height and top-shoot traits, which include the shoot's leaf-blades and non-leafy mass, its total leaf-blade area and the length and basal diameter of the shoot's stem. We examine the allometric characteristics of open-grown current-year leader shoots at the tops of forest tree crowns up to 24 m high and quantify their responses to tree height in 13 co-occurring deciduous hardwood species in a cool-temperate forest in northern Japan. Key Results Dry mass allocated to leaf blades in a leader shoot increased with tree height in all 13 species. Specific leaf area decreased with tree height. Stem basal area was almost proportional to total leaf area in a leader shoot, where the proportionality constant did not depend on tree height, irrespective of species. Stem length for a given stem diameter decreased with tree height. Conclusions In the 13 species observed, height-dependent changes in allometry of leader shoots were convergent. This finding suggests that there is a common functional constraint in tree-height development. Under full-light conditions, leader shoots of tall trees naturally experience more severe water stress than those of short trees. We hypothesize that the height dependence of shoot allometry detected reflects an integrated response to height-associated water stress, which contributes to successful crown expansion and height gain. PMID:21914698

PhyloTreePruner: A Phylogenetic Tree-Based Approach for Selection of Orthologous Sequences for Phylogenomics.

PubMed

Kocot, Kevin M; Citarella, Mathew R; Moroz, Leonid L; Halanych, Kenneth M

2013-01-01

Molecular phylogenetics relies on accurate identification of orthologous sequences among the taxa of interest. Most orthology inference programs available for use in phylogenomics rely on small sets of pre-defined orthologs from model organisms or phenetic approaches such as all-versus-all sequence comparisons followed by Markov graph-based clustering. Such approaches have high sensitivity but may erroneously include paralogous sequences. We developed PhyloTreePruner, a software utility that uses a phylogenetic approach to refine orthology inferences made using phenetic methods. PhyloTreePruner checks single-gene trees for evidence of paralogy and generates a new alignment for each group containing only sequences inferred to be orthologs. Importantly, PhyloTreePruner takes into account support values on the tree and avoids unnecessarily deleting sequences in cases where a weakly supported tree topology incorrectly indicates paralogy. A test of PhyloTreePruner on a dataset generated from 11 completely sequenced arthropod genomes identified 2,027 orthologous groups sampled for all taxa. Phylogenetic analysis of the concatenated supermatrix yielded a generally well-supported topology that was consistent with the current understanding of arthropod phylogeny. PhyloTreePruner is freely available from http://sourceforge.net/projects/phylotreepruner/.

Evolutionary tree reconstruction

NASA Technical Reports Server (NTRS)

Cheeseman, Peter; Kanefsky, Bob

1990-01-01

It is described how Minimum Description Length (MDL) can be applied to the problem of DNA and protein evolutionary tree reconstruction. If there is a set of mutations that transform a common ancestor into a set of the known sequences, and this description is shorter than the information to encode the known sequences directly, then strong evidence for an evolutionary relationship has been found. A heuristic algorithm is described that searches for the simplest tree (smallest MDL) that finds close to optimal trees on the test data. Various ways of extending the MDL theory to more complex evolutionary relationships are discussed.

Learning classification trees

NASA Technical Reports Server (NTRS)

Buntine, Wray

1991-01-01

Algorithms for learning classification trees have had successes in artificial intelligence and statistics over many years. How a tree learning algorithm can be derived from Bayesian decision theory is outlined. This introduces Bayesian techniques for splitting, smoothing, and tree averaging. The splitting rule turns out to be similar to Quinlan's information gain splitting rule, while smoothing and averaging replace pruning. Comparative experiments with reimplementations of a minimum encoding approach, Quinlan's C4 and Breiman et al. Cart show the full Bayesian algorithm is consistently as good, or more accurate than these other approaches though at a computational price.

Arthropod but Not Bird Predation in Ethiopian Homegardens Is Higher in Tree-Poor than in Tree-Rich Landscapes

PubMed Central

Lemessa, Debissa; Hambäck, Peter A.; Hylander, Kristoffer

2015-01-01

Bird and arthropod predation is often associated with natural pest control in agricultural landscapes, but the rates of predation may vary with the amount of tree cover or other environmental factors. We examined bird and arthropod predation in three tree-rich and three tree-poor landscapes across southwestern Ethiopia. Within each landscape we selected three tree-rich and three tree-poor homegardens in which we recorded the number of tree species and tree stems within 100 × 100 m surrounding the central house. To estimate predation rates, we attached plasticine caterpillars on leaves of two coffee and two avocado shrubs in each homegarden, and recorded the number of attacked caterpillars for 7–9 consecutive weeks. The overall mean daily predation rate was 1.45% for birds and 1.60% for arthropods. The rates of arthropod predation varied among landscapes and were higher in tree-poor landscapes. There was no such difference for birds. Within landscapes, predation rates from birds and arthropods did not vary between tree-rich and tree-poor homegardens in either tree-rich or tree-poor landscapes. The most surprising result was the lack of response by birds to tree cover at either spatial scale. Our results suggest that in tree-poor landscapes there are still enough non-crop habitats to support predatory arthropods and birds to deliver strong top-down effect on crop pests. PMID:25961306

Gene-Tree Reconciliation with MUL-Trees to Resolve Polyploidy Events.

PubMed

Gregg, W C Thomas; Ather, S Hussain; Hahn, Matthew W

2017-11-01

Polyploidy can have a huge impact on the evolution of species, and it is a common occurrence, especially in plants. The two types of polyploids-autopolyploids and allopolyploids-differ in the level of divergence between the genes that are brought together in the new polyploid lineage. Because allopolyploids are formed via hybridization, the homoeologous copies of genes within them are at least as divergent as orthologs in the parental species that came together to form them. This means that common methods for estimating the parental lineages of allopolyploidy events are not accurate, and can lead to incorrect inferences about the number of gene duplications and losses. Here, we have adapted an algorithm for topology-based gene-tree reconciliation to work with multi-labeled trees (MUL-trees). By definition, MUL-trees have some tips with identical labels, which makes them a natural representation of the genomes of polyploids. Using this new reconciliation algorithm we can: accurately place allopolyploidy events on a phylogeny, identify the parental lineages that hybridized to form allopolyploids, distinguish between allo-, auto-, and (in most cases) no polyploidy, and correctly count the number of duplications and losses in a set of gene trees. We validate our method using gene trees simulated with and without polyploidy, and revisit the history of polyploidy in data from the clades including both baker's yeast and bread wheat. Our re-analysis of the yeast data confirms the allopolyploid origin and parental lineages previously identified for this group. The method presented here should find wide use in the growing number of genomes from species with a history of polyploidy. [Polyploidy; reconciliation; whole-genome duplication.]. © The Author(s) 2017. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Tree nut oils

USDA-ARS?s Scientific Manuscript database

The major tree nuts include almonds, Brazil nuts, cashew nuts, hazelnuts, macadamia nuts, pecans, pine nuts, pistachio nuts, and walnuts. Tree nut oils are appreciated in food applications because of their flavors and are generally more expensive than other gourmet oils. Research during the last de...

Fault Tree Analysis.

PubMed

McElroy, Lisa M; Khorzad, Rebeca; Rowe, Theresa A; Abecassis, Zachary A; Apley, Daniel W; Barnard, Cynthia; Holl, Jane L

The purpose of this study was to use fault tree analysis to evaluate the adequacy of quality reporting programs in identifying root causes of postoperative bloodstream infection (BSI). A systematic review of the literature was used to construct a fault tree to evaluate 3 postoperative BSI reporting programs: National Surgical Quality Improvement Program (NSQIP), Centers for Medicare and Medicaid Services (CMS), and The Joint Commission (JC). The literature review revealed 699 eligible publications, 90 of which were used to create the fault tree containing 105 faults. A total of 14 identified faults are currently mandated for reporting to NSQIP, 5 to CMS, and 3 to JC; 2 or more programs require 4 identified faults. The fault tree identifies numerous contributing faults to postoperative BSI and reveals substantial variation in the requirements and ability of national quality data reporting programs to capture these potential faults. Efforts to prevent postoperative BSI require more comprehensive data collection to identify the root causes and develop high-reliability improvement strategies.

Felling small trees with a drive-to-tree feller-buncher

Treesearch

Dana Mitchell

2008-01-01

Conventional forestry equipment is often used to harvest small-diameter trees. The typical ground-based logging operation is highly mechanized, with the most common using feller-bunchers, grapple skidders, and a chipper or grinder. But these machines may not be economical when used in pre-commercial or unmerchantable thinning operations in which the number of trees to...

Water, gravity and trees: Relationship of tree-ring widths and total water storage dynamics

NASA Astrophysics Data System (ADS)

Creutzfeldt, B.; Heinrich, I.; Merz, B.; Blume, T.; Güntner, A.

2012-04-01

Water stored in the subsurface as groundwater or soil moisture is the main fresh water source not only for drinking water and food production but also for the natural vegetation. In a changing environment water availability becomes a critical issue in many different regions. Long-term observations of the past are needed to improve the understanding of the hydrological system and the prediction of future developments. Tree ring data have repeatedly proved to be valuable sources for reconstructing long-term climate dynamics, e.g. temperature, precipitation and different hydrological variables. In water-limited environments, tree growth is primarily influenced by total water stored in the subsurface and hence, tree-ring records usually contain information about subsurface water storage. The challenge is to retrieve the information on total water storage from tree rings, because a training dataset of water stored in the sub-surface is required for calibration against the tree-ring series. However, measuring water stored in the subsurface is notoriously difficult. We here present high-precision temporal gravimeter measurements which allow for the depth-integrated quantification of total water storage dynamics at the field scale. In this study, we evaluate the relationship of total water storage change and tree ring growth also in the context of the complex interactions of other meteorological forcing factors. A tree-ring chronology was derived from a Norway spruce stand in the Bavarian Forest, Germany. Total water storage dynamics were measured directly by the superconducting gravimeter of the Geodetic Observatory Wettzell for a 9-years period. Time series were extended to 63-years period by a hydrological model using gravity data as the only calibration constrain. Finally, water storage changes were reconstructed based on the relationship between the hydrological model and the tree-ring chronology. Measurement results indicate that tree-ring growth is primarily

The potential of the tree water potential.

PubMed

Steppe, Kathy

2018-06-12

Non-invasive quantification of tree water potential is one of the grand challenges for assessing the fate of trees and forests in the coming decades. Tree water potential is a robust and direct indicator of tree water status and is preferably used to track how trees, forests and vegetation in general respond to changes in climate and drought. In this issue of Tree Physiology, Dietrich et al. (2018) predict the daily canopy water potential of mature temperate trees from tree water deficit derived from stem diameter variation measurements.

Complementarity effects on tree growth are contingent on tree size and climatic conditions across Europe

PubMed Central

Madrigal-González, Jaime; Ruiz-Benito, Paloma; Ratcliffe, Sophia; Calatayud, Joaquín; Kändler, Gerald; Lehtonen, Aleksi; Dahlgren, Jonas; Wirth, Christian; Zavala, Miguel A.

2016-01-01

Neglecting tree size and stand structure dynamics might bias the interpretation of the diversity-productivity relationship in forests. Here we show evidence that complementarity is contingent on tree size across large-scale climatic gradients in Europe. We compiled growth data of the 14 most dominant tree species in 32,628 permanent plots covering boreal, temperate and Mediterranean forest biomes. Niche complementarity is expected to result in significant growth increments of trees surrounded by a larger proportion of functionally dissimilar neighbours. Functional dissimilarity at the tree level was assessed using four functional types: i.e. broad-leaved deciduous, broad-leaved evergreen, needle-leaved deciduous and needle-leaved evergreen. Using Linear Mixed Models we show that, complementarity effects depend on tree size along an energy availability gradient across Europe. Specifically: (i) complementarity effects at low and intermediate positions of the gradient (coldest-temperate areas) were stronger for small than for large trees; (ii) in contrast, at the upper end of the gradient (warmer regions), complementarity is more widespread in larger than smaller trees, which in turn showed negative growth responses to increased functional dissimilarity. Our findings suggest that the outcome of species mixing on stand productivity might critically depend on individual size distribution structure along gradients of environmental variation. PMID:27571971

Size matters a lot: tree height and prior growth predict drought-induced tree death in Italian oak forests

NASA Astrophysics Data System (ADS)

Ripullone, F.; Colangelo, M.; Camarero, J. J.; Gazol, A.; Borghetti, M.; Gentilesca, T.

2016-12-01

Climate warming is expected to amplify drought stress resulting in the occurrence of more widespread dieback episodes and increasing mortality rates. This has pushed the search of reliable and robust early-warning indicators of impending drought-triggered tree death. Recent studies highlight how level of defoliation or age of trees strictly coact with drought in leading to forest decline. In addition, tree size and the tree-to-tree competition for water could also contribute to tree death in drought-prone sites. In this regard, it has been predicted that tall trees with isohydric stomatal regulation are most likely to die due to drought stress. Here, we test this hypothesis by analyzing size, age, competition and growth data in a Mediterranean oak species characterized by anisohydric behaviour, showing recent drought-induced mortality in two Italian forest sites. At both study sites, tree height was associated to the probability of dying. However, this association was opposite to published predictions because living trees were taller than dead trees at both sites. Neither age nor competition intensity played significant roles as drivers of tree mortality. Regarding growth data, trends in basal area increment were significantly smaller in dead than in living trees. Differences were most marked at mid (15 years prior to death) than at short (10 years) or long-term (35 year) scales. This is probably not related to intrinsic growth features of the study species but it can be explained because the most severe drought since 1950 occurred in 2000 at the study area, i.e. 15 years prior to the increase of tree mortality and when growth of living and dead trees started diverging. Lastly, we discuss potential factors which may explain why smaller individuals of anisohydric tree species such as Mediterranean oaks are prone to drought-induced tree death.

Influence of Tree-Scale Environmental Variability on Tree-Ring Reconstructions of Temperature at Sonora Pass, CA

NASA Astrophysics Data System (ADS)

Ma, L.; Stine, A.

2016-12-01

Tree-ring width from treeline environments tend to covary with local interannual temperature variabilities. However, other environmental factors such as moisture and light availability may further modulate tree growth in cold climates. We investigate the influence of various environmental factors on a tree-ring record from a research plot near Sonora Pass, CA (38.32N, 119.64W; elev. 3130 m). This treeline ecotone is dominated by whitebark pine (Pinus albicaulis) growing as individuals and as stands, and at the transition between tree form and krummholtz. We surveyed all trees in the 160m x 90m site, mapping and coring all trees with a diameter at breast height greater than 10 cm. We use survey data to test for an influence of inter-tree competition on growth. We also test for modulation of growth by variation in distance from surface water, aspect and slope, and soil types. Initial result shows a relationship between tree ring width and local May-July temperature (R = 0.33, p < 0.01), suggesting summer temperature as a large-scale control on growth. Incorporating the tree-level metadata, we test for the effect of spatial variability on mean growth rate and on reconstructed temperatures. Trees that have larger or closer neighboring trees experience greater competition, and we hypothesize that competition will be inversely related to average growth rate. Further, we test the sensitivity of ring-width interannual variability to other non-temperature environmental drivers such as moisture availability, light competition, and spatial relations in the microenvironment. We hypothesize that trees that have ready access to light and water will likely produce ring records more closely correlated with the temperature record, and thus will produce a temperature reconstruction with a higher signal-to-noise ratio; whereas trees that experience more microenvironment limitations or competition will produce ring records resembling temperature and additional environmental factors or

Current and Potential Tree Locations in Tree Line Ecotone of Changbai Mountains, Northeast China: The Controlling Effects of Topography

PubMed Central

Zong, Shengwei; Wu, Zhengfang; Xu, Jiawei; Li, Ming; Gao, Xiaofeng; He, Hongshi; Du, Haibo; Wang, Lei

2014-01-01

Tree line ecotone in the Changbai Mountains has undergone large changes in the past decades. Tree locations show variations on the four sides of the mountains, especially on the northern and western sides, which has not been fully explained. Previous studies attributed such variations to the variations in temperature. However, in this study, we hypothesized that topographic controls were responsible for causing the variations in the tree locations in tree line ecotone of the Changbai Mountains. To test the hypothesis, we used IKONOS images and WorldView-1 image to identify the tree locations and developed a logistic regression model using topographical variables to identify the dominant controls of the tree locations. The results showed that aspect, wetness, and slope were dominant controls for tree locations on western side of the mountains, whereas altitude, SPI, and aspect were the dominant factors on northern side. The upmost altitude a tree can currently reach was 2140 m asl on the northern side and 2060 m asl on western side. The model predicted results showed that habitats above the current tree line on the both sides were available for trees. Tree recruitments under the current tree line may take advantage of the available habitats at higher elevations based on the current tree location. Our research confirmed the controlling effects of topography on the tree locations in the tree line ecotone of Changbai Mountains and suggested that it was essential to assess the tree response to topography in the research of tree line ecotone. PMID:25170918

Current and potential tree locations in tree line ecotone of Changbai Mountains, Northeast China: the controlling effects of topography.

PubMed

Zong, Shengwei; Wu, Zhengfang; Xu, Jiawei; Li, Ming; Gao, Xiaofeng; He, Hongshi; Du, Haibo; Wang, Lei

2014-01-01

Tree line ecotone in the Changbai Mountains has undergone large changes in the past decades. Tree locations show variations on the four sides of the mountains, especially on the northern and western sides, which has not been fully explained. Previous studies attributed such variations to the variations in temperature. However, in this study, we hypothesized that topographic controls were responsible for causing the variations in the tree locations in tree line ecotone of the Changbai Mountains. To test the hypothesis, we used IKONOS images and WorldView-1 image to identify the tree locations and developed a logistic regression model using topographical variables to identify the dominant controls of the tree locations. The results showed that aspect, wetness, and slope were dominant controls for tree locations on western side of the mountains, whereas altitude, SPI, and aspect were the dominant factors on northern side. The upmost altitude a tree can currently reach was 2140 m asl on the northern side and 2060 m asl on western side. The model predicted results showed that habitats above the current tree line on the both sides were available for trees. Tree recruitments under the current tree line may take advantage of the available habitats at higher elevations based on the current tree location. Our research confirmed the controlling effects of topography on the tree locations in the tree line ecotone of Changbai Mountains and suggested that it was essential to assess the tree response to topography in the research of tree line ecotone.

New tree-measurement concepts: height accumulation, giant tree, taper and shape

Treesearch

L. R. Grosenbaugh

1954-01-01

An entirely new concept of tree measurment was announced by the author in 1948 (11). Since the original theory and applications have subsequently been b roadened considerably, it seems advisable to publish the entire development in readily usable form, along with other material helpful in tree measurement.

