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PubMed2006

TreeFam: a curated database of phylogenetic trees of animal gene families.

TreeFam is a database of phylogenetic trees of gene families found in animals. It aims to develop a curated resource that presents the accurate evolutionary history of all animal gene families, as well as reliable ortholog and paralog assignments. Curated families are being added progressively, based on seed alignments and trees in a similar fashion to Pfam. Release 1.1 of TreeFam contains curated trees for 690 families and automatically generated trees for another 11 646 families. These represent over 128 000 genes from nine fully sequenced animal genomes and over 45 000 other animal proteins from UniProt; approximately 40-85% of proteins encoded in the fully sequenced animal genomes are included in TreeFam. TreeFam is freely available at http://www.treefam.org and http://treefam.genomics.org.cn.

Animals↗
PubMed2006

VOMBAT: prediction of transcription factor binding sites using variable order Bayesian trees.

Variable order Markov models and variable order Bayesian trees have been proposed for the recognition of transcription factor binding sites, and it could be demonstrated that they outperform traditional models, such as position weight matrices, Markov models and Bayesian trees. We develop a web server for the recognition of DNA binding sites based on variable order Markov models and variable order Bayesian trees offering the following functionality: (i) given datasets with annotated binding sites and genomic background sequences, variable order Markov models and variable order Bayesian trees can be trained; (ii) given a set of trained models, putative DNA binding sites can be predicted in a given set of genomic sequences and (iii) given a dataset with annotated binding sites and a dataset with genomic background sequences, cross-validation experiments for different model combinations with different parameter settings can be performed. Several of the offered services are computationally demanding, such as genome-wide predictions of DNA binding sites in mammalian genomes or sets of 10(4)-fold cross-validation experiments for different model combinations based on problem-specific data sets. In order to execute these jobs, and in order to serve multiple users at the same time, the web server is attached to a Linux cluster with 150 processors. VOMBAT is available at http://pdw-24.ipk-gatersleben.de:8080/VOMBAT/.

Algorithms↗
PubMed1996

Recognizing the forest for the trees: testing temporal patterns of cladogenesis using a null model of stochastic diversification.

Computer simulations are developed and employed to examine the expected temporal distributions of nodes under a null model of stochastic lineage bifurcation and extinction. These Markovian models of phylogenetic process were constructed so as to permit direct comparisons against empirical phylogenetic trees generated from molecular or other information available solely from extant species. For replicate simulated phylads with n extant species, cumulative distribution functions (cdf's) of branching times were calculated, and compared (using the Kolmogorov-Smirnov test statistic D) to those from three published empirical trees. Molecular phylogenies for columbine plants and avian cranes showed statistically significant departures from the null expectations, in directions indicating recent and ancient species' radiations, respectively, whereas a molecular phylogeny for the Drosophila virilis species group showed no apparent historical clustering of branching events. Effects of outgroup choice and phylogenetic frame of reference were investigated for the columbines and found to have a predictable influence on the types of conclusions to be drawn from such analyses. To enable other investigators to statistically test for nonrandomness in temporal cladogenetic pattern in empirical trees generated from data on extant species, we present tables of mean cdf's and associated probabilities under the null model for expected branching times in phylads of varying size. The approaches developed in this report complement and extend those of other recent methods for employing null models to assess the statistical significance of pattern in evolutionary trees.

Animals↗
PubMed1998

Nuclear gene trees and the phylogenetic relationships of the mangabeys (Primates: Papionini).

Phylogenetic relationships of mangabeys within the Old World monkey tribe Papionini are inferred from analyses of nuclear DNA sequences from five unlinked loci. The following conclusions are strongly supported, based on congruence among trees derived for the five separate gene regions: (1) mangabeys are polyphyletic within the Papionini; (2) Cercocebus is the sister taxon to the genus Mandrillus; and (3) Lophocebus belongs to a clade with Papio and Theropithecus, with Papio as its most likely sister taxon. Morphologically based phylogenies positing mangabey monophyly were evaluated by mapping the sequences for each locus on these trees. The data seem to fit these trees poorly in both maximum-parsimony and likelihood analyses. Incongruence among nuclear gene trees occurred in the interrelationships among Lophocebus, Papio, and Theropithecus. Several factors that may account for this incongruence are discussed, including sampling error, random lineage sorting, and introgression.