Trees Are Terrific!

ERIC Educational Resources Information Center

Braus, Judy, Ed.

1992-01-01

Ranger Rick's NatureScope is a creative education series dedicated to inspiring in children an understanding and appreciation of the natural world while developing the skills they will need to make responsible decisions about the environment. Contents are organized into the following sections: (1) "What Makes a Tree a Tree?," including…

Extended Full Computation-Tree Logic with Sequence Modal Operator: Representing Hierarchical Tree Structures

NASA Astrophysics Data System (ADS)

Kamide, Norihiro; Kaneiwa, Ken

An extended full computation-tree logic, CTLS*, is introduced as a Kripke semantics with a sequence modal operator. This logic can appropriately represent hierarchical tree structures where sequence modal operators in CTLS* are applied to tree structures. An embedding theorem of CTLS* into CTL* is proved. The validity, satisfiability and model-checking problems of CTLS* are shown to be decidable. An illustrative example of biological taxonomy is presented using CTLS* formulas.

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

PubMed

Franklin, Oskar; Palmroth, Sari; Näsholm, Torgny

2014-11-01

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

Tree Species Richness Promotes Invertebrate Herbivory on Congeneric Native and Exotic Tree Saplings in a Young Diversity Experiment.

PubMed

Wein, Annika; Bauhus, Jürgen; Bilodeau-Gauthier, Simon; Scherer-Lorenzen, Michael; Nock, Charles; Staab, Michael

2016-01-01

Tree diversity in forests is an important driver of ecological processes including herbivory. Empirical evidence suggests both negative and positive effects of tree diversity on herbivory, which can be, respectively, attributed to associational resistance or associational susceptibility. Tree diversity experiments allow testing for associational effects, but evidence regarding which pattern predominates is mixed. Furthermore, it is unknown if herbivory on tree species of native vs. exotic origin is influenced by changing tree diversity in a similar way, or if exotic tree species escape natural enemies, resulting in lower damage that is unrelated to tree diversity. To address these questions, we established a young tree diversity experiment in temperate southwestern Germany that uses high planting density (49 trees per plot; plot size 13 m2). The species pool consists of six congeneric species pairs of European and North American origin (12 species in total) planted in monocultures and mixtures (1, 2, 4, 6 species). We assessed leaf damage by leaf-chewing insects on more than 5,000 saplings of six broadleaved tree species. Plot-level tree species richness increased leaf damage, which more than doubled from monocultures to six-species mixtures, strongly supporting associational susceptibility. However, leaf damage among congeneric native and exotic species pairs was similar. There were marked differences in patterns of leaf damage across tree genera, and only the genera likely having a predominately generalist herbivore community showed associational susceptibility, irrespective of the geographical origin of a tree species. In conclusion, an increase in tree species richness in young temperate forests may result in associational susceptibility to feeding by generalist herbivores.

Anatomical modeling of the bronchial tree

NASA Astrophysics Data System (ADS)

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

2010-02-01

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

Tree colonization by the Asian longhorn beetle, Anoplophora glabripennis (Coleoptera: Cerambycidae): effect of habitat and tree suitability.

PubMed

Faccoli, Massimo; Favaro, Riccardo; Concheri, Giuseppe; Squartini, Andrea; Battisti, Andrea

2016-04-01

Tree colonization and feeding activity of the invasive wood-borer Asian longhorn beetle (Anoplophora glabripennis), an Asian pest introduced into North America and Europe, was studied in a newly invaded area in Italy. The hypothesis being tested was that the reproductive success of the insect depend on habitat type and tree suitability. Adult beetles were caged on branches of host and nonhost species, in both urban and forest habitats. Two months later, number and size of feeding patches on plant tissues, eggs laid, and surviving larvae were assessed. Bark concentration of C and N was also measured from the same trees. Results indicated that the mean area of plant tissues consumed by adult feeding was significantly larger on trees growing in forest than in urban habitat, although within the same habitat there were no differences between susceptible and nonsusceptible trees. ALB tree colonization, in terms of number of eggs laid and young larvae survival, was not affected by habitat while it was higher on susceptible trees. Although trees growing in forests had a lower nitrogen concentration, they allowed colonization rates similar to those of trees growing in the urban habitat. Hence, the amount of carbon and nitrogen did not fully explain tree suitability or habitat selection. We suggest compensatory feeding as a potential mechanism that might explain this peculiar situation, as supported by a more intensive feeding activity recorded on trees in the forest. Suitability of different trees may be due to other factors, such as secondary chemical compounds. © 2014 Institute of Zoology, Chinese Academy of Sciences.

Growing a Forest for the Trees.

ERIC Educational Resources Information Center

Growing Ideas, 2001

2001-01-01

Describes a tree studies program in a fourth-grade classroom. Students collected local tree seeds and seeds from supermarket fruits, researched growing conditions, and grew seeds under various conditions. Students kept journals on local trees, observing seed dispersal mechanisms and examining rings on trunk slices. Inquiry-based tree studies…

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

PubMed

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

2007-11-01

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

Remeasuring tree heights on permanent plots using rectangular coordinates and one angle per tree

Treesearch

Robert L. Neal

1973-01-01

Heights of permanent sample trees with tops visible from any point can be measured from that point with any clinometer, measuring one vertical angle per tree. Two horizontal angles and one additional vertical angle per observation point are necessary to orient the point to the plot. Permanently recorded coordinates and elevations of tree locations are used with the...

Moon tree ceremony

NASA Image and Video Library

2011-02-03

Apollo 13 astronaut Fred Haise stands with Rosemary Roosa, daughter of late Apollo 14 astronaut Stuart Roosa, beside a 'moon tree' planted at the INFINITY science center on Feb. 3, 2011. The moon tree is a descendent of seeds carried into space by Stuart Roosa on the Apollo 14 mission in 1971.

Individual tree control

Treesearch

Harvey A. Holt

1989-01-01

Controlling individual unwanted trees in forest stands is a readily accepted method for improving the value of future harvests. The practice is especially important in mixed hardwood forests where species differ considerably in value and within species individual trees differ in quality. Individual stem control is a mechanical or chemical weeding operation that...

Tree growth visualization

Treesearch

L. Linsen; B.J. Karis; E.G. McPherson; B. Hamann

2005-01-01

In computer graphics, models describing the fractal branching structure of trees typically exploit the modularity of tree structures. The models are based on local production rules, which are applied iteratively and simultaneously to create a complex branching system. The objective is to generate three-dimensional scenes of often many realistic- looking and non-...

iGLASS: An Improvement to the GLASS Method for Estimating Species Trees from Gene Trees

PubMed Central

Rosenberg, Noah A.

2012-01-01

Abstract Several methods have been designed to infer species trees from gene trees while taking into account gene tree/species tree discordance. Although some of these methods provide consistent species tree topology estimates under a standard model, most either do not estimate branch lengths or are computationally slow. An exception, the GLASS method of Mossel and Roch, is consistent for the species tree topology, estimates branch lengths, and is computationally fast. However, GLASS systematically overestimates divergence times, leading to biased estimates of species tree branch lengths. By assuming a multispecies coalescent model in which multiple lineages are sampled from each of two taxa at L independent loci, we derive the distribution of the waiting time until the first interspecific coalescence occurs between the two taxa, considering all loci and measuring from the divergence time. We then use the mean of this distribution to derive a correction to the GLASS estimator of pairwise divergence times. We show that our improved estimator, which we call iGLASS, consistently estimates the divergence time between a pair of taxa as the number of loci approaches infinity, and that it is an unbiased estimator of divergence times when one lineage is sampled per taxon. We also show that many commonly used clustering methods can be combined with the iGLASS estimator of pairwise divergence times to produce a consistent estimator of the species tree topology. Through simulations, we show that iGLASS can greatly reduce the bias and mean squared error in obtaining estimates of divergence times in a species tree. PMID:22216756

Using tree diversity to compare phylogenetic heuristics.

PubMed

Sul, Seung-Jin; Matthews, Suzanne; Williams, Tiffani L

2009-04-29

Evolutionary trees are family trees that represent the relationships between a group of organisms. Phylogenetic heuristics are used to search stochastically for the best-scoring trees in tree space. Given that better tree scores are believed to be better approximations of the true phylogeny, traditional evaluation techniques have used tree scores to determine the heuristics that find the best scores in the fastest time. We develop new techniques to evaluate phylogenetic heuristics based on both tree scores and topologies to compare Pauprat and Rec-I-DCM3, two popular Maximum Parsimony search algorithms. Our results show that although Pauprat and Rec-I-DCM3 find the trees with the same best scores, topologically these trees are quite different. Furthermore, the Rec-I-DCM3 trees cluster distinctly from the Pauprat trees. In addition to our heatmap visualizations of using parsimony scores and the Robinson-Foulds distance to compare best-scoring trees found by the two heuristics, we also develop entropy-based methods to show the diversity of the trees found. Overall, Pauprat identifies more diverse trees than Rec-I-DCM3. Overall, our work shows that there is value to comparing heuristics beyond the parsimony scores that they find. Pauprat is a slower heuristic than Rec-I-DCM3. However, our work shows that there is tremendous value in using Pauprat to reconstruct trees-especially since it finds identical scoring but topologically distinct trees. Hence, instead of discounting Pauprat, effort should go in improving its implementation. Ultimately, improved performance measures lead to better phylogenetic heuristics and will result in better approximations of the true evolutionary history of the organisms of interest.

Measuring (bio)physical tree properties using accelerometers

NASA Astrophysics Data System (ADS)

van Emmerik, Tim; Steele-Dunne, Susan; Hut, Rolf; Gentine, Pierre; Selker, John; van de Giesen, Nick

2017-04-01

Trees play a crucial role in the water, carbon and nitrogen cycle on local, regional and global scales. Understanding the exchange of heat, water, and CO2 between trees and the atmosphere is important to assess the impact of drought, deforestation and climate change. Unfortunately, ground measurements of tree dynamics are often expensive, or difficult due to challenging environments. We demonstrate the potential of measuring (bio)physical properties of trees using robust and affordable acceleration sensors. Tree sway is dependent on e.g. mass and wind energy absorption of the tree. By measuring tree acceleration we can relate the tree motion to external loads (e.g. precipitation), and tree (bio)physical properties (e.g. mass). Using five months of acceleration data of 19 trees in the Brazilian Amazon, we show that the frequency spectrum of tree sway is related to mass, precipitation, and canopy drag. This presentation aims to show the concept of using accelerometers to measure tree dynamics, and we acknowledge that the presented example applications is not an exhaustive list. Further analyses are the scope of current research, and we hope to inspire others to explore additional applications.

Structural Equation Model Trees

PubMed Central

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

2015-01-01

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 structures that separate a data set recursively into subsets with significantly different parameter estimates in a SEM. SEM Trees provide means for finding covariates and covariate interactions that predict differences in structural parameters in observed as well as in latent space and facilitate theory-guided exploration of empirical data. We describe the methodology, discuss theoretical and practical implications, and demonstrate applications to a factor model and a linear growth curve model. PMID:22984789

DLRS: gene tree evolution in light of a species tree.

PubMed

Sjöstrand, Joel; Sennblad, Bengt; Arvestad, Lars; Lagergren, Jens

2012-11-15

PrIME-DLRS (or colloquially: 'Delirious') is a phylogenetic software tool to simultaneously infer and reconcile a gene tree given a species tree. It accounts for duplication and loss events, a relaxed molecular clock and is intended for the study of homologous gene families, for example in a comparative genomics setting involving multiple species. PrIME-DLRS uses a Bayesian MCMC framework, where the input is a known species tree with divergence times and a multiple sequence alignment, and the output is a posterior distribution over gene trees and model parameters. PrIME-DLRS is available for Java SE 6+ under the New BSD License, and JAR files and source code can be downloaded from http://code.google.com/p/jprime/. There is also a slightly older C++ version available as a binary package for Ubuntu, with download instructions at http://prime.sbc.su.se. The C++ source code is available upon request. joel.sjostrand@scilifelab.se or jens.lagergren@scilifelab.se. PrIME-DLRS is based on a sound probabilistic model (Åkerborg et al., 2009) and has been thoroughly validated on synthetic and biological datasets (Supplementary Material online).

Effects of tree-to-tree variations on sap flux-based transpiration estimates in a forested watershed

NASA Astrophysics Data System (ADS)

Kume, Tomonori; Tsuruta, Kenji; Komatsu, Hikaru; Kumagai, Tomo'omi; Higashi, Naoko; Shinohara, Yoshinori; Otsuki, Kyoichi

2010-05-01

To estimate forest stand-scale water use, we assessed how sample sizes affect confidence of stand-scale transpiration (E) estimates calculated from sap flux (Fd) and sapwood area (AS_tree) measurements of individual trees. In a Japanese cypress plantation, we measured Fd and AS_tree in all trees (n = 58) within a 20 × 20 m study plot, which was divided into four 10 × 10 subplots. We calculated E from stand AS_tree (AS_stand) and mean stand Fd (JS) values. Using Monte Carlo analyses, we examined potential errors associated with sample sizes in E, AS_stand, and JS by using the original AS_tree and Fd data sets. Consequently, we defined optimal sample sizes of 10 and 15 for AS_stand and JS estimates, respectively, in the 20 × 20 m plot. Sample sizes greater than the optimal sample sizes did not decrease potential errors. The optimal sample sizes for JS changed according to plot size (e.g., 10 × 10 m and 10 × 20 m), while the optimal sample sizes for AS_stand did not. As well, the optimal sample sizes for JS did not change in different vapor pressure deficit conditions. In terms of E estimates, these results suggest that the tree-to-tree variations in Fd vary among different plots, and that plot size to capture tree-to-tree variations in Fd is an important factor. This study also discusses planning balanced sampling designs to extrapolate stand-scale estimates to catchment-scale estimates.

Individual tree crown delineation using localized contour tree method and airborne LiDAR data in coniferous forests

NASA Astrophysics Data System (ADS)

Wu, Bin; Yu, Bailang; Wu, Qiusheng; Huang, Yan; Chen, Zuoqi; Wu, Jianping

2016-10-01

Individual tree crown delineation is of great importance for forest inventory and management. The increasing availability of high-resolution airborne light detection and ranging (LiDAR) data makes it possible to delineate the crown structure of individual trees and deduce their geometric properties with high accuracy. In this study, we developed an automated segmentation method that is able to fully utilize high-resolution LiDAR data for detecting, extracting, and characterizing individual tree crowns with a multitude of geometric and topological properties. The proposed approach captures topological structure of forest and quantifies topological relationships of tree crowns by using a graph theory-based localized contour tree method, and finally segments individual tree crowns by analogy of recognizing hills from a topographic map. This approach consists of five key technical components: (1) derivation of canopy height model from airborne LiDAR data; (2) generation of contours based on the canopy height model; (3) extraction of hierarchical structures of tree crowns using the localized contour tree method; (4) delineation of individual tree crowns by segmenting hierarchical crown structure; and (5) calculation of geometric and topological properties of individual trees. We applied our new method to the Medicine Bow National Forest in the southwest of Laramie, Wyoming and the HJ Andrews Experimental Forest in the central portion of the Cascade Range of Oregon, U.S. The results reveal that the overall accuracy of individual tree crown delineation for the two study areas achieved 94.21% and 75.07%, respectively. Our method holds great potential for segmenting individual tree crowns under various forest conditions. Furthermore, the geometric and topological attributes derived from our method provide comprehensive and essential information for forest management.

Tests with VHR images for the identification of olive trees and other fruit trees in the European Union

NASA Astrophysics Data System (ADS)

Masson, Josiane; Soille, Pierre; Mueller, Rick

2004-10-01

In the context of the Common Agricultural Policy (CAP) there is a strong interest of the European Commission for counting and individually locating fruit trees. An automatic counting algorithm developed by the JRC (OLICOUNT) was used in the past for olive trees only, on 1m black and white orthophotos but with limits in case of young trees or irregular groves. This study investigates the improvement of fruit tree identification using VHR images on a large set of data in three test sites, one in Creta (Greece; one in the south-east of France with a majority of olive trees and associated fruit trees, and the last one in Florida on citrus trees. OLICOUNT was compared with two other automatic tree counting, applications, one using the CRISP software on citrus trees and the other completely automatic based on regional minima (morphological image analysis). Additional investigation was undertaken to refine the methods. This paper describes the automatic methods and presents the results derived from the tests.

Voxel-Based 3-D Tree Modeling from Lidar Images for Extracting Tree Structual Information

NASA Astrophysics Data System (ADS)

Hosoi, F.

2014-12-01

Recently, lidar (light detection and ranging) has been used to extracting tree structural information. Portable scanning lidar systems can capture the complex shape of individual trees as a 3-D point-cloud image. 3-D tree models reproduced from the lidar-derived 3-D image can be used to estimate tree structural parameters. We have proposed the voxel-based 3-D modeling for extracting tree structural parameters. One of the tree parameters derived from the voxel modeling is leaf area density (LAD). We refer to the method as the voxel-based canopy profiling (VCP) method. In this method, several measurement points surrounding the canopy and optimally inclined laser beams are adopted for full laser beam illumination of whole canopy up to the internal. From obtained lidar image, the 3-D information is reproduced as the voxel attributes in the 3-D voxel array. Based on the voxel attributes, contact frequency of laser beams on leaves is computed and LAD in each horizontal layer is obtained. This method offered accurate LAD estimation for individual trees and woody canopy trees. For more accurate LAD estimation, the voxel model was constructed by combining airborne and portable ground-based lidar data. The profiles obtained by the two types of lidar complemented each other, thus eliminating blind regions and yielding more accurate LAD profiles than could be obtained by using each type of lidar alone. Based on the estimation results, we proposed an index named laser beam coverage index, Ω, which relates to the lidar's laser beam settings and a laser beam attenuation factor. It was shown that this index can be used for adjusting measurement set-up of lidar systems and also used for explaining the LAD estimation error using different types of lidar systems. Moreover, we proposed a method to estimate woody material volume as another application of the voxel tree modeling. In this method, voxel solid model of a target tree was produced from the lidar image, which is composed of

New Life From Dead Trees

ERIC Educational Resources Information Center

DeGraaf, Richard M.

1978-01-01

There are numerous bird species that will nest only in dead or dying trees. Current forestry practices include clearing forests of these snags, or dead trees. This practice is driving many species out of the forests. An illustrated example of bird succession in and on a tree is given. (MA)

The Hopi Fruit Tree Book.

ERIC Educational Resources Information Center

Nyhuis, Jane

Referring as often as possible to traditional Hopi practices and to materials readily available on the reservation, the illustrated booklet provides information on the care and maintenance of young fruit trees. An introduction to fruit trees explains the special characteristics of new trees, e.g., grafting, planting pits, and watering. The…

Christmas Tree Pest Manual, Third Edition

Treesearch

Steven Katovich; Deborah McCullough; Michael Ostry; Jill O’Donnell; Isabel Munck; Cliff Sadof

2014-01-01

Continuing mortality of red pine from an unknown cause has been observed in 30 to 40 year old plantations in southern and west central Wisconsin. A single tree or small group of trees die, followed by mortality of adjacent trees. These circular pockets of dead trees expand up to 0.3 acre per year.

Heterogeneous Compression of Large Collections of Evolutionary Trees.

PubMed

Matthews, Suzanne J

2015-01-01

Compressing heterogeneous collections of trees is an open problem in computational phylogenetics. In a heterogeneous tree collection, each tree can contain a unique set of taxa. An ideal compression method would allow for the efficient archival of large tree collections and enable scientists to identify common evolutionary relationships over disparate analyses. In this paper, we extend TreeZip to compress heterogeneous collections of trees. TreeZip is the most efficient algorithm for compressing homogeneous tree collections. To the best of our knowledge, no other domain-based compression algorithm exists for large heterogeneous tree collections or enable their rapid analysis. Our experimental results indicate that TreeZip averages 89.03 percent (72.69 percent) space savings on unweighted (weighted) collections of trees when the level of heterogeneity in a collection is moderate. The organization of the TRZ file allows for efficient computations over heterogeneous data. For example, consensus trees can be computed in mere seconds. Lastly, combining the TreeZip compressed (TRZ) file with general-purpose compression yields average space savings of 97.34 percent (81.43 percent) on unweighted (weighted) collections of trees. Our results lead us to believe that TreeZip will prove invaluable in the efficient archival of tree collections, and enables scientists to develop novel methods for relating heterogeneous collections of trees.

Grading hardwood trees

Treesearch

Robert L. Brisbin

1989-01-01

Tree grading provides a way to evaluate the quality characteristics and value of standing hardwood trees. This is important because the differences in price between high-quality and low-quality end products can be very large. Since hardwood timber varies greatly in quality and value among species, within species, and even within specific geographic areas, timber...

Factors that influence Christmas tree sales

Treesearch

Thomas H. Pendleton; Lawrence D. Garrett

1970-01-01

An analysis of the metropolitan Christmas tree market in Winston-Salem, N. C., shows that to sell more trees, Christmas tree retailers should locate their lots on heavily traveled streets in business areas, have adequate parking facilities, advertise, and have attractive displays of trees. Retailers who follow these practices can expect to receive higher prices for...

Pocket guide to Christmas tree diseases

Treesearch

Thomas H. Nicholls; Robert D. Wray

1989-01-01

Each year more than 30 million American families bring a live Christmas tree into their homes to become the warm and glowing center of their Christmas celebration. Years ago, most Christmas trees were cut wild. But, as demand increased and the supply of suitable wild trees decreased, growing Christmas trees in plantations became more and more common.

Imaging tree roots with borehole radar

Treesearch

John R. Butnor; Kurt H. Johnsen; Per Wikstrom; Tomas Lundmark; Sune Linder

2006-01-01

Ground-penetrating radar has been used to de-tect and map tree roots using surface-based antennas in reflection mode. On amenable soils these methods can accurately detect lateral tree roots. In some tree species (e.g. Pinus taeda, Pinus palustris), vertically orientated tap roots directly beneath the tree, comprise most of the root mass. It is...

The View from the Trees: Nocturnal Bull Ants, Myrmecia midas, Use the Surrounding Panorama While Descending from Trees

PubMed Central

Freas, Cody A.; Wystrach, Antione; Narendra, Ajay; Cheng, Ken

2018-01-01

Solitary foraging ants commonly use visual cues from their environment for navigation. Foragers are known to store visual scenes from the surrounding panorama for later guidance to known resources and to return successfully back to the nest. Several ant species travel not only on the ground, but also climb trees to locate resources. The navigational information that guides animals back home during their descent, while their body is perpendicular to the ground, is largely unknown. Here, we investigate in a nocturnal ant, Myrmecia midas, whether foragers travelling down a tree use visual information to return home. These ants establish nests at the base of a tree on which they forage and in addition, they also forage on nearby trees. We collected foragers and placed them on the trunk of the nest tree or a foraging tree in multiple compass directions. Regardless of the displacement location, upon release ants immediately moved to the side of the trunk facing the nest during their descent. When ants were released on non-foraging trees near the nest, displaced foragers again travelled around the tree to the side facing the nest. All the displaced foragers reached the correct side of the tree well before reaching the ground. However, when the terrestrial cues around the tree were blocked, foragers were unable to orient correctly, suggesting that the surrounding panorama is critical to successful orientation on the tree. Through analysis of panoramic pictures, we show that views acquired at the base of the foraging tree nest can provide reliable nest-ward orientation up to 1.75 m above the ground. We discuss, how animals descending from trees compare their current scene to a memorised scene and report on the similarities in visually guided behaviour while navigating on the ground and descending from trees. PMID:29422880

The View from the Trees: Nocturnal Bull Ants, Myrmecia midas, Use the Surrounding Panorama While Descending from Trees.

PubMed

Freas, Cody A; Wystrach, Antione; Narendra, Ajay; Cheng, Ken

2018-01-01

Solitary foraging ants commonly use visual cues from their environment for navigation. Foragers are known to store visual scenes from the surrounding panorama for later guidance to known resources and to return successfully back to the nest. Several ant species travel not only on the ground, but also climb trees to locate resources. The navigational information that guides animals back home during their descent, while their body is perpendicular to the ground, is largely unknown. Here, we investigate in a nocturnal ant, Myrmecia midas , whether foragers travelling down a tree use visual information to return home. These ants establish nests at the base of a tree on which they forage and in addition, they also forage on nearby trees. We collected foragers and placed them on the trunk of the nest tree or a foraging tree in multiple compass directions. Regardless of the displacement location, upon release ants immediately moved to the side of the trunk facing the nest during their descent. When ants were released on non-foraging trees near the nest, displaced foragers again travelled around the tree to the side facing the nest. All the displaced foragers reached the correct side of the tree well before reaching the ground. However, when the terrestrial cues around the tree were blocked, foragers were unable to orient correctly, suggesting that the surrounding panorama is critical to successful orientation on the tree. Through analysis of panoramic pictures, we show that views acquired at the base of the foraging tree nest can provide reliable nest-ward orientation up to 1.75 m above the ground. We discuss, how animals descending from trees compare their current scene to a memorised scene and report on the similarities in visually guided behaviour while navigating on the ground and descending from trees.

Encoding phylogenetic trees in terms of weighted quartets.

PubMed

Grünewald, Stefan; Huber, Katharina T; Moulton, Vincent; Semple, Charles

2008-04-01

One of the main problems in phylogenetics is to develop systematic methods for constructing evolutionary or phylogenetic trees. For a set of species X, an edge-weighted phylogenetic X-tree or phylogenetic tree is a (graph theoretical) tree with leaf set X and no degree 2 vertices, together with a map assigning a non-negative length to each edge of the tree. Within phylogenetics, several methods have been proposed for constructing such trees that work by trying to piece together quartet trees on X, i.e. phylogenetic trees each having four leaves in X. Hence, it is of interest to characterise when a collection of quartet trees corresponds to a (unique) phylogenetic tree. Recently, Dress and Erdös provided such a characterisation for binary phylogenetic trees, that is, phylogenetic trees all of whose internal vertices have degree 3. Here we provide a new characterisation for arbitrary phylogenetic trees.

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

USGS Publications Warehouse

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

2007-01-01

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

Microwave sensing of tree trunks

NASA Astrophysics Data System (ADS)

Jezova, Jana; Mertens, Laurence; Lambot, Sebastien

2015-04-01

The main subject of this research is the observation of the inner part of living tree trunks using ground-penetrating radar (GPR). Trees are everyday part of human life and therefore it is important to pay attention to the tree conditions. The most obvious consequence of the poor tree condition is dead or injury caused by falling tree. The trunk internal structure is divided into three main parts: heartwood, sapwood and bark, which make this medium highly anisotropic and heterogeneous. Furthermore, the properties of the wood are not only specie-dependent but also depend on genetic and on environmental conditions. In urban areas the main problem for the stability of the trees relies in the apparition of decays provoked by fungi, insect or birds. This results in cavities or decreasing of the support capacity of the tree. GPR has proved itself to be a very powerful electromagnetic tool for non-destructive detection of buried objects. Since the beginning of the 20th century it has been used in several different areas (archaeology, landmine detection, civil engineering, ...). GPR uses the principle of the scattering of the electromagnetic waves that are radiated from a transmitting antenna. Then the waves propagate through the medium and are reflected from the object and then they are received by a receiving antenna. The velocity of the scattered signal is determined primarily by the permittivity of the material. The optimal functionality of the GPR was investigated using the numerical simulation tool gprMax2D. This tool is based on a Finite-Difference Time-Domain (FDTD) numerical model. Subsequently, the GPR functionality was tested using the laboratory model of a decayed tree trunk. Afterwards, the results and lessons learnt in the simplified tests will be used in the processing of the real data and will help to achieve deeper understanding of them. The laboratory model of the tree trunk was made by plastic or carton pipes and filled by sand. Space inside the model

TREE2FASTA: a flexible Perl script for batch extraction of FASTA sequences from exploratory phylogenetic trees.

PubMed

Sauvage, Thomas; Plouviez, Sophie; Schmidt, William E; Fredericq, Suzanne

2018-03-05

The body of DNA sequence data lacking taxonomically informative sequence headers is rapidly growing in user and public databases (e.g. sequences lacking identification and contaminants). In the context of systematics studies, sorting such sequence data for taxonomic curation and/or molecular diversity characterization (e.g. crypticism) often requires the building of exploratory phylogenetic trees with reference taxa. The subsequent step of segregating DNA sequences of interest based on observed topological relationships can represent a challenging task, especially for large datasets. We have written TREE2FASTA, a Perl script that enables and expedites the sorting of FASTA-formatted sequence data from exploratory phylogenetic trees. TREE2FASTA takes advantage of the interactive, rapid point-and-click color selection and/or annotations of tree leaves in the popular Java tree-viewer FigTree to segregate groups of FASTA sequences of interest to separate files. TREE2FASTA allows for both simple and nested segregation designs to facilitate the simultaneous preparation of multiple data sets that may overlap in sequence content.

Tree and shrub expansion over the past 34 years at the tree-line near Abisko, Sweden.

PubMed

Rundqvist, Sara; Hedenås, Henrik; Sandström, Anneli; Emanuelsson, Urban; Eriksson, Håkan; Jonasson, Christer; Callaghan, Terry V

2011-09-01

Shrubs and trees are expected to expand in the sub-Arctic due to global warming. Our study was conducted in Abisko, sub-arctic Sweden. We recorded the change in coverage of shrub and tree species over a 32- to 34-year period, in three 50 x 50 m plots; in the alpine-tree-line ecotone. The cover of shrubs and trees (<3.5 cm diameter at breast height) were estimated during 2009-2010 and compared with historical documentation from 1976 to 1977. Similarly, all tree stems (> or =3.5 cm) were noted and positions determined. There has been a substantial increase of cover of shrubs and trees, particularly dwarf birch (Betula nana), and mountain birch (Betula pubescens ssp. czerepanovii), and an establishment of aspen (Populus tremula). The other species willows (Salix spp.), juniper (Juniperus communis), and rowan (Sorbus aucuparia) revealed inconsistent changes among the plots. Although this study was unable to identify the causes for the change in shrubs and small trees, they are consistent with anticipated changes due to climate change and reduced herbivory.

Tree-Based Unrooted Phylogenetic Networks.

PubMed

Francis, A; Huber, K T; Moulton, V

2018-02-01

Phylogenetic networks are a generalization of phylogenetic trees that are used to represent non-tree-like evolutionary histories that arise in organisms such as plants and bacteria, or uncertainty in evolutionary histories. An unrooted phylogenetic network on a non-empty, finite set X of taxa, or network, is a connected, simple graph in which every vertex has degree 1 or 3 and whose leaf set is X. It is called a phylogenetic tree if the underlying graph is a tree. In this paper we consider properties of tree-based networks, that is, networks that can be constructed by adding edges into a phylogenetic tree. We show that although they have some properties in common with their rooted analogues which have recently drawn much attention in the literature, they have some striking differences in terms of both their structural and computational properties. We expect that our results could eventually have applications to, for example, detecting horizontal gene transfer or hybridization which are important factors in the evolution of many organisms.

Tree Height and DBH Growth Model Establishment of Main Tree Species in Wuling Mountain Small Watershed

NASA Astrophysics Data System (ADS)

Luo, Jia; Zhang, Min; Zhou, Xiaoling; Chen, Jianhua; Tian, Yuxin

2018-01-01

Taken 4 main tree species in the Wuling mountain small watershed as research objects, 57 typical sample plots were set up according to the stand type, site conditions and community structure. 311 goal diameter-class sample trees were selected according to diameter-class groups of different tree-height grades, and the optimal fitting models of tree height and DBH growth of main tree species were obtained by stem analysis using Richard, Logistic, Korf, Mitscherlich, Schumacher, Weibull theoretical growth equations, and the correlation coefficient of all optimal fitting models reached above 0.9. Through the evaluation and test, the optimal fitting models possessed rather good fitting precision and forecast dependability.

Mapping tree density at a global scale

NASA Astrophysics Data System (ADS)

Crowther, T. W.; Glick, H. B.; Covey, K. R.; Bettigole, C.; Maynard, D. S.; Thomas, S. M.; Smith, J. R.; Hintler, G.; Duguid, M. C.; Amatulli, G.; Tuanmu, M.-N.; Jetz, W.; Salas, C.; Stam, C.; Piotto, D.; Tavani, R.; Green, S.; Bruce, G.; Williams, S. J.; Wiser, S. K.; Huber, M. O.; Hengeveld, G. M.; Nabuurs, G.-J.; Tikhonova, E.; Borchardt, P.; Li, C.-F.; Powrie, L. W.; Fischer, M.; Hemp, A.; Homeier, J.; Cho, P.; Vibrans, A. C.; Umunay, P. M.; Piao, S. L.; Rowe, C. W.; Ashton, M. S.; Crane, P. R.; Bradford, M. A.

2015-09-01

The global extent and distribution of forest trees is central to our understanding of the terrestrial biosphere. We provide the first spatially continuous map of forest tree density at a global scale. This map reveals that the global number of trees is approximately 3.04 trillion, an order of magnitude higher than the previous estimate. Of these trees, approximately 1.39 trillion exist in tropical and subtropical forests, with 0.74 trillion in boreal regions and 0.61 trillion in temperate regions. Biome-level trends in tree density demonstrate the importance of climate and topography in controlling local tree densities at finer scales, as well as the overwhelming effect of humans across most of the world. Based on our projected tree densities, we estimate that over 15 billion trees are cut down each year, and the global number of trees has fallen by approximately 46% since the start of human civilization.

Mapping tree density at a global scale.

PubMed

Crowther, T W; Glick, H B; Covey, K R; Bettigole, C; Maynard, D S; Thomas, S M; Smith, J R; Hintler, G; Duguid, M C; Amatulli, G; Tuanmu, M-N; Jetz, W; Salas, C; Stam, C; Piotto, D; Tavani, R; Green, S; Bruce, G; Williams, S J; Wiser, S K; Huber, M O; Hengeveld, G M; Nabuurs, G-J; Tikhonova, E; Borchardt, P; Li, C-F; Powrie, L W; Fischer, M; Hemp, A; Homeier, J; Cho, P; Vibrans, A C; Umunay, P M; Piao, S L; Rowe, C W; Ashton, M S; Crane, P R; Bradford, M A

2015-09-10

The global extent and distribution of forest trees is central to our understanding of the terrestrial biosphere. We provide the first spatially continuous map of forest tree density at a global scale. This map reveals that the global number of trees is approximately 3.04 trillion, an order of magnitude higher than the previous estimate. Of these trees, approximately 1.39 trillion exist in tropical and subtropical forests, with 0.74 trillion in boreal regions and 0.61 trillion in temperate regions. Biome-level trends in tree density demonstrate the importance of climate and topography in controlling local tree densities at finer scales, as well as the overwhelming effect of humans across most of the world. Based on our projected tree densities, we estimate that over 15 billion trees are cut down each year, and the global number of trees has fallen by approximately 46% since the start of human civilization.

Improved prediction of hardwood tree biomass derived from wood density estimates and form factors for whole trees

Treesearch

David W. MacFarlane; Neil R. Ver Planck

2012-01-01

Data from hardwood trees in Michigan were analyzed to investigate how differences in whole-tree form and wood density between trees of different stem diameter relate to residual error in standard-type biomass equations. The results suggested that whole-tree wood density, measured at breast height, explained a significant proportion of residual error in standard-type...

Atmospheric carbon reduction by urban trees

Treesearch

David J. Nowak

1993-01-01

Trees, because they sequester atmospheric carbon through their growth process and conserve energy in urban areas, have been suggested as one means to combat increasing levels of atmospheric carbon. Analysis of the urban forest in Oakland, California (21% tree cover), reveals a tree carbon storage level of 11.0 metric tons/hectare. Trees in the area of the 1991 fire in...

Hardwood Regeneration After Seed Tree Cutting

Treesearch

Robert L. Johnson; R. M. Krinard

1976-01-01

Seed trees left at two sites did not appear to influence the establishment or development of reproduction . Seed trees were mainly sweetgum and red oaks. Most reproduction was from sprouting of the stumps and roots of cut trees or from advanced seedlings present in the understory at the time of cutting. Eighteen years after cutting, dominant trees of the reproduction...

Guide to the measurement of tree characteristics important to the quality classification for young hardwood trees

Treesearch

David L. Sonderman

1979-01-01

A procedure is shown for measuring external tree characteristics that are important in determining the current and future quality of young hardwood trees. This guide supplements a precious study which describes the quality classification system for young hardwood trees

Prioritizing trees for global conservation action: BGCI’s tree conservation agenda

Treesearch

K. Shaw; M. Rivers; E. Beech

2017-01-01

Botanic Gardens Conservation International (BGCI) is a global voice for plant conservation via its worldwide network of botanic gardens and partners. Tree conservation has been a strong focus of BGCI’s program for many years. In collaboration with Fauna & Flora International, BGCI runs the Global Trees Campaign (GTC, www.globaltrees.org), the only international...