Animals↗
PubMed1999

Generalized neighbor-joining: more reliable phylogenetic tree reconstruction.

We have developed a phylogenetic tree reconstruction method that detects and reports multiple topologically distant low-cost solutions. Our method is a generalization of the neighbor-joining method of Saitou and Nei and affords a more thorough sampling of the solution space by keeping track of multiple partial solutions during its execution. The scope of the solution space sampling is controlled by a pair of user-specified parameters--the total number of alternate solutions and the number of alternate solutions that are randomly selected--effecting a smooth trade-off between run time and solution quality and diversity. This method can discover topologically distinct low-cost solutions. In tests on biological and synthetic data sets using either the least-squares distance or minimum-evolution criterion, the method consistently performed as well as, or better than, both the neighbor-joining heuristic and the PHYLIP implementation of the Fitch-Margoliash distance measure. In addition, the method identified alternative tree topologies with costs within 1% or 2% of the best, but with topological distances of 9 or more partitions from the best solution (16 taxa); with 32 taxa, topologies were obtained 17 (least-squares) and 22 (minimum-evolution) partitions from the best topology when 200 partial solutions were retained. Thus, the method can find lower-cost tree topologies and near-best tree topologies that are significantly different from the best topology.

Algorithms↗
PubMed1992

Statistical method for estimating the standard errors of branch lengths in a phylogenetic tree reconstructed without assuming equal rates of nucleotide substitution among different lineages.

A statistical method is developed for estimating the standard errors of branch lengths in a phylogenetic tree reconstructed without assuming equal rates of nucleotide substitution among different lineages. This method can be easily used for testing whether the length of an interior branch in a reconstructed tree is positive, i.e., whether the topology of the tree is correct. Computer simulations indicate that this method is appropriate for a statistical test. As an example, this method is applied to phylogenetic trees reconstructed for the four hominoid species: human, chimpanzee, gorilla, and orangutan. The results obtained show that the present method provides a powerful statistical test.

Animals↗
PubMed2002

Characterization of polypeptides accumulated in the latex cytosol of rubber trees affected by the tapping panel dryness syndrome.

The tapping panel dryness (TPD) syndrome of rubber is characterized by the reduction or ultimately total cessation of latex flow upon tapping, due to physiological disorders in the bark tissue. The protein pattern in the cytoplasm from healthy and TPD tree latex cells was compared by electrophoresis. Two polypeptides (P15 and P22) of 15 and 22 kDa, respectively, were found to accumulate in the cytosol of the TPD-affected trees, whereas a 29 kDa polypeptide (P29) appeared de novo. P15 and P22 were identified as REF (Hev b1) and SRPP (Hev b3), respectively, two proteins proposed to be involved in rubber biosynthesis. P29 appeared to be a new member of the patatin-like protein family. Specific molecular probes were designed for a detailed characterization of REF and SRPP gene expression and RFLP mapping. This allowed the demonstration that REF and SRPP display very similar expression profiles. They are highly over-expressed by the tapping-induced metabolic activation, although not by wounding per se, or ethylene or ABA. In addition to this similarity in gene expression, they were found to share one common locus in the genome. No significant difference in REF and SRPP gene expression was observed between healthy and TPD trees, indicating that their TPD-related accumulation in the cytosol was not transcriptionally regulated. Western blot analysis demonstrated that osmotic lysis of the sedimentable organelles (lutoids) in vitro caused the release of REF and SRPP from the rubber particle membrane into the cytosol. A mechanism of cellular delocalization as a consequence of the lutoids instability is proposed to explain REF and SRPP accumulation in the cytosol of TPD trees.

Allergens↗
PubMed1986

Precision weighing lysimetry for trees, using a simplified tared-balance design.