Autumn frost hardiness in Norway spruce plus tree progeny and trees of the local and transferred provenances in central Sweden.

PubMed

Hannerz, Mats; Westin, Johan

2005-09-01

Reforestation with provenances from locations remote from the planting site (transferred provenances) or the progeny of trees of local provenances selected for superior form and vigor (plus trees) offer alternative means to increase yield over that obtained by the use of seed from unselected trees of the local provenance. Under Swedish conditions, Norway spruce (Picea abies (L.) Karst.) of certain transferred provenances generally has an advantage in productivity relative to the local provenance comparable to that of progeny of plus trees. The aim of this study was to explore the extent to which productivity gains achieved by provenance transfer or the use of plus tree progeny are associated with reductions in autumn frost hardiness, relative to that of trees of the local provenance. In a field trial with 19-year-old trees in central Sweden, bud hardiness was tested on four occasions during the autumn of 2002. Trees of the local provenance were compared with trees of a south Swedish provenance originating 3 degrees of latitude to the south, a Belarusian provenance and the progeny of plus trees of local origin. The Belarusian provenance was the least hardy and the local provenance the most hardy, with plus tree progeny and the south Swedish provenance being intermediate in hardiness. Both the Belarusian provenance and the plus tree progeny were significantly taller than trees of the other populations. Within provenances, tree height was negatively correlated with autumn frost hardiness. Among the plus tree progeny, however, no such correlation between tree height and autumn frost hardiness was found. It is concluded that although the gain in productivity achieved by provenance transfer from Belarus was comparable to that achieved by using the progeny of plus trees of the local provenance, the use of trees of the Belarus provenance involved an increased risk of autumn frost damage because of later hardening.

Inferences from growing trees backwards

Treesearch

David W. Green; Kent A. McDonald

1997-01-01

The objective of this paper is to illustrate how longitudinal stress wave techniques can be useful in tracking the future quality of a growing tree. Monitoring the quality of selected trees in a plantation forest could provide early input to decisions on the effectiveness of management practices, or future utilization options, for trees in a plantation. There will...

The Tree Worker's Manual. [Revised.

ERIC Educational Resources Information Center

Lilly, S. J.

This manual acquaints readers with the general operations of the tree care industry. The manual covers subjects important to a tree worker and serves as a training aid for workers at the entry level as tree care professionals. Each chapter begins with a set of objectives and may include figures, tables, and photographs. Ten chapters are included:…

Our Air: Unfit for Trees.

ERIC Educational Resources Information Center

Dochinger, Leon S.

To help urban, suburban, and rural tree owners know about air pollution's effects on trees and their tolerance and intolerance to pollutants, the USDA Forest Service has prepared this booklet. It answers the following questions about atmospheric pollution: Where does it come from? What can it do to trees? and What can we do about it? In addition,…

The stopping rules for winsorized tree

NASA Astrophysics Data System (ADS)

Ch'ng, Chee Keong; Mahat, Nor Idayu

2017-11-01

Winsorized tree is a modified tree-based classifier that is able to investigate and to handle all outliers in all nodes along the process of constructing the tree. It overcomes the tedious process of constructing a classical tree where the splitting of branches and pruning go concurrently so that the constructed tree would not grow bushy. This mechanism is controlled by the proposed algorithm. In winsorized tree, data are screened for identifying outlier. If outlier is detected, the value is neutralized using winsorize approach. Both outlier identification and value neutralization are executed recursively in every node until predetermined stopping criterion is met. The aim of this paper is to search for significant stopping criterion to stop the tree from further splitting before overfitting. The result obtained from the conducted experiment on pima indian dataset proved that the node could produce the final successor nodes (leaves) when it has achieved the range of 70% in information gain.

CSI for Trees

ERIC Educational Resources Information Center

Rubino, Darrin L.; Hanson, Deborah

2009-01-01

The circles and patterns in a tree's stem tell a story, but that story can be a mystery. Interpreting the story of tree rings provides a way to heighten the natural curiosity of students and help them gain insight into the interaction of elements in the environment. It also represents a wonderful opportunity to incorporate the nature of science.…

Accounting for Uncertainty in Gene Tree Estimation: Summary-Coalescent Species Tree Inference in a Challenging Radiation of Australian Lizards.

PubMed

Blom, Mozes P K; Bragg, Jason G; Potter, Sally; Moritz, Craig

2017-05-01

Accurate gene tree inference is an important aspect of species tree estimation in a summary-coalescent framework. Yet, in empirical studies, inferred gene trees differ in accuracy due to stochastic variation in phylogenetic signal between targeted loci. Empiricists should, therefore, examine the consistency of species tree inference, while accounting for the observed heterogeneity in gene tree resolution of phylogenomic data sets. Here, we assess the impact of gene tree estimation error on summary-coalescent species tree inference by screening ${\\sim}2000$ exonic loci based on gene tree resolution prior to phylogenetic inference. We focus on a phylogenetically challenging radiation of Australian lizards (genus Cryptoblepharus, Scincidae) and explore effects on topology and support. We identify a well-supported topology based on all loci and find that a relatively small number of high-resolution gene trees can be sufficient to converge on the same topology. Adding gene trees with decreasing resolution produced a generally consistent topology, and increased confidence for specific bipartitions that were poorly supported when using a small number of informative loci. This corroborates coalescent-based simulation studies that have highlighted the need for a large number of loci to confidently resolve challenging relationships and refutes the notion that low-resolution gene trees introduce phylogenetic noise. Further, our study also highlights the value of quantifying changes in nodal support across locus subsets of increasing size (but decreasing gene tree resolution). Such detailed analyses can reveal anomalous fluctuations in support at some nodes, suggesting the possibility of model violation. By characterizing the heterogeneity in phylogenetic signal among loci, we can account for uncertainty in gene tree estimation and assess its effect on the consistency of the species tree estimate. We suggest that the evaluation of gene tree resolution should be incorporated

Phylogenetic trees and Euclidean embeddings.

PubMed

Layer, Mark; Rhodes, John A

2017-01-01

It was recently observed by de Vienne et al. (Syst Biol 60(6):826-832, 2011) that a simple square root transformation of distances between taxa on a phylogenetic tree allowed for an embedding of the taxa into Euclidean space. While the justification for this was based on a diffusion model of continuous character evolution along the tree, here we give a direct and elementary explanation for it that provides substantial additional insight. We use this embedding to reinterpret the differences between the NJ and BIONJ tree building algorithms, providing one illustration of how this embedding reflects tree structures in data.

Mapping Tree Density at the Global Scale

NASA Astrophysics Data System (ADS)

Covey, K. R.; Crowther, T. W.; Glick, H.; Bettigole, C.; Bradford, M.

2015-12-01

The global extent and distribution of forest trees is central to our understanding of the terrestrial biosphere. We provide the first spatially continuous map of forest tree density at a global-scale. This map reveals that the global number of trees is approximately 3.04 trillion, an order of magnitude higher than the previous estimate. Of these trees, approximately 1.39 trillion exist in tropical and subtropical regions, with 0.74, and 0.61 trillion in boreal and temperate regions, respectively. Biome-level trends in tree density demonstrate the importance of climate and topography in controlling local tree densities at finer scales, as well as the overwhelming impact of humans across most of the world. Based on our projected tree densities, we estimate that deforestation is currently responsible for removing over 15 billion trees each year, and the global number of trees has fallen by approximately 46% since the start of human civilization.

Modeling stem profile of Triadica Sebifera in southern forestlands of Mississippi

Treesearch

Nana Tian; Zhaofei Fan

2016-01-01

Chinese tallow (Triadica sebifera) is one of the most aggressive invasive species in the southern forestlands of United States. To explore the stem taper of tallow, outside-and-inside bark stem profile equations were fitted using Max and Burkhart (1976), Cao (2009) modified Max and Burkhart, andClark, Souter, and Schlaegel (1991) segmented...

Utility of tree crown condition indicators to predict tree survival using remeasured Forest Inventory and Analysis data

Treesearch

Randall S. Morin; Jim Steinman; KaDonna C. Randolph

2012-01-01

The condition of tree crowns is an important indicator of tree and forest health. Crown conditions have been evaluated during surveys of Forest Inventory and Analysis (FIA) Phase 3 (P3) plots since 1999. In this study, remeasured data from 39,357 trees in the northern United States were used to assess the probability of survival among various tree species using the...

Anatomy of the Pythagoras' Tree

ERIC Educational Resources Information Center

Teia, Luis

2016-01-01

The architecture of nature can be seen at play in a tree: no two are alike. The Pythagoras' tree behaves just as a "tree" in that the root plus the same movement repeated over and over again grows from a seed, to a plant, to a tree. In human life, this movement is termed cell division. With triples, this movement is a geometrical and…

Tree diversity and the role of non-host neighbour tree species in reducing fungal pathogen infestation

PubMed Central

Hantsch, Lydia; Bien, Steffen; Radatz, Stine; Braun, Uwe; Auge, Harald; Bruelheide, Helge

2014-01-01

The degree to which plant pathogen infestation occurs in a host plant is expected to be strongly influenced by the level of species diversity among neighbouring host and non-host plant species. Since pathogen infestation can negatively affect host plant performance, it can mediate the effects of local biodiversity on ecosystem functioning. We tested the effects of tree diversity and the proportion of neighbouring host and non-host species with respect to the foliar fungal pathogens of Tilia cordata and Quercus petraea in the Kreinitz tree diversity experiment in Germany. We hypothesized that fungal pathogen richness increases while infestation decreases with increasing local tree diversity. In addition, we tested whether fungal pathogen richness and infestation are dependent on the proportion of host plant species present or on the proportion of particular non-host neighbouring tree species. Leaves of the two target species were sampled across three consecutive years with visible foliar fungal pathogens on the leaf surface being identified macro- and microscopically. Effects of diversity among neighbouring trees were analysed: (i) for total fungal species richness and fungal infestation on host trees and (ii) for infestation by individual fungal species. We detected four and five fungal species on T. cordata and Q. petraea, respectively. High local tree diversity reduced (i) total fungal species richness and infestation of T. cordata and fungal infestation of Q. petraea and (ii) infestation by three host-specialized fungal pathogen species. These effects were brought about by local tree diversity and were independent of host species proportion. In general, host species proportion had almost no effect on fungal species richness and infestation. Strong effects associated with the proportion of particular non-host neighbouring tree species on fungal species richness and infestation were, however, recorded. Synthesis. For the first time, we experimentally

Tree diversity and the role of non-host neighbour tree species in reducing fungal pathogen infestation.

PubMed

Hantsch, Lydia; Bien, Steffen; Radatz, Stine; Braun, Uwe; Auge, Harald; Bruelheide, Helge

2014-11-01

The degree to which plant pathogen infestation occurs in a host plant is expected to be strongly influenced by the level of species diversity among neighbouring host and non-host plant species. Since pathogen infestation can negatively affect host plant performance, it can mediate the effects of local biodiversity on ecosystem functioning.We tested the effects of tree diversity and the proportion of neighbouring host and non-host species with respect to the foliar fungal pathogens of Tilia cordata and Quercus petraea in the Kreinitz tree diversity experiment in Germany. We hypothesized that fungal pathogen richness increases while infestation decreases with increasing local tree diversity. In addition, we tested whether fungal pathogen richness and infestation are dependent on the proportion of host plant species present or on the proportion of particular non-host neighbouring tree species.Leaves of the two target species were sampled across three consecutive years with visible foliar fungal pathogens on the leaf surface being identified macro- and microscopically. Effects of diversity among neighbouring trees were analysed: (i) for total fungal species richness and fungal infestation on host trees and (ii) for infestation by individual fungal species.We detected four and five fungal species on T. cordata and Q. petraea , respectively. High local tree diversity reduced (i) total fungal species richness and infestation of T. cordata and fungal infestation of Q. petraea and (ii) infestation by three host-specialized fungal pathogen species. These effects were brought about by local tree diversity and were independent of host species proportion. In general, host species proportion had almost no effect on fungal species richness and infestation. Strong effects associated with the proportion of particular non-host neighbouring tree species on fungal species richness and infestation were, however, recorded. Synthesis . For the first time, we experimentally

Are There Infinite Irrigation Trees?

NASA Astrophysics Data System (ADS)

Bernot, M.; Caselles, V.; Morel, J. M.

2006-08-01

In many natural or artificial flow systems, a fluid flow network succeeds in irrigating every point of a volume from a source. Examples are the blood vessels, the bronchial tree and many irrigation and draining systems. Such systems have raised recently a lot of interest and some attempts have been made to formalize their description, as a finite tree of tubes, and their scaling laws [25], [26]. In contrast, several mathematical models [5], [22], [10], propose an idealization of these irrigation trees, where a countable set of tubes irrigates any point of a volume with positive Lebesgue measure. There is no geometric obstruction to this infinitesimal model and general existence and structure theorems have been proved. As we show, there may instead be an energetic obstruction. Under Poiseuille law R(s) = s -2 for the resistance of tubes with section s, the dissipated power of a volume irrigating tree cannot be finite. In other terms, infinite irrigation trees seem to be impossible from the fluid mechanics viewpoint. This also implies that the usual principle analysis performed for the biological models needs not to impose a minimal size for the tubes of an irrigating tree; the existence of the minimal size can be proven from the only two obvious conditions for such irrigation trees, namely the Kirchhoff and Poiseuille laws.

Trees and highway safety.

DOT National Transportation Integrated Search

2011-03-01

To minimize the severity of run-off-road collisions of vehicles with trees, departments of transportation (DOTs) : commonly establish clear zones for trees and other fixed objects. Caltrans clear zone on freeways is 30 feet : minimum (40 feet pref...

Interim hardwood tree grades for factory lumber

Treesearch

Leland F. Hanks; Leland F. Hanks

1971-01-01

Hardwood trees have for many years been measured in such a way that tree volume could be estimated; and in recent years the prediction of tree quality by using tree grades has become of interest to owners, sellers, and buyers of timber. Several tree-grading systems have been developed, but none has been publicized and used on a widespread scale. The Forest Service...

A comparison of supplemental calcium soap of palm fatty acids versus tallow in a corn-based finishing diet for feedlot steers.

PubMed

Warner, Crystal M; Hahm, Sahng-Wook; Archibeque, Shawn L; Wagner, John J; Engle, Terry E; Roman-Muniz, Ivette N; Woerner, Dale; Sponsler, Mark; Han, Hyungchul

2015-01-01

Rumen bypass fat is commonly added to increase energy intake in dairy cattle. The objective of this study is to examine the addition of rumen bypass fat during finishing period on performance and carcass characteristics in grain fed steers. This study was conducted as a completely randomized block design with 126 cross-bred steer calves (initial BW 471.5 ± 7.5 kg) randomly assigned to pens with 9 steers/pen (n = 7 pens/treatment). Each pen was randomly assigned to one of two treatment groups; rumen bypass fat treatment (CCS, calcium soap of palm fatty acids) and control diet (CT, tallow). The diets were formulated to be isonitrogenous and isocaloric. Animals were fed twice daily at 110 % of the previous daily ad libitum intake. Blood from each sample was taken from the jugular vein. Muscle and adipose samples were collected from the longissimus dorsi regions. Feedlot performance and carcass characteristics were assessed. To examine adipogenic gene expression, quantitative real-time PCR was completed. Steers fed the CT had a greater level of performance for most of the parameters measured. The CT group had greater DMI (P < 0.05) and tended to have greater ADG (P < 0.10). Marbling score (P < 0.05) and quality grade (P < 0.05) were greater for steers fed the CT diet than those fed CCS. The longissimus muscle area tended to be greater (P < 0.10) in steers fed CT (87.60 cm(2)) than those fed CCS (84.88 cm(2)). The leptin mRNA expression was down-regulated (P < 0.05) in adipose tissue of steers fed a CCS when compared to those fed CT. These data suggest that calcium soap of palm fatty acids can be added to finishing diets without significant reduction in final body weight, although there may be modest reductions in marbling and quality scores.

Tree-Substrate Water Relations and Root Development in Tree Plantations Used for Mine Tailings Reclamation.

PubMed

Guittonny-Larchevêque, Marie; Bussière, Bruno; Pednault, Carl

2016-05-01

Tree water uptake relies on well-developed root systems. However, mine wastes can restrict root growth, in particular metalliferous mill tailings, which consist of the finely crushed ore that remains after valuable metals are removed. Thus, water stress could limit plantation success in reclaimed mine lands. This study evaluates the effect of substrates varying in quality (topsoil, overburden, compost and tailings mixture, and tailings alone) and quantity (50- or 20-cm-thick topsoil layer vs. 1-m plantation holes) on root development and water stress exposure of trees planted in low-sulfide mine tailings under boreal conditions. A field experiment was conducted over 2 yr with two tree species: basket willow ( L.) and hybrid poplar ( Moench × A. Henry). Trees developed roots in the tailings underlying the soil treatments despite tailings' low macroporosity. However, almost no root development occurred in tailings underlying a compost and tailings mixture. Because root development and associated water uptake was not limited to the soil, soil volume influenced neither short-term (water potential and instantaneous transpiration) nor long-term (δC) water stress exposure in trees. However, trees were larger and had greater total leaf area when grown in thicker topsoil. Despite a volumetric water content that always remained above permanent wilting point in the tailings colonized by tree roots, measured foliar water potentials at midday were lower than drought thresholds reported for both tested tree species. Copyright © by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.

VC-dimension of univariate decision trees.

PubMed

Yildiz, Olcay Taner

2015-02-01

In this paper, we give and prove the lower bounds of the Vapnik-Chervonenkis (VC)-dimension of the univariate decision tree hypothesis class. The VC-dimension of the univariate decision tree depends on the VC-dimension values of its subtrees and the number of inputs. Via a search algorithm that calculates the VC-dimension of univariate decision trees exhaustively, we show that our VC-dimension bounds are tight for simple trees. To verify that the VC-dimension bounds are useful, we also use them to get VC-generalization bounds for complexity control using structural risk minimization in decision trees, i.e., pruning. Our simulation results show that structural risk minimization pruning using the VC-dimension bounds finds trees that are more accurate as those pruned using cross validation.

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

USGS Publications Warehouse

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

2013-01-01

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

Tree decay an expanded concept

Treesearch

Alex L. Shigo

1979-01-01

This publication is the final one in a series on tree decay developed in cooperation with Harold G. Marx, Research Application Staff Assistant, U.S. Department of Agriculture, Forest Service, Washington, D.C. The purpose of this publication is to clarify further the tree decay concept that expands the classical concept to include the orderly response of the tree to...

Rx for wounded trees

Treesearch

Hal Marx

1976-01-01

This booklet offers guidelines on how to care for trees to keep them healthy and to protect them from wounds. It also prescribes ways to prevent, recognize, and minimize damage by decay that most often sets in after tree wounding.

Fuzzy tree automata and syntactic pattern recognition.

PubMed

Lee, E T

1982-04-01

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

Folding and unfolding phylogenetic trees and networks.

PubMed

Huber, Katharina T; Moulton, Vincent; Steel, Mike; Wu, Taoyang

2016-12-01

Phylogenetic networks are rooted, labelled directed acyclic graphswhich are commonly used to represent reticulate evolution. There is a close relationship between phylogenetic networks and multi-labelled trees (MUL-trees). Indeed, any phylogenetic network N can be "unfolded" to obtain a MUL-tree U(N) and, conversely, a MUL-tree T can in certain circumstances be "folded" to obtain aphylogenetic network F(T) that exhibits T. In this paper, we study properties of the operations U and F in more detail. In particular, we introduce the class of stable networks, phylogenetic networks N for which F(U(N)) is isomorphic to N, characterise such networks, and show that they are related to the well-known class of tree-sibling networks. We also explore how the concept of displaying a tree in a network N can be related to displaying the tree in the MUL-tree U(N). To do this, we develop aphylogenetic analogue of graph fibrations. This allows us to view U(N) as the analogue of the universal cover of a digraph, and to establish a close connection between displaying trees in U(N) and reconciling phylogenetic trees with networks.

Estimating phylogenetic trees from genome-scale data.

PubMed

Liu, Liang; Xi, Zhenxiang; Wu, Shaoyuan; Davis, Charles C; Edwards, Scott V

2015-12-01

The heterogeneity of signals in the genomes of diverse organisms poses challenges for traditional phylogenetic analysis. Phylogenetic methods known as "species tree" methods have been proposed to directly address one important source of gene tree heterogeneity, namely the incomplete lineage sorting that occurs when evolving lineages radiate rapidly, resulting in a diversity of gene trees from a single underlying species tree. Here we review theory and empirical examples that help clarify conflicts between species tree and concatenation methods, and misconceptions in the literature about the performance of species tree methods. Considering concatenation as a special case of the multispecies coalescent model helps explain differences in the behavior of the two methods on phylogenomic data sets. Recent work suggests that species tree methods are more robust than concatenation approaches to some of the classic challenges of phylogenetic analysis, including rapidly evolving sites in DNA sequences and long-branch attraction. We show that approaches, such as binning, designed to augment the signal in species tree analyses can distort the distribution of gene trees and are inconsistent. Computationally efficient species tree methods incorporating biological realism are a key to phylogenetic analysis of whole-genome data. © 2015 New York Academy of Sciences.

Environmental fate of emamectin benzoate after tree micro injection of horse chestnut trees.

PubMed

Burkhard, Rene; Binz, Heinz; Roux, Christian A; Brunner, Matthias; Ruesch, Othmar; Wyss, Peter

2015-02-01

Emamectin benzoate, an insecticide derived from the avermectin family of natural products, has a unique translocation behavior in trees when applied by tree micro injection (TMI), which can result in protection from insect pests (foliar and borers) for several years. Active ingredient imported into leaves was measured at the end of season in the fallen leaves of treated horse chestnut (Aesculus hippocastanum) trees. The dissipation of emamectin benzoate in these leaves seems to be biphasic and depends on the decomposition of the leaf. In compost piles, where decomposition of leaves was fastest, a cumulative emamectin benzoate degradation half-life time of 20 d was measured. In leaves immersed in water, where decomposition was much slower, the degradation half-life time was 94 d, and in leaves left on the ground in contact with soil, where decomposition was slowest, the degradation half-life time was 212 d. The biphasic decline and the correlation with leaf decomposition might be attributed to an extensive sorption of emamectin benzoate residues to leaf macromolecules. This may also explain why earthworms ingesting leaves from injected trees take up very little emamectin benzoate and excrete it with the feces. Furthermore, no emamectin benzoate was found in water containing decomposing leaves from injected trees. It is concluded, that emamectin benzoate present in abscised leaves from horse chestnut trees injected with the insecticide is not available to nontarget organisms present in soil or water bodies. Published 2014 SETAC.

Long tree-ring chronologies provide evidence of recent tree growth decrease in a Central African tropical forest.

PubMed

Battipaglia, Giovanna; Zalloni, Enrica; Castaldi, Simona; Marzaioli, Fabio; Cazzolla-Gatti, Roberto; Lasserre, Bruno; Tognetti, Roberto; Marchetti, Marco; Valentini, Riccardo

2015-01-01

It is still unclear whether the exponential rise of atmospheric CO2 concentration has produced a fertilization effect on tropical forests, thus incrementing their growth rate, in the last two centuries. As many factors affect tree growth patterns, short -term studies might be influenced by the confounding effect of several interacting environmental variables on plant growth. Long-term analyses of tree growth can elucidate long-term trends of plant growth response to dominant drivers. The study of annual rings, applied to long tree-ring chronologies in tropical forest trees enables such analysis. Long-term tree-ring chronologies of three widespread African species were measured in Central Africa to analyze the growth of trees over the last two centuries. Growth trends were correlated to changes in global atmospheric CO2 concentration and local variations in the main climatic drivers, temperature and rainfall. Our results provided no evidence for a fertilization effect of CO2 on tree growth. On the contrary, an overall growth decline was observed for all three species in the last century, which appears to be significantly correlated to the increase in local temperature. These findings provide additional support to the global observations of a slowing down of C sequestration in the trunks of forest trees in recent decades. Data indicate that the CO2 increase alone has not been sufficient to obtain a tree growth increase in tropical trees. The effect of other changing environmental factors, like temperature, may have overridden the fertilization effect of CO2.

Long Tree-Ring Chronologies Provide Evidence of Recent Tree Growth Decrease in a Central African Tropical Forest

PubMed Central

Battipaglia, Giovanna; Zalloni, Enrica; Castaldi, Simona; Marzaioli, Fabio; Cazzolla- Gatti, Roberto; Lasserre, Bruno; Tognetti, Roberto; Marchetti, Marco; Valentini, Riccardo

2015-01-01

It is still unclear whether the exponential rise of atmospheric CO2 concentration has produced a fertilization effect on tropical forests, thus incrementing their growth rate, in the last two centuries. As many factors affect tree growth patterns, short -term studies might be influenced by the confounding effect of several interacting environmental variables on plant growth. Long-term analyses of tree growth can elucidate long-term trends of plant growth response to dominant drivers. The study of annual rings, applied to long tree-ring chronologies in tropical forest trees enables such analysis. Long-term tree-ring chronologies of three widespread African species were measured in Central Africa to analyze the growth of trees over the last two centuries. Growth trends were correlated to changes in global atmospheric CO2 concentration and local variations in the main climatic drivers, temperature and rainfall. Our results provided no evidence for a fertilization effect of CO2 on tree growth. On the contrary, an overall growth decline was observed for all three species in the last century, which appears to be significantly correlated to the increase in local temperature. These findings provide additional support to the global observations of a slowing down of C sequestration in the trunks of forest trees in recent decades. Data indicate that the CO2 increase alone has not been sufficient to obtain a tree growth increase in tropical trees. The effect of other changing environmental factors, like temperature, may have overridden the fertilization effect of CO2. PMID:25806946

Decision Tree Phytoremediation

DTIC Science & Technology

1999-12-01

aromatic hydrocarbons, and landfill leachates . Phytoremediation has been used for point and nonpoint source hazardous waste control. 1.2 Types of... Phytoremediation Prepared by Interstate Technology and Regulatory Cooperation Work Group Phytoremediation Work Team December 1999 Decision Tree...1999 2. REPORT TYPE N/A 3. DATES COVERED - 4. TITLE AND SUBTITLE Phytoremediation Decision Tree 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c

ETE: a python Environment for Tree Exploration.

PubMed

Huerta-Cepas, Jaime; Dopazo, Joaquín; Gabaldón, Toni

2010-01-13

Many bioinformatics analyses, ranging from gene clustering to phylogenetics, produce hierarchical trees as their main result. These are used to represent the relationships among different biological entities, thus facilitating their analysis and interpretation. A number of standalone programs are available that focus on tree visualization or that perform specific analyses on them. However, such applications are rarely suitable for large-scale surveys, in which a higher level of automation is required. Currently, many genome-wide analyses rely on tree-like data representation and hence there is a growing need for scalable tools to handle tree structures at large scale. Here we present the Environment for Tree Exploration (ETE), a python programming toolkit that assists in the automated manipulation, analysis and visualization of hierarchical trees. ETE libraries provide a broad set of tree handling options as well as specific methods to analyze phylogenetic and clustering trees. Among other features, ETE allows for the independent analysis of tree partitions, has support for the extended newick format, provides an integrated node annotation system and permits to link trees to external data such as multiple sequence alignments or numerical arrays. In addition, ETE implements a number of built-in analytical tools, including phylogeny-based orthology prediction and cluster validation techniques. Finally, ETE's programmable tree drawing engine can be used to automate the graphical rendering of trees with customized node-specific visualizations. ETE provides a complete set of methods to manipulate tree data structures that extends current functionality in other bioinformatic toolkits of a more general purpose. ETE is free software and can be downloaded from http://ete.cgenomics.org.

ETE: a python Environment for Tree Exploration

PubMed Central

2010-01-01

Background Many bioinformatics analyses, ranging from gene clustering to phylogenetics, produce hierarchical trees as their main result. These are used to represent the relationships among different biological entities, thus facilitating their analysis and interpretation. A number of standalone programs are available that focus on tree visualization or that perform specific analyses on them. However, such applications are rarely suitable for large-scale surveys, in which a higher level of automation is required. Currently, many genome-wide analyses rely on tree-like data representation and hence there is a growing need for scalable tools to handle tree structures at large scale. Results Here we present the Environment for Tree Exploration (ETE), a python programming toolkit that assists in the automated manipulation, analysis and visualization of hierarchical trees. ETE libraries provide a broad set of tree handling options as well as specific methods to analyze phylogenetic and clustering trees. Among other features, ETE allows for the independent analysis of tree partitions, has support for the extended newick format, provides an integrated node annotation system and permits to link trees to external data such as multiple sequence alignments or numerical arrays. In addition, ETE implements a number of built-in analytical tools, including phylogeny-based orthology prediction and cluster validation techniques. Finally, ETE's programmable tree drawing engine can be used to automate the graphical rendering of trees with customized node-specific visualizations. Conclusions ETE provides a complete set of methods to manipulate tree data structures that extends current functionality in other bioinformatic toolkits of a more general purpose. ETE is free software and can be downloaded from http://ete.cgenomics.org. PMID:20070885

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

Irrational exuberance for resolved species trees.

PubMed

Hahn, Matthew W; Nakhleh, Luay

2016-01-01

Phylogenomics has largely succeeded in its aim of accurately inferring species trees, even when there are high levels of discordance among individual gene trees. These resolved species trees can be used to ask many questions about trait evolution, including the direction of change and number of times traits have evolved. However, the mapping of traits onto trees generally uses only a single representation of the species tree, ignoring variation in the gene trees used to construct it. Recognizing that genes underlie traits, these results imply that many traits follow topologies that are discordant with the species topology. As a consequence, standard methods for character mapping will incorrectly infer the number of times a trait has evolved. This phenomenon, dubbed "hemiplasy," poses many problems in analyses of character evolution. Here we outline these problems, explaining where and when they are likely to occur. We offer several ways in which the possible presence of hemiplasy can be diagnosed, and discuss multiple approaches to dealing with the problems presented by underlying gene tree discordance when carrying out character mapping. Finally, we discuss the implications of hemiplasy for general phylogenetic inference, including the possible drawbacks of the widespread push for "resolved" species trees. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

Long-term monitoring of Sacramento Shade program trees: tree survival, growth and energy-saving performance

Treesearch

Yekang Ko; Jun-Hak Lee; E. Gregory McPherson; Lara A. Roman

2015-01-01

Long-term survival and growth of urban forests are critical to achieve the targeted benefits of urban tree planting programs, such as building energy savings from tree shade. However, little is known about how trees perform in the long-term, especially in residential areas. Given this gap in the literature, we monitored 22-years of post-planting survival, growth, and...

Nodal distances for rooted phylogenetic trees.

PubMed

Cardona, Gabriel; Llabrés, Mercè; Rosselló, Francesc; Valiente, Gabriel

2010-08-01

Dissimilarity measures for (possibly weighted) phylogenetic trees based on the comparison of their vectors of path lengths between pairs of taxa, have been present in the systematics literature since the early seventies. For rooted phylogenetic trees, however, these vectors can only separate non-weighted binary trees, and therefore these dissimilarity measures are metrics only on this class of rooted phylogenetic trees. In this paper we overcome this problem, by splitting in a suitable way each path length between two taxa into two lengths. We prove that the resulting splitted path lengths matrices single out arbitrary rooted phylogenetic trees with nested taxa and arcs weighted in the set of positive real numbers. This allows the definition of metrics on this general class of rooted phylogenetic trees by comparing these matrices through metrics in spaces M(n)(R) of real-valued n x n matrices. We conclude this paper by establishing some basic facts about the metrics for non-weighted phylogenetic trees defined in this way using L(p) metrics on M(n)(R), with p [epsilon] R(>0).

Compartmentalization of decay in trees

Treesearch

Alex L. Shigo

1985-01-01

Trees have a spectacular survival record. Over a period of more than 400 million years they have evolved as the tallest, most massive and longest-lived organisms ever to inhabit the earth. Yet trees lack a means of defense that almost every animal has: trees cannot move away from destructive forces. Because they cannot move, all types of living and nonliving enemies—...

Barking up the Right Tree

ERIC Educational Resources Information Center

Houston, Paul D.

2006-01-01

There is a childhood saying about a confused dog who thinks he sees a possum in a tree. The problem is that the possum is actually in a different tree so the dog barks up the wrong tree. American education is constantly playing both dog and possum. Sometimes they are the prey, and sometimes they are just confused about what and where the prey is.…

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.

Hydraulic limits on tree performance: transpiration, carbon gain and growth of trees

Treesearch

Melvin T. Tyree

2003-01-01

The state of knowledge concerning the influences of tree size, xylem dysfunction, growth conditions, and within-species and between species genetics is reviewed. It is concluded that high plant hydraulic conductance is necessary for high productivity in forest trees, and this being the case, the implications for commercial forestry require further study.

Tree-centered spot firing - a technique for prescribed burning beneath standing trees.

Treesearch

C. Phillip Weatherspoon; George A. Almond; Carl N. Skinner

1989-01-01

Prescribed burning beneath standing trees normally requires efforts to protect residual trees from excessive fire damage. Damage to both crowns and boles is strongly influenced by flame length, a fire characteristic functionally related to fireline intensity (Albini 1976). In a good prescribed burn, therefore, the prescription specifies desired or maximum flame lengths...

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

NASA Astrophysics Data System (ADS)

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

2011-12-01

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

Tree demography dominates long-term growth trends inferred from tree rings.

PubMed

Brienen, Roel J W; Gloor, Manuel; Ziv, Guy

2017-02-01

Understanding responses of forests to increasing CO 2 and temperature is an important challenge, but no easy task. Tree rings are increasingly used to study such responses. In a recent study, van der Sleen et al. (2014) Nature Geoscience, 8, 4 used tree rings from 12 tropical tree species and find that despite increases in intrinsic water use efficiency, no growth stimulation is observed. This challenges the idea that increasing CO 2 would stimulate growth. Unfortunately, tree ring analysis can be plagued by biases, resulting in spurious growth trends. While their study evaluated several biases, it does not account for all. In particular, one bias may have seriously affected their results. Several of the species have recruitment patterns, which are not uniform, but clustered around one specific year. This results in spurious negative growth trends if growth rates are calculated in fixed size classes, as 'fast-growing' trees reach the sampling diameter earlier compared to slow growers and thus fast growth rates tend to have earlier calendar dates. We assessed the effect of this 'nonuniform age bias' on observed growth trends and find that van der Sleen's conclusions of a lack of growth stimulation do not hold. Growth trends are - at least partially - driven by underlying recruitment or age distributions. Species with more clustered age distributions show more negative growth trends, and simulations to estimate the effect of species' age distributions show growth trends close to those observed. Re-evaluation of the growth data and correction for the bias result in significant positive growth trends of 1-2% per decade for the full period, and 3-7% since 1950. These observations, however, should be taken cautiously as multiple biases affect these trend estimates. In all, our results highlight that tree ring studies of long-term growth trends can be strongly influenced by biases if demographic processes are not carefully accounted for. © 2016 The Authors. Global

Comparative Use of Tree Leaves, Needles, Tree Barks and Lichens for Air Pollution Biomonitoring

NASA Astrophysics Data System (ADS)

El Khoukhi, T.; Cherkaoui El Moursli, R.; Chouak, A.; Moutia, Z.; Lferde, M.; Senhou, A.; Gaudry, A.; Ayrault, S.; Chakir, M.

2005-01-01

The aim of this work is to determine the most suitable bioaccumulators for air pollution survey in Morocco. For this, we compare in this paper heavy metals uptake efficiencies for different types of biomonitors: leaves of oak and eucalyptus trees, needles of coniferous trees, tree-barks and lichens collected at the same site. Instrumental neutron activation analysis using the k0 method (INAA-k0) was used for its adequate characteristics to analyze accurately a wide number of elements. Reference materials were analyzed to check the reliability and the accuracy of this technique. The results obtained for all these bioaccumulators lead to the following conclusions. For the major elements, leaves and needles are more accumulating than tree barks and lichens. While for the intermediate and trace elements, there is an obvious accumulation in lichens in comparison with tree barks, leaves and needles. This work shows the possibility to use these four bioaccumulators according to their availability in an area. It will be useful however to set up an inter calibration between these bioaccumulators.

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.

The dynamics of strangling among forest trees.

PubMed

Okamoto, Kenichi W

2015-11-07

Strangler trees germinate and grow on other trees, eventually enveloping and potentially even girdling their hosts. This allows them to mitigate fitness costs otherwise incurred by germinating and competing with other trees on the forest floor, as well as minimize risks associated with host tree-fall. If stranglers can themselves host other strangler trees, they may not even seem to need non-stranglers to persist. Yet despite their high fitness potential, strangler trees neither dominate the communities in which they occur nor is the strategy particularly common outside of figs (genus Ficus). Here we analyze how dynamic interactions between strangling and non-strangling trees can shape the adaptive landscape for strangling mutants and mutant trees that have lost the ability to strangle. We find a threshold which strangler germination rates must exceed for selection to favor the evolution of strangling, regardless of how effectively hemiepiphytic stranglers may subsequently replace their hosts. This condition describes the magnitude of the phenotypic displacement in the ability to germinate on other trees necessary for invasion by a mutant tree that could potentially strangle its host following establishment as an epiphyte. We show how the relative abilities of strangling and non-strangling trees to occupy empty sites can govern whether strangling is an evolutionarily stable strategy, and obtain the conditions for strangler coexistence with non-stranglers. We then elucidate when the evolution of strangling can disrupt stable coexistence between commensal epiphytic ancestors and their non-strangling host trees. This allows us to highlight parallels between the invasion fitness of strangler trees arising from commensalist ancestors, and cases where strangling can arise in concert with the evolution of hemiepiphytism among free-standing ancestors. Finally, we discuss how our results can inform the evolutionary ecology of antagonistic interactions more generally

Tree Height Calculator: An Android App for Estimating Tree Height

NASA Astrophysics Data System (ADS)

Burca, V. S.; Htet, N. M.; Huang, X.; de Lanerolle, T. R.; Morelli, R.; Gourley, J. R.

2011-12-01

Conventionally, measuring tree height requires a collection of different tools - clinometer, transit, pencil, paper, laptop computer. Results are recorded manually and entered into a spreadsheet or database for future calculation and analysis. Tree Height Calculator is a mobile Android app the integrates the various steps in this process thereby improving the accuracy and dramatically reducing the time required to go from taking measurements to analyzing data. Given the user's height and the distance from the base of the tree (which can be downloaded into the app from a server), the app uses the phone's orientation sensor to calculate the angle of elevation. A simple trigonometric formula is then used to calculate and record the tree's height in the phone's database. When the phone has a WiFi connection, the data are transmitted to a server, from where they can be downloaded directly into a spreadsheet. The application was first tested in an Environmental Science laboratory at Trinity College. On the first trial, 103 data samples were collected, stored, and uploaded to the online database with only couple of dropped data points. On the second trial, 98 data samples were gathered with no loss of data. The app combined the individual measurements taken by the students in the lab, reducing the time required to produce a graph of the class's results from days to hours.

Using fragmentation trees and mass spectral trees for identifying unknown compounds in metabolomics.

PubMed

Vaniya, Arpana; Fiehn, Oliver

2015-06-01

Identification of unknown metabolites is the bottleneck in advancing metabolomics, leaving interpretation of metabolomics results ambiguous. The chemical diversity of metabolism is vast, making structure identification arduous and time consuming. Currently, comprehensive analysis of mass spectra in metabolomics is limited to library matching, but tandem mass spectral libraries are small compared to the large number of compounds found in the biosphere, including xenobiotics. Resolving this bottleneck requires richer data acquisition and better computational tools. Multi-stage mass spectrometry (MSn) trees show promise to aid in this regard. Fragmentation trees explore the fragmentation process, generate fragmentation rules and aid in sub-structure identification, while mass spectral trees delineate the dependencies in multi-stage MS of collision-induced dissociations. This review covers advancements over the past 10 years as a tool for metabolite identification, including algorithms, software and databases used to build and to implement fragmentation trees and mass spectral annotations.

Flow around a Living Tree

NASA Astrophysics Data System (ADS)

Ishikawa, Hitoshi; Amano, Suguru; Yakushiji, Kenta

Flow around a living tree was investigated as basic research of a windbreak forest. A type of conifer, which is named “goldcrest, ” was used as the test piece in a wind tunnel experiment. The drag coefficient of the living tree was measured in the range of a mean flow velocity of 5˜15m/s. The drag coefficient of the living tree was less than that of a two-dimensional circular cylinder. Because flow passes through the tree’s crown which has the permeability of branches and leaves, the drag coefficient was decreased as the flow velocity was increased. Moreover, the flexibility is that the bole of a living tree also plays an important role in drag reduction, bending itself so as to decrease the projected area. In the wake behind the living tree, reverse flow was found at further downstream region than the case of a circular cylinder.

An efficient and extensible approach for compressing phylogenetic trees.

PubMed

Matthews, Suzanne J; Williams, Tiffani L

2011-10-18

Biologists require new algorithms to efficiently compress and store their large collections of phylogenetic trees. Our previous work showed that TreeZip is a promising approach for compressing phylogenetic trees. In this paper, we extend our TreeZip algorithm by handling trees with weighted branches. Furthermore, by using the compressed TreeZip file as input, we have designed an extensible decompressor that can extract subcollections of trees, compute majority and strict consensus trees, and merge tree collections using set operations such as union, intersection, and set difference. On unweighted phylogenetic trees, TreeZip is able to compress Newick files in excess of 98%. On weighted phylogenetic trees, TreeZip is able to compress a Newick file by at least 73%. TreeZip can be combined with 7zip with little overhead, allowing space savings in excess of 99% (unweighted) and 92%(weighted). Unlike TreeZip, 7zip is not immune to branch rotations, and performs worse as the level of variability in the Newick string representation increases. Finally, since the TreeZip compressed text (TRZ) file contains all the semantic information in a collection of trees, we can easily filter and decompress a subset of trees of interest (such as the set of unique trees), or build the resulting consensus tree in a matter of seconds. We also show the ease of which set operations can be performed on TRZ files, at speeds quicker than those performed on Newick or 7zip compressed Newick files, and without loss of space savings. TreeZip is an efficient approach for compressing large collections of phylogenetic trees. The semantic and compact nature of the TRZ file allow it to be operated upon directly and quickly, without a need to decompress the original Newick file. We believe that TreeZip will be vital for compressing and archiving trees in the biological community.

7 CFR 1214.3 - Christmas tree.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 7 Agriculture 10 2013-01-01 2013-01-01 false Christmas tree. 1214.3 Section 1214.3 Agriculture... AND ORDERS; MISCELLANEOUS COMMODITIES), DEPARTMENT OF AGRICULTURE CHRISTMAS TREE PROMOTION, RESEARCH, AND INFORMATION ORDER Christmas Tree Promotion, Research, and Information Order Definitions § 1214.3...

7 CFR 1214.3 - Christmas tree.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 7 Agriculture 10 2012-01-01 2012-01-01 false Christmas tree. 1214.3 Section 1214.3 Agriculture... AND ORDERS; MISCELLANEOUS COMMODITIES), DEPARTMENT OF AGRICULTURE CHRISTMAS TREE PROMOTION, RESEARCH, AND INFORMATION ORDER Christmas Tree Promotion, Research, and Information Order Definitions § 1214.3...

7 CFR 1214.3 - Christmas tree.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 7 Agriculture 10 2014-01-01 2014-01-01 false Christmas tree. 1214.3 Section 1214.3 Agriculture... AND ORDERS; MISCELLANEOUS COMMODITIES), DEPARTMENT OF AGRICULTURE CHRISTMAS TREE PROMOTION, RESEARCH, AND INFORMATION ORDER Christmas Tree Promotion, Research, and Information Order Definitions § 1214.3...

Tree injuries from mechanized logging

Treesearch

Richard M. Godman

1992-01-01

Small trees in even-aged northern hardwood stands suffer the most mechanical damage when stands are thinned for the first time. From 15 to 35 percent of the trees may be damaged; a quarter of the trees (but usually less than 20 per acre) can be seriously damaged by having at least 50 square inches of the cambium exposed. Bole damage is most common, followed by root and...

Environmental Fate of Emamectin Benzoate After Tree Micro Injection of Horse Chestnut Trees

PubMed Central

Burkhard, Rene; Binz, Heinz; Roux, Christian A; Brunner, Matthias; Ruesch, Othmar; Wyss, Peter

2015-01-01

Emamectin benzoate, an insecticide derived from the avermectin family of natural products, has a unique translocation behavior in trees when applied by tree micro injection (TMI), which can result in protection from insect pests (foliar and borers) for several years. Active ingredient imported into leaves was measured at the end of season in the fallen leaves of treated horse chestnut (Aesculus hippocastanum) trees. The dissipation of emamectin benzoate in these leaves seems to be biphasic and depends on the decomposition of the leaf. In compost piles, where decomposition of leaves was fastest, a cumulative emamectin benzoate degradation half-life time of 20 d was measured. In leaves immersed in water, where decomposition was much slower, the degradation half-life time was 94 d, and in leaves left on the ground in contact with soil, where decomposition was slowest, the degradation half-life time was 212 d. The biphasic decline and the correlation with leaf decomposition might be attributed to an extensive sorption of emamectin benzoate residues to leaf macromolecules. This may also explain why earthworms ingesting leaves from injected trees take up very little emamectin benzoate and excrete it with the feces. Furthermore, no emamectin benzoate was found in water containing decomposing leaves from injected trees. It is concluded, that emamectin benzoate present in abscised leaves from horse chestnut trees injected with the insecticide is not available to nontarget organisms present in soil or water bodies. Environ Toxicol Chem 2014;9999:1–6. © 2014 The Authors. Published 2014 SETAC PMID:25363584

Regolith properties under trees and the biomechanical effects caused by tree root systems as recognized by electrical resistivity tomography (ERT)

NASA Astrophysics Data System (ADS)

Pawlik, Łukasz; Kasprzak, Marek

2018-01-01

Following previous findings regarding the influence of vascular plants (mainly trees) on weathering, soil production and hillslope stability, in this study, we attempted to test a hypothesis regarding significant impacts of tree root systems on soil and regolith properties. Different types of impacts from tree root system (direct and indirect) are commonly gathered under the key term of "biomechanical effects". To add to the discussion of the biomechanical effects of trees, we used a non-invasive geophysical method, electrical resistivity tomography (ERT), to investigate the profiles of four different configurations at three study sites within the Polish section of the Outer Western Carpathians. At each site, one long profile (up to 189 m) of a large section of a hillslope and three short profiles (up to 19.5 m), that is, microsites occupied by trees or their remnants, were made. Short profiles included the tree root zone of a healthy large tree, the tree stump of a decaying tree and the pit-and-mound topography formed after a tree uprooting. The resistivity of regolith and bedrock presented on the long profiles and in comparison with the short profiles through the microsites it can be seen how tree roots impact soil and regolith properties and add to the complexity of the whole soil/regolith profile. Trees change soil and regolith properties directly through root channels and moisture migration and indirectly through the uprooting of trees and the formation of pit-and-mound topography. Within tree stump microsites, the impact of tree root systems, evaluated by a resistivity model, was smaller compared to microsites with living trees or those with pit-and-mound topography but was still visible even several decades after the trees were windbroken or cut down. The ERT method is highly useful for quick evaluation of the impact of tree root systems on soils and regolith. This method, in contrast to traditional soil analyses, offers a continuous dataset for the entire

Looking/Learning Drawing: Trees.

ERIC Educational Resources Information Center

Hurwitz, Al; Blume, Sharon

1985-01-01

Secondary students are asked to study and compare three reproductions--Van Gogh's "Grove of Cypresses," Da Vinci's "Study of a Tree," and Mondrian's "Tree II." The activity will help students develop their powers of observation and analysis, powers that can be applied to their own drawings. (RM)

Trees for Mother Earth.

ERIC Educational Resources Information Center

Greer, Sandy

1993-01-01

Describes Trees for Mother Earth, a program in which secondary students raise funds to buy fruit trees to plant during visits to the Navajo Reservation. Benefits include developing feelings of self-worth among participants, promoting cultural exchange and understanding, and encouraging self-sufficiency among the Navajo. (LP)

The space of ultrametric phylogenetic trees.

PubMed

Gavryushkin, Alex; Drummond, Alexei J

2016-08-21

The reliability of a phylogenetic inference method from genomic sequence data is ensured by its statistical consistency. Bayesian inference methods produce a sample of phylogenetic trees from the posterior distribution given sequence data. Hence the question of statistical consistency of such methods is equivalent to the consistency of the summary of the sample. More generally, statistical consistency is ensured by the tree space used to analyse the sample. In this paper, we consider two standard parameterisations of phylogenetic time-trees used in evolutionary models: inter-coalescent interval lengths and absolute times of divergence events. For each of these parameterisations we introduce a natural metric space on ultrametric phylogenetic trees. We compare the introduced spaces with existing models of tree space and formulate several formal requirements that a metric space on phylogenetic trees must possess in order to be a satisfactory space for statistical analysis, and justify them. We show that only a few known constructions of the space of phylogenetic trees satisfy these requirements. However, our results suggest that these basic requirements are not enough to distinguish between the two metric spaces we introduce and that the choice between metric spaces requires additional properties to be considered. Particularly, that the summary tree minimising the square distance to the trees from the sample might be different for different parameterisations. This suggests that further fundamental insight is needed into the problem of statistical consistency of phylogenetic inference methods. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

Differences in xylogenesis between dominant and suppressed trees.

PubMed

Liu, Shushan; Li, Xiaoxia; Rossi, Sergio; Wang, Lily; Li, Wei; Liang, Eryuan; Leavitt, Steven W

2018-05-01

Most dendroecological studies focus on dominant trees, but little is known about the growing season of trees belonging to different size classes and their sensitivity to biotic factors. The objective of this study was to compare the dynamics of xylem formation between dominant and suppressed trees of Abies fabri of similar age growing in the Gongga Mountains, southeastern Tibetan Plateau, and to identify the association between xylem growth and climate. The timing and duration of xylogenesis in histological sections were investigated weekly during the 2013-2015 growing seasons. Our investigation found that timing and duration of xylogenesis varied with canopy position and its associated tree size. Xylogenesis started 6-14 days earlier, and ended 5-11 days later in dominant trees than in suppressed trees, resulting in a significantly longer growing season. Dominant trees also exhibited higher temperature sensitivity of tracheid production rate than suppressed trees. The observed differences in xylogenesis among trees suggested that competition affects tree growth by reducing the growing period in suppressed trees. Representative climate-growth relationships should involve trees of all size classes when evaluating the effects of the environment on forest dynamics. © 2018 Botanical Society of America.

75 FR 25103 - Tree Assistance Program

Federal Register 2010, 2011, 2012, 2013, 2014

2010-05-07

... 1416 RIN 0560-AH96 Tree Assistance Program AGENCY: Farm Service Agency and Commodity Credit Corporation, USDA. ACTION: Final rule. SUMMARY: This rule implements specific requirements for the Tree Assistance... provides disaster assistance to eligible orchardists and nursery tree growers to replant or rehabilitate...

Genomics of Tropical Fruit Tree Crops

USDA-ARS?s Scientific Manuscript database

The genetic improvement of tropical fruit trees is limited when compared to progress achieved in temperate fruit trees and annual crops. Tropical fruit tree breeding programs require significant resources to develop new cultivars that are adapted to modern shipping and storage requirements. The use...

TreeQ-VISTA: An Interactive Tree Visualization Tool withFunctional Annotation Query Capabilities

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

Gu, Shengyin; Anderson, Iain; Kunin, Victor

2007-05-07

Summary: We describe a general multiplatform exploratorytool called TreeQ-Vista, designed for presenting functional annotationsin a phylogenetic context. Traits, such as phenotypic and genomicproperties, are interactively queried from a relational database with auser-friendly interface which provides a set of tools for users with orwithout SQL knowledge. The query results are projected onto aphylogenetic tree and can be displayed in multiple color groups. A richset of browsing, grouping and query tools are provided to facilitatetrait exploration, comparison and analysis.Availability: The program,detailed tutorial and examples are available online athttp://genome-test.lbl.gov/vista/TreeQVista.

Objective consensus from decision trees.

PubMed

Putora, Paul Martin; Panje, Cedric M; Papachristofilou, Alexandros; Dal Pra, Alan; Hundsberger, Thomas; Plasswilm, Ludwig

2014-12-05

Consensus-based approaches provide an alternative to evidence-based decision making, especially in situations where high-level evidence is limited. Our aim was to demonstrate a novel source of information, objective consensus based on recommendations in decision tree format from multiple sources. Based on nine sample recommendations in decision tree format a representative analysis was performed. The most common (mode) recommendations for each eventuality (each permutation of parameters) were determined. The same procedure was applied to real clinical recommendations for primary radiotherapy for prostate cancer. Data was collected from 16 radiation oncology centres, converted into decision tree format and analyzed in order to determine the objective consensus. Based on information from multiple sources in decision tree format, treatment recommendations can be assessed for every parameter combination. An objective consensus can be determined by means of mode recommendations without compromise or confrontation among the parties. In the clinical example involving prostate cancer therapy, three parameters were used with two cut-off values each (Gleason score, PSA, T-stage) resulting in a total of 27 possible combinations per decision tree. Despite significant variations among the recommendations, a mode recommendation could be found for specific combinations of parameters. Recommendations represented as decision trees can serve as a basis for objective consensus among multiple parties.

snpTree--a web-server to identify and construct SNP trees from whole genome sequence data.

PubMed

Leekitcharoenphon, Pimlapas; Kaas, Rolf S; Thomsen, Martin Christen Frølund; Friis, Carsten; Rasmussen, Simon; Aarestrup, Frank M

2012-01-01

The advances and decreasing economical cost of whole genome sequencing (WGS), will soon make this technology available for routine infectious disease epidemiology. In epidemiological studies, outbreak isolates have very little diversity and require extensive genomic analysis to differentiate and classify isolates. One of the successfully and broadly used methods is analysis of single nucletide polymorphisms (SNPs). Currently, there are different tools and methods to identify SNPs including various options and cut-off values. Furthermore, all current methods require bioinformatic skills. Thus, we lack a standard and simple automatic tool to determine SNPs and construct phylogenetic tree from WGS data. Here we introduce snpTree, a server for online-automatic SNPs analysis. This tool is composed of different SNPs analysis suites, perl and python scripts. snpTree can identify SNPs and construct phylogenetic trees from WGS as well as from assembled genomes or contigs. WGS data in fastq format are aligned to reference genomes by BWA while contigs in fasta format are processed by Nucmer. SNPs are concatenated based on position on reference genome and a tree is constructed from concatenated SNPs using FastTree and a perl script. The online server was implemented by HTML, Java and python script.The server was evaluated using four published bacterial WGS data sets (V. cholerae, S. aureus CC398, S. Typhimurium and M. tuberculosis). The evaluation results for the first three cases was consistent and concordant for both raw reads and assembled genomes. In the latter case the original publication involved extensive filtering of SNPs, which could not be repeated using snpTree. The snpTree server is an easy to use option for rapid standardised and automatic SNP analysis in epidemiological studies also for users with limited bioinformatic experience. The web server is freely accessible at http://www.cbs.dtu.dk/services/snpTree-1.0/.

Reconciliation of Gene and Species Trees

PubMed Central

Rusin, L. Y.; Lyubetskaya, E. V.; Gorbunov, K. Y.; Lyubetsky, V. A.

2014-01-01

The first part of the paper briefly overviews the problem of gene and species trees reconciliation with the focus on defining and algorithmic construction of the evolutionary scenario. Basic ideas are discussed for the aspects of mapping definitions, costs of the mapping and evolutionary scenario, imposing time scales on a scenario, incorporating horizontal gene transfers, binarization and reconciliation of polytomous trees, and construction of species trees and scenarios. The review does not intend to cover the vast diversity of literature published on these subjects. Instead, the authors strived to overview the problem of the evolutionary scenario as a central concept in many areas of evolutionary research. The second part provides detailed mathematical proofs for the solutions of two problems: (i) inferring a gene evolution along a species tree accounting for various types of evolutionary events and (ii) trees reconciliation into a single species tree when only gene duplications and losses are allowed. All proposed algorithms have a cubic time complexity and are mathematically proved to find exact solutions. Solving algorithms for problem (ii) can be naturally extended to incorporate horizontal transfers, other evolutionary events, and time scales on the species tree. PMID:24800245

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

PubMed

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

2018-01-01

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

How To Select and Plant a Tree.

ERIC Educational Resources Information Center

Fazio, James R., Ed.

1991-01-01

This bulletin furnishes information about selecting and planting trees. The tree selection process includes being aware of the physical characteristics of bare root seedlings, containerized seedlings, balled and burlapped, or potted trees and determining the proper size and root ball proportions. The section on tree planting discusses how to: (1)…

Single-tree nut immunotherapy attenuates allergic reactions in mice with hypersensitivity to multiple tree nuts.

PubMed

Kulis, Mike; Li, Yifan; Lane, Hannah; Pons, Laurent; Burks, Wesley

2011-01-01

Allergic reactions to tree nuts are often severe and are outgrown in less than 10% of diagnosed patients. To determine whether treatment of underlying tree nut sensitization will prevent allergic reactions to cross-reacting tree nuts and to determine the effects of single-tree nut immunotherapy on true multi-tree nut sensitization. Cross-reactivity model: Cashew-sensitized mice underwent immunotherapy with cashew and were subsequently challenged with cashew and pistachio. Multisensitization model: Cashew plus walnut-sensitized mice were treated with cashew alone, walnut alone, or both cashew and walnut and then underwent challenges to cashew and walnut. Challenges were assessed on the basis of symptoms, changes in body temperature, and mouse mast cell protease-1 release. In the cross-reactivity model, cashew immunotherapy completely prevented allergic reactions on challenges with cashew or the cross-reactive pistachio. In the multisensitization model, mice with cashew plus walnut allergy were significantly protected from anaphylactic reactions on cashew challenge in both the cashew-alone and walnut-alone immunotherapy groups. Results from the walnut challenge demonstrated significantly decreased allergic responses in the walnut immunotherapy group, whereas mice in the cashew immunotherapy group experienced significantly lower symptoms. In the cross-reactivity model, immunotherapy effectively decreased IL-4 and IL-5 production and increased IL-12 relative to placebo while also inducing a 5-fold increase in specific IgG(1). Single-tree nut immunotherapy can effectively decrease allergic responses in both the cross-reactivity and multisensitization mouse models. Further studies are needed to determine which single-tree nut immunotherapies will be most effective for specific multi-tree nut allergy profiles. Copyright © 2010 American Academy of Allergy, Asthma & Immunology. Published by Mosby, Inc. All rights reserved.

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.

Clustering Tree-structured Data on Manifold

PubMed Central

Lu, Na; Miao, Hongyu

2016-01-01

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

An efficient and extensible approach for compressing phylogenetic trees

PubMed Central

2011-01-01

Background Biologists require new algorithms to efficiently compress and store their large collections of phylogenetic trees. Our previous work showed that TreeZip is a promising approach for compressing phylogenetic trees. In this paper, we extend our TreeZip algorithm by handling trees with weighted branches. Furthermore, by using the compressed TreeZip file as input, we have designed an extensible decompressor that can extract subcollections of trees, compute majority and strict consensus trees, and merge tree collections using set operations such as union, intersection, and set difference. Results On unweighted phylogenetic trees, TreeZip is able to compress Newick files in excess of 98%. On weighted phylogenetic trees, TreeZip is able to compress a Newick file by at least 73%. TreeZip can be combined with 7zip with little overhead, allowing space savings in excess of 99% (unweighted) and 92%(weighted). Unlike TreeZip, 7zip is not immune to branch rotations, and performs worse as the level of variability in the Newick string representation increases. Finally, since the TreeZip compressed text (TRZ) file contains all the semantic information in a collection of trees, we can easily filter and decompress a subset of trees of interest (such as the set of unique trees), or build the resulting consensus tree in a matter of seconds. We also show the ease of which set operations can be performed on TRZ files, at speeds quicker than those performed on Newick or 7zip compressed Newick files, and without loss of space savings. Conclusions TreeZip is an efficient approach for compressing large collections of phylogenetic trees. The semantic and compact nature of the TRZ file allow it to be operated upon directly and quickly, without a need to decompress the original Newick file. We believe that TreeZip will be vital for compressing and archiving trees in the biological community. PMID:22165819

Can live tree size-density relationships provide a mechanism for predicting down and dead tree resources?

Treesearch

Christopher Woodall; James Westfall

2009-01-01

Live tree size-density relationships in forests have long provided a framework for understanding stand dynamics. There has been little examination of the relationship between the size-density attributes of live and standing/down dead trees (e.g., number and mean tree size per unit area, such information could help in large-scale efforts to estimate dead wood resources...

Object-based methods for individual tree identification and tree species classification from high-spatial resolution imagery

NASA Astrophysics Data System (ADS)

Wang, Le

2003-10-01

Modern forest management poses an increasing need for detailed knowledge of forest information at different spatial scales. At the forest level, the information for tree species assemblage is desired whereas at or below the stand level, individual tree related information is preferred. Remote Sensing provides an effective tool to extract the above information at multiple spatial scales in the continuous time domain. To date, the increasing volume and readily availability of high-spatial-resolution data have lead to a much wider application of remotely sensed products. Nevertheless, to make effective use of the improving spatial resolution, conventional pixel-based classification methods are far from satisfactory. Correspondingly, developing object-based methods becomes a central challenge for researchers in the field of Remote Sensing. This thesis focuses on the development of methods for accurate individual tree identification and tree species classification. We develop a method in which individual tree crown boundaries and treetop locations are derived under a unified framework. We apply a two-stage approach with edge detection followed by marker-controlled watershed segmentation. Treetops are modeled from radiometry and geometry aspects. Specifically, treetops are assumed to be represented by local radiation maxima and to be located near the center of the tree-crown. As a result, a marker image was created from the derived treetop to guide a watershed segmentation to further differentiate overlapping trees and to produce a segmented image comprised of individual tree crowns. The image segmentation method developed achieves a promising result for a 256 x 256 CASI image. Then further effort is made to extend our methods to the multiscales which are constructed from a wavelet decomposition. A scale consistency and geometric consistency are designed to examine the gradients along the scale-space for the purpose of separating true crown boundary from unwanted

The impact of tree age on biomass growth and carbon accumulation capacity: A retrospective analysis using tree ring data of three tropical tree species grown in natural forests of Suriname

PubMed Central

Neupane, Prem R.

2017-01-01

The world’s forests play a pivotal role in the mitigation of global climate change. By photosynthesis they remove CO2 from the atmosphere and store carbon in their biomass. While old trees are generally acknowledged for a long carbon residence time, there is no consensus on their contribution to carbon accumulation due to a lack of long-term individual tree data. Tree ring analyses, which use anatomical differences in the annual formation of wood for dating growth zones, are a retrospective approach that provides growth patterns of individual trees over their entire lifetime. We developed time series of diameter growth and related annual carbon accumulation for 61 trees of the species Cedrela odorata L. (Meliacea), Hymenaea courbaril L. (Fabacea) and Goupia glabra Aubl. (Goupiacea). The trees grew in unmanaged tropical wet-forests of Suriname and reached ages from 84 to 255 years. Most of the trees show positive trends of diameter growth and carbon accumulation over time. For some trees we observed fluctuating growth—periods of lower growth alternate with periods of increased growth. In the last quarter of their lifetime trees accumulate on average between 39 percent (C. odorata) and 50 percent (G. glabra) of their final carbon stock. This suggests that old-growth trees in tropical forests do not only contribute to carbon stocks by long carbon resistance times, but maintain high rates of carbon accumulation at later stages of their life time. PMID:28813429

The impact of tree age on biomass growth and carbon accumulation capacity: A retrospective analysis using tree ring data of three tropical tree species grown in natural forests of Suriname.

PubMed

Köhl, Michael; Neupane, Prem R; Lotfiomran, Neda

2017-01-01

The world's forests play a pivotal role in the mitigation of global climate change. By photosynthesis they remove CO2 from the atmosphere and store carbon in their biomass. While old trees are generally acknowledged for a long carbon residence time, there is no consensus on their contribution to carbon accumulation due to a lack of long-term individual tree data. Tree ring analyses, which use anatomical differences in the annual formation of wood for dating growth zones, are a retrospective approach that provides growth patterns of individual trees over their entire lifetime. We developed time series of diameter growth and related annual carbon accumulation for 61 trees of the species Cedrela odorata L. (Meliacea), Hymenaea courbaril L. (Fabacea) and Goupia glabra Aubl. (Goupiacea). The trees grew in unmanaged tropical wet-forests of Suriname and reached ages from 84 to 255 years. Most of the trees show positive trends of diameter growth and carbon accumulation over time. For some trees we observed fluctuating growth-periods of lower growth alternate with periods of increased growth. In the last quarter of their lifetime trees accumulate on average between 39 percent (C. odorata) and 50 percent (G. glabra) of their final carbon stock. This suggests that old-growth trees in tropical forests do not only contribute to carbon stocks by long carbon resistance times, but maintain high rates of carbon accumulation at later stages of their life time.

The gravity apple tree

NASA Astrophysics Data System (ADS)

Espinosa Aldama, Mariana

2015-04-01

The gravity apple tree is a genealogical tree of the gravitation theories developed during the past century. The graphic representation is full of information such as guides in heuristic principles, names of main proponents, dates and references for original articles (See under Supplementary Data for the graphic representation). This visual presentation and its particular classification allows a quick synthetic view for a plurality of theories, many of them well validated in the Solar System domain. Its diachronic structure organizes information in a shape of a tree following similarities through a formal concept analysis. It can be used for educational purposes or as a tool for philosophical discussion.

Relationships between tree size, crown shape, gender segregation and sex allocation in Pinus halepensis, a Mediterranean pine tree.

PubMed

Ne'eman, Gidi; Goubitz, Shirrinka; Werger, Marinus J A; Shmida, Avi

2011-07-01

Sex allocation has been studied mainly in small herbaceous plants but much less in monoecious wind-pollinated trees. The aim of this study was to explore changes in gender segregation and sex allocation by Pinus halepensis, a Mediterranean lowland pine tree, within tree crowns and between trees differing in their size or crown shape. The production of new male and female cones and sex allocation of biomass, nitrogen and phosphorus were studied. The relationship between branch location, its reproductive status and proxies of branch vigour was also studied. Small trees produced only female cones, but, as trees grew, they produced both male and female cones. Female cones were produced mainly in the upper part of the crown, and male cones in its middle and lower parts. Lateral branch density was correlated with the number of male but not female cones; lateral branches were more dense in large than in small trees and even denser in hemispherical trees. Apical branches grew faster, were thicker and their phosphorus concentration was higher than in lateral shoots. Nitrogen concentration was higher in cone-bearing apical branches than in apical vegetative branches and in lateral branches with or without cones. Allocation to male relative to female function increased with tree size as predicted by sex allocation theory. The adaptive values of sex allocation and gender segregation patterns in P. halepensis, in relation to its unique life history, are demonstrated and discussed. Small trees produce only female cones that have a higher probability of being pollinated than the probability of male cones pollinating; the female-first strategy enhances population spread. Hemispherical old trees are loaded with serotinous cones that supply enough seeds for post-fire germination; thus, allocation to males is more beneficial than to females.

Trees as templates for tropical litter arthropod diversity.

PubMed

Donoso, David A; Johnston, Mary K; Kaspari, Michael

2010-09-01

Increased tree species diversity in the tropics is associated with even greater herbivore diversity, but few tests of tree effects on litter arthropod diversity exist. We studied whether tree species influence patchiness in diversity and abundance of three common soil arthropod taxa (ants, gamasid mites, and oribatid mites) in a Panama forest. The tree specialization hypothesis proposes that tree-driven habitat heterogeneity maintains litter arthropod diversity. We tested whether tree species differed in resource quality and quantity of their leaf litter and whether more heterogeneous litter supports more arthropod species. Alternatively, the abundance-extinction hypothesis states that arthropod diversity increases with arthropod abundance, which in turn tracks resource quantity (e.g., litter depth). We found little support for the hypothesis that tropical trees are templates for litter arthropod diversity. Ten tree species differed in litter depth, chemistry, and structural variability. However, the extent of specialization of invertebrates on particular tree taxa was low and the more heterogeneous litter between trees failed to support higher arthropod diversity. Furthermore, arthropod diversity did not track abundance or litter depth. The lack of association between tree species and litter arthropods suggests that factors other than tree species diversity may better explain the high arthropod diversity in tropical forests.

Tree biology and dendrochemistry

Treesearch

Kevin T. Smith; Walter C. Shortle

1996-01-01

Dendrochemistry, the interpretation of elemental analysis of dated tree rings, can provide a temporal record of environmental change. Using the dendrochemical record requires an understanding of tree biology. In this review, we pose four questions concerning assumptions that underlie recent dendrochemical research: 1) Does the chemical composition of the wood directly...

Does predation contribute to tree diversity?

Treesearch

Brian Beckage; James S. Clark

2005-01-01

Seed and seedling predation may differentially affect competitively superior tree species to increase the relative recruitment success of poor competitors and contribute to the coexistence of tree species. We examined the effect of seed and seedling predation on the seedling recruitment of three tree species, Acer rubrum (red maple), ...

Tree biomass in the Swiss landscape: nationwide modelling for improved accounting for forest and non-forest trees.

PubMed

Price, B; Gomez, A; Mathys, L; Gardi, O; Schellenberger, A; Ginzler, C; Thürig, E

2017-03-01

Trees outside forest (TOF) can perform a variety of social, economic and ecological functions including carbon sequestration. However, detailed quantification of tree biomass is usually limited to forest areas. Taking advantage of structural information available from stereo aerial imagery and airborne laser scanning (ALS), this research models tree biomass using national forest inventory data and linear least-square regression and applies the model both inside and outside of forest to create a nationwide model for tree biomass (above ground and below ground). Validation of the tree biomass model against TOF data within settlement areas shows relatively low model performance (R 2 of 0.44) but still a considerable improvement on current biomass estimates used for greenhouse gas inventory and carbon accounting. We demonstrate an efficient and easily implementable approach to modelling tree biomass across a large heterogeneous nationwide area. The model offers significant opportunity for improved estimates on land use combination categories (CC) where tree biomass has either not been included or only roughly estimated until now. The ALS biomass model also offers the advantage of providing greater spatial resolution and greater within CC spatial variability compared to the current nationwide estimates.

A whole-tree chamber system for examining tree-level physiological responses of field-grown trees to environmental variation and climate change.

PubMed

Medhurst, Jane; Parsby, Jan; Linder, Sune; Wallin, Göran; Ceschia, Eric; Slaney, Michelle

2006-09-01

A whole-tree chamber (WTC) system was installed at Flakaliden in northern Sweden to examine the long-term physiological responses of field-grown 40-year-old Norway spruce trees [Picea abies (L.) Karst.] to climate change. The WTCs were designed as large cuvettes to allow the net tree-level CO(2) and water fluxes to be measured on a continuous basis. A total of 12 WTCs were used to impose combinations of atmospheric carbon dioxide concentration, [CO(2)], and air temperature treatments. The air inside the ambient and elevated [CO(2)] WTCs was maintained at 365 and 700 micromol mol(-1), respectively. The air temperature inside the ambient temperature WTCs tracked air temperature outside the WTCs. Elevated temperatures were altered on a monthly time-step and ranged between +2.8 and +5.6 degrees C above ambient temperature. The system allowed continuous, long-term measurement of whole-tree photosynthesis, night-time respiration and transpiration. The performance of the WTCs was assessed using winter and spring data sets. The ability of the WTC system to measure tree-level physiological responses is demonstrated. All WTCs displayed a high level of control over tracking of air temperatures. The set target of 365 micromol mol(-1) in the ambient [CO(2)] chambers was too low to be maintained during winter because of tree dormancy and the high natural increase in [CO(2)] over winter at high latitudes such as the Flakaliden site. Accurate control over [CO(2)] in the ambient [CO(2)] chambers was restored during the spring and the system maintained the elevated [CO(2)] target of 700 micromol mol(-1) for both measurement periods. Air water vapour deficit (VPD) was accurately tracked in ambient temperature WTCs. However, as water vapour pressure in all 12 WTCs was maintained at the level of non-chambered (reference) air, VPD of elevated temperature WTCs was increased.

7 CFR 1437.306 - Christmas tree crops.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 7 Agriculture 10 2010-01-01 2010-01-01 false Christmas tree crops. 1437.306 Section 1437.306... Determining Coverage Using Value § 1437.306 Christmas tree crops. (a) A Christmas tree is a value loss crop and may generate a claim for benefits under this part only if the tree was grown exclusively for...

Molecular basis of angiosperm tree architecture.

PubMed

Hollender, Courtney A; Dardick, Chris

2015-04-01

The architecture of trees greatly impacts the productivity of orchards and forestry plantations. Amassing greater knowledge on the molecular genetics that underlie tree form can benefit these industries, as well as contribute to basic knowledge of plant developmental biology. This review describes the fundamental components of branch architecture, a prominent aspect of tree structure, as well as genetic and hormonal influences inferred from studies in model plant systems and from trees with non-standard architectures. The bulk of the molecular and genetic data described here is from studies of fruit trees and poplar, as these species have been the primary subjects of investigation in this field of science. No claim to original US Government works. New Phytologist © 2014 New Phytologist Trust.

Surveying Dead Trees and CO2-Induced Stressed Trees Using AVIRIS in the Long Valley Caldera

NASA Technical Reports Server (NTRS)

deJong, Steven M.

1996-01-01

Since 1980 the Long Valley Caldera in the eastern Sierra Nevada (California) has shown signs of renewed volcanic activity. Frequent earthquakes, a re-inflation of the caldera, hydrothermal activity and gas emissions are the outer symptoms of this renewed activity. In 1990 and 1991 several areas of dying trees were found around Mammoth Mountain. The cause of the die off of the trees was first sought in the persistent drought in the preceding years. However, the trees died regardless of age and species. Farrar et al. (1995) started a soil-gas survey in 1994 in the dead-tree areas and found carbon dioxide concentrations ranging from 30 to 96% at soil depths between 30 and 60 cm. CO2 concentrations in the atmosphere are usually around 0.03% and in the soil profile CO2 levels do commonly not exceed 4 to 5%. Although not much is known about the effect of high levels of carbon dioxide in the soil profile on roots, it is most likely that the trees are dying due to oxygen deprivation: the CO2 drives the oxygen out of the soil. So far, four sites of dead trees have been mapped around Mammoth Mountain. The two largest dying trees sites are located near Horseshoe Lake and near Mammoth Mountain Main Lodge covering approximately an area of 10 and 8 ha respectively. Analysis of the gas composition regarding the He-3/He-4 ratio and the percentage biogenic carbon reveals the source of the gas: the magma body beneath the Long Valley Caldera. Until recently it was not known that volcanoes release abundant carbon dioxide from their flanks as diffuse soil emanations. As a result of the magma gas emission around Mammoth Mountain there is an excellent sequence of dead trees, stressed trees, healthy trees and bare soil surfaces. This research site provides excellent opportunities to: (1) Study the capabilities of imaging spectrometry to map stressed (and dead) pine and fir species; (2) Study methods to separate the vivid vegetation, stressed vegetation and dead vegetation from the soil

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

PubMed Central

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

2018-01-01

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

Decision tree modeling using R.

PubMed

Zhang, Zhongheng

2016-08-01

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

Whole-tree water transport scales with sapwood capacitance in tropical forest canopy trees.

Treesearch

F.C. Meinzer; S.A. James; G. Goldstein; D. Woodruff

2003-01-01

The present study examines the manner in which several whole-tree water transport properties scale with species specific variation in sapwood water storage capacity. The hypothesis that constraints on relationships between sapwood capacitance and other water relations characteristics lead to predictable scaling relationships between intrinsic capacitance and whole-tree...

Modeling Caribbean tree stem diameters from tree height and crown width measurements

Treesearch

Thomas Brandeis; KaDonna Randolph; Mike Strub

2009-01-01

Regression models to predict diameter at breast height (DBH) as a function of tree height and maximum crown radius were developed for Caribbean forests based on data collected by the U.S. Forest Service in the Commonwealth of Puerto Rico and Territory of the U.S. Virgin Islands. The model predicting DBH from tree height fit reasonably well (R2 = 0.7110), with...

Field guide to red tree vole nests

Treesearch

Damon B. Lesmeister; James K. Swingle

2017-01-01

Surveys for red tree vole (Arborimus longicaudus) nests require tree climbing because the species is a highly specialized arboreal rodent that live in the tree canopy of coniferous forests in western Oregon and northwestern California. Tree voles are associated with old coniferous forest (≥80 years old) that are structurally complex, but are often...

Visualization of time-varying natural tree data

Treesearch

S. Brasch; L. Linsen; E.G. McPherson

2007-01-01

Given a set of global (natural) tree parameters measured for many specimens of different ages for a range of species, we have developed a tool that visualizes these parameters over time. The parameters include measures of tree dimensions like heights, diameters, and crown shape, and measures of costs and benefits for growing the tree. We visualize the tree dimensions...

7 CFR 1437.306 - Christmas tree crops.

Code of Federal Regulations, 2014 CFR

2014-01-01

... commercial use as a Christmas tree, and only if other requirements of this section are met. (b) The unit of... 7 Agriculture 10 2014-01-01 2014-01-01 false Christmas tree crops. 1437.306 Section 1437.306... Determining Coverage Using Value § 1437.306 Christmas tree crops. (a) A Christmas tree is a value loss crop...

7 CFR 1437.306 - Christmas tree crops.

Code of Federal Regulations, 2013 CFR

2013-01-01

... commercial use as a Christmas tree, and only if other requirements of this section are met. (b) The unit of... 7 Agriculture 10 2013-01-01 2013-01-01 false Christmas tree crops. 1437.306 Section 1437.306... Determining Coverage Using Value § 1437.306 Christmas tree crops. (a) A Christmas tree is a value loss crop...

7 CFR 1437.306 - Christmas tree crops.

Code of Federal Regulations, 2011 CFR

2011-01-01

... commercial use as a Christmas tree, and only if other requirements of this section are met. (b) The unit of... 7 Agriculture 10 2011-01-01 2011-01-01 false Christmas tree crops. 1437.306 Section 1437.306... Determining Coverage Using Value § 1437.306 Christmas tree crops. (a) A Christmas tree is a value loss crop...

7 CFR 1437.306 - Christmas tree crops.

Code of Federal Regulations, 2012 CFR

2012-01-01

... commercial use as a Christmas tree, and only if other requirements of this section are met. (b) The unit of... 7 Agriculture 10 2012-01-01 2012-01-01 false Christmas tree crops. 1437.306 Section 1437.306... Determining Coverage Using Value § 1437.306 Christmas tree crops. (a) A Christmas tree is a value loss crop...

The '06 trap trees in '07

Treesearch

Andrea C. Anulewicz; Deborah G. McCullough; Therese M. Poland; David Cappaert

2008-01-01

To date, use of girdled trap trees remain the most effective method employed by regulatory and resource management agencies for detecting low-density populations of emerald ash borer (EAB), Agrilus planipennis Fairmaire. Locating suitable trees can be difficult, and felling and debarking trap trees is expensive. Alternative options for EAB detection...

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…

California tree seed zones

Treesearch

John M. Buck; Ronald S. Adams; Jerrold Cone; M. Thompson Conkle; William J. Libby; Cecil J. Eden; Michel J. Knight

1970-01-01

California forest tree seed zones were established originally by Fowells (1946), with revisions proposed by Roy (1963) and Schubert (1966). The Forest Tree Seed Committee of the Northern California Section, Society of American Foresters, has revised the original zones and updated the recording system described in the earlier reports. Fowells' (1946) Research Note...

The tree BVOC index

Treesearch

J.R. Simpson; E.G. McPherson

2011-01-01

Urban trees can produce a number of benefits, among them improved air quality. Biogenic volatile organic compounds (BVOCs) emitted by some species are ozone precursors. Modifying future tree planting to favor lower-emitting species can reduce these emissions and aid air management districts in meeting federally mandated emissions reductions for these compounds. Changes...

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

Uncertain decision tree inductive inference

NASA Astrophysics Data System (ADS)

Zarban, L.; Jafari, S.; Fakhrahmad, S. M.

2011-10-01

Induction is the process of reasoning in which general rules are formulated based on limited observations of recurring phenomenal patterns. Decision tree learning is one of the most widely used and practical inductive methods, which represents the results in a tree scheme. Various decision tree algorithms have already been proposed such as CLS, ID3, Assistant C4.5, REPTree and Random Tree. These algorithms suffer from some major shortcomings. In this article, after discussing the main limitations of the existing methods, we introduce a new decision tree induction algorithm, which overcomes all the problems existing in its counterparts. The new method uses bit strings and maintains important information on them. This use of bit strings and logical operation on them causes high speed during the induction process. Therefore, it has several important features: it deals with inconsistencies in data, avoids overfitting and handles uncertainty. We also illustrate more advantages and the new features of the proposed method. The experimental results show the effectiveness of the method in comparison with other methods existing in the literature.

Nitrogen nutrition of poplar trees.

PubMed

Rennenberg, H; Wildhagen, H; Ehlting, B

2010-03-01

Many forest ecosystems have evolved at sites with growth-limiting nitrogen (N) availability, low N input from external sources and high ecosystem internal cycling of N. By contrast, many poplar species are frequent constituents of floodplain forests where they are exposed to a significant ecosystem external supply of N, mainly nitrate, in the moving water table. Therefore, nitrate is much more important for N nutrition of these poplar species than for many other tree species. We summarise current knowledge of nitrate uptake and its regulation by tree internal signals, as well as acquisition of ammonium and organic N from the soil. Unlike herbaceous plants, N nutrition of trees is sustained by seasonal, tree internal cycling. Recent advances in the understanding of seasonal storage and mobilisation in poplar bark and regulation of these processes by temperature and daylength are addressed. To explore consequences of global climate change on N nutrition of poplar trees, responses of N uptake and metabolism to increased atmospheric CO(2) and O(3) concentrations, increased air and soil temperatures, drought and salt stress are highlighted.

Clarifying the effects of dwarfing rootstock on vegetative and reproductive growth during tree development: a study on apple trees.

PubMed

Costes, E; García-Villanueva, E

2007-08-01

Despite the widespread use of dwarfing rootstocks in the fruit-tree industry, their impact on tree architectural development and possible role in the within-tree balance between growth and flowering are still poorly understood, in particular during the early years of growth. The present study addressed this question in apple trees, through a detailed analysis of shoot populations, i.e. both vegetative and flowering shoots, during tree development. Architectural databases were constructed for trees of two cultivars that were either own-rooted or grafted on dwarfing rootstock. Within-tree shoot demographics and annual shoot characteristics, i.e. their dimensions, number of laterals and flowering, were observed from the first to the fifth year of growth and compared among scion/root system combinations. Differences in axis demographics appeared among scion/root system combinations after the second year of growth. Differences were found (a) in the number of long axes and (b) the number of medium axes. Dwarfing rootstock reduced the total number of axes developed in a tree, and this reduction resulted from proportionally more medium axes and spurs than long axes. The life span of spurs was also shortened. These phenomena appeared after an increase in flowering that started in the second year of growth and involved both axillary and terminal positions. Flowering regularity was also increased in grafted trees. These results confirm that the number of long shoots and flowering potential depend on the cultivar. They indicate that tree architectural plasticity in response to its root system mainly derives from the number of medium shoots developed and follows priorities within the whole tree axis population. There was also evidence for dwarfing rootstock involvement in adjusting the flowering abundance and that differences in flowering occurrence take precedence over those regarding vegetative growth during tree development.

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

PubMed

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

2016-01-01

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

Tree-Structured Infinite Sparse Factor Model

PubMed Central

Zhang, XianXing; Dunson, David B.; Carin, Lawrence

2013-01-01

A tree-structured multiplicative gamma process (TMGP) is developed, for inferring the depth of a tree-based factor-analysis model. This new model is coupled with the nested Chinese restaurant process, to nonparametrically infer the depth and width (structure) of the tree. In addition to developing the model, theoretical properties of the TMGP are addressed, and a novel MCMC sampler is developed. The structure of the inferred tree is used to learn relationships between high-dimensional data, and the model is also applied to compressive sensing and interpolation of incomplete images. PMID:25279389

Analyzing and synthesizing phylogenies using tree alignment graphs.

PubMed

Smith, Stephen A; Brown, Joseph W; Hinchliff, Cody E

2013-01-01

Phylogenetic trees are used to analyze and visualize evolution. However, trees can be imperfect datatypes when summarizing multiple trees. This is especially problematic when accommodating for biological phenomena such as horizontal gene transfer, incomplete lineage sorting, and hybridization, as well as topological conflict between datasets. Additionally, researchers may want to combine information from sets of trees that have partially overlapping taxon sets. To address the problem of analyzing sets of trees with conflicting relationships and partially overlapping taxon sets, we introduce methods for aligning, synthesizing and analyzing rooted phylogenetic trees within a graph, called a tree alignment graph (TAG). The TAG can be queried and analyzed to explore uncertainty and conflict. It can also be synthesized to construct trees, presenting an alternative to supertrees approaches. We demonstrate these methods with two empirical datasets. In order to explore uncertainty, we constructed a TAG of the bootstrap trees from the Angiosperm Tree of Life project. Analysis of the resulting graph demonstrates that areas of the dataset that are unresolved in majority-rule consensus tree analyses can be understood in more detail within the context of a graph structure, using measures incorporating node degree and adjacency support. As an exercise in synthesis (i.e., summarization of a TAG constructed from the alignment trees), we also construct a TAG consisting of the taxonomy and source trees from a recent comprehensive bird study. We synthesized this graph into a tree that can be reconstructed in a repeatable fashion and where the underlying source information can be updated. The methods presented here are tractable for large scale analyses and serve as a basis for an alternative to consensus tree and supertree methods. Furthermore, the exploration of these graphs can expose structures and patterns within the dataset that are otherwise difficult to observe.

Analyzing and Synthesizing Phylogenies Using Tree Alignment Graphs

PubMed Central

Smith, Stephen A.; Brown, Joseph W.; Hinchliff, Cody E.

2013-01-01

Phylogenetic trees are used to analyze and visualize evolution. However, trees can be imperfect datatypes when summarizing multiple trees. This is especially problematic when accommodating for biological phenomena such as horizontal gene transfer, incomplete lineage sorting, and hybridization, as well as topological conflict between datasets. Additionally, researchers may want to combine information from sets of trees that have partially overlapping taxon sets. To address the problem of analyzing sets of trees with conflicting relationships and partially overlapping taxon sets, we introduce methods for aligning, synthesizing and analyzing rooted phylogenetic trees within a graph, called a tree alignment graph (TAG). The TAG can be queried and analyzed to explore uncertainty and conflict. It can also be synthesized to construct trees, presenting an alternative to supertrees approaches. We demonstrate these methods with two empirical datasets. In order to explore uncertainty, we constructed a TAG of the bootstrap trees from the Angiosperm Tree of Life project. Analysis of the resulting graph demonstrates that areas of the dataset that are unresolved in majority-rule consensus tree analyses can be understood in more detail within the context of a graph structure, using measures incorporating node degree and adjacency support. As an exercise in synthesis (i.e., summarization of a TAG constructed from the alignment trees), we also construct a TAG consisting of the taxonomy and source trees from a recent comprehensive bird study. We synthesized this graph into a tree that can be reconstructed in a repeatable fashion and where the underlying source information can be updated. The methods presented here are tractable for large scale analyses and serve as a basis for an alternative to consensus tree and supertree methods. Furthermore, the exploration of these graphs can expose structures and patterns within the dataset that are otherwise difficult to observe. PMID:24086118

Epicormic branching on hardwood trees bordering forest openings

Treesearch

G.R., Jr. Trimble; Donald W. Seegrist; Donald W. Seegrist

1973-01-01

Epicormic branching in hardwoods can degrade logs and reduce the dollar returns from growing trees. A study made around clearcut openings of various sizes showed that the following variables were related to the degree of epicormic branching on trees bordering the openings: size of opening, species, tree dominance class, exposure of tree bole, and position on tree bole...

Do trees smart from ozone

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

Not Available

Douglas-firs near Eatonville, Washington - 70 miles south of Seattle - are getting doses of ozone pollution at levels regularly found in Los Angeles. Ozone levels of 220 parts per billion (ppb) can make your eyes smart and give your Aunt Edna a doozy of a headache. University of Washington researchers are now trying to find if Douglas-fir is adversely affected by 220 ppb of ozone. They are also studying whether individual branches can reveal how whole trees respond to pollutants. Studying entire trees is tough so researchers hope to take the pulse of a tree by examining its branches.more » At the university's experimental forest, researchers have placed 12-foot-tall plastic-covered corrals around six Douglas-firs, each nine or 10 years old and up to 15 feet tall. Three of the trees receive filtered air while three others are blasted with 220 ppb of ozone for eight hours each day. Four individual branches on each tree are encased in their own plastic chambers. Two are dosed with filtered air and two with ozone. To date, the UW research is the only study in the US combining branch chambers with whole tree measurements. Now in its second year, the experiment is expected to yield information about growth and foliage health by measuring respiration, chlorophyll, photosynthesis, and nutrient uptake. Loss of tree vigor could lead to increased problems with pathogens and insects. In the summer of '88, surprisingly high levels of ozone - up to 196 ppb - were detected in forests downwind from Seattle, worse than the urban areas themselves.« less

Food webs of two intermittently open estuaries receiving 15N-enriched sewage effluent

NASA Astrophysics Data System (ADS)

Hadwen, Wade L.; Arthington, Angela H.

2007-01-01

Carbon and nitrogen stable isotope signatures were used to assess the response of food webs to sewage effluent discharged into two small intermittently open estuaries in northern New South Wales, Australia. One of these systems, Tallows Creek, has a history of direct sewage inputs, whilst the other, Belongil Creek, receives wastewater via an extensive wetland treatment system. The food webs of both systems were driven by algal sources of carbon, reflecting high autotrophic productivity in response to the nutrients entering the system from sewage effluent. All aquatic biota collected from Tallows Creek had significantly enriched δ15N signatures relative to their conspecifics from Belongil Creek, indicating that sewage nitrogen had been assimilated and transferred throughout the Tallows Creek food web. These δ15N values were higher than those reported from studies in permanently open estuaries receiving sewage effluent. We suggest that these enriched signatures and the transfer of nitrogen throughout the entire food web reflect differences in hydrology and associated nitrogen cycling processes between permanently open and intermittently open estuaries. Although all organisms in Tallows Creek were generally 15N-enriched, isotopically light (less 15N-enriched) individuals of estuary perchlet ( Ambassis marianus) and sea mullet ( Mugil cephalus) were also collected. These individuals were most likely recent immigrants into Tallows Creek, as this system had only recently been opened to the ocean. This isotopic discrimination between resident (enriched) and immigrant (significantly less enriched) individuals can provide information on fish movement patterns and the role of heavily polluted intermittently open estuaries in supporting commercially and recreationally valuable estuarine species.

Climate variability drives recent tree mortality in Europe.

PubMed

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

2017-11-01

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

Reclamation: what about trees

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

Kolar, C.A.; Ashby, W.C.

A five-year research programme was started in 1978 in the Botany Department of Southern Illinois University to evaluate the effect of reclamation practices on tree survival and growth. The project was initiated as a direct result of reports from Illinois and Indiana of tree-planting failures on mined lands reclaimed to current regulation standards.

Northern Mountain and Prairie Community Tree Guide

Treesearch

E.G. McPherson; J.R. Simpson; P.J. Peper; S.E. Maco; Q. Xiao; P.J. Hoefer

2003-01-01

This tree guide quantifies benefits and costs for typical large-, medium-, small-stature, deciduous trees, as well as a conifer. The analysis assumed that trees were planted in a residential yard site or a public (street/park) site, under a 40-year time frame, and having a 60% survival rate. Tree care costs were based on findings from a survey of municipal and...