Four weighing lysimeters (1.8 m diameter, 1 m depth, weight 3.5-4.5 Mg) were used to estimate transpiration from single, isolated trees. The weighing mechanism incorporated a simple, new system of wire ropes around torsion tubes, producing a lever action through which most of the weight was tared off with a counter weight. Weight differences measured by load cell under the main lever arm were unaffected by hysteresis or temperature change. Sensitivity better than 100 g was achieved in windless conditions. Daily measurements over yearly periods (trees could be regularly replaced using extra pots) revealed both sigmoid seasonal patterns, and sigmoid diurnal changes closely related to micrometeorological variables, for a range of tree species. Measurements taken during rainfall demonstrated that an isolated tree intercepts considerably more precipitation than does a uniform crop covering the same ground area, and that substantial evaporation from the canopy takes place while it is raining.

Journal Article↗
PubMed1992

Effects of varying crop load on photosynthesis, dry matter production and partitioning of Crispin/M.27 apple trees.

Fruit load was altered by flower thinning on three- and four-year-old, field-grown apple trees. Increasing fruit load led to increases in dry matter production per unit leaf area and partitioning to fruit and to decreases in fruit size, percentage fruit dry matter, dry matter partitioning to new shoot growth, thickening of existing woody tissue and root growth. Flower bud production for the following spring was also negatively affected by an increase in fruit load. Leaf photosynthesis was increased in cropping trees in July and August at the time of maximum fruit dry weight increase. Calculated light interception was linearly related to leaf area. The efficiency of conversion of intercepted photosynthetic active radiation to dry matter energy equivalents was 3.3% in heavily cropping trees and 1.8% in non-cropping trees. Total dry matter production was linearly related to both leaf area and light interception, but the variance accounted for by the regression was more than doubled if fruit dry matter or fruit number was included in the regression.

Journal Article↗
PubMedDate not supplied

Relationship between CO(2)-dependent O(2) evolution and photosystem II activity in oak (Quercus petraea) trees grown in the field and in seedlings grown in ambient or elevated CO(2).

The light-response of the apparent quantum yield of photosynthetic O(2) evolution (Phi(O(2) )) under non-photorespiratory conditions was measured together with the photochemical efficiency of PS II (DeltaF/F(m)'), the photochemical efficiency of open PS II reaction centers (F(v)'/F(m)') and the photochemical fluorescence quenching (q(p)) of leaf disks punched from oak leaves of seedlings grown in ambient (350 micro mol mol(-1)) or elevated (700 micro mol mol(-1)) CO(2) in a greenhouse, and from sunlit leaves of mature oak trees (Quercus petraea (Matt.) Liebl.). There were marked differences between seedlings and trees. In seedlings, CO(2) concentration during growth did not modify the light response of photosynthesis or PS II activity. There was a single linear relationship between Phi(O(2) ) and DeltaF/F(m)' in seedling leaves that was independent of the CO(2) concentration imposed during growth. In contrast, this relationship was curvilinear in sunlit leaves of adult trees. In seedling leaves, the decrease in q(p) (i.e., the proportion of open PS II reaction centers) largely accounted for the decrease in DeltaF/F(m)', whereas the decrease in DeltaF/F(m)' in sunlit leaves of mature oak trees was dependent on both q(p) and F(v)'/F(m)'.

Journal Article↗
PubMed1995

Effects of light availability and tree size on the architecture of assimilative surface in the canopy of Picea abies: variation in needle morphology.

Needle dimensions, needle surface area, needle dry weight per area (LWA) and needle density (ND, needle weight per volume) were measured in terminal current-year shoots in a natural canopy of variably sized Picea abies (L.) Karst. trees growing along a light gradient. Needle shape was described as a rhomboid. Needle width (D(2)) increased with increasing diffuse site factor, a(d) (relative amount of penetrating diffuse solar radiation), whereas needle thickness (D(1)) remained nearly constant, resulting in an inverse relationship between D(1)/D(2) and a(d) and an increase in the ratio of total (TLA) to projected needle surface area (PLA) with increasing a(d). Because of the variations in needle morphology with respect to light availability, the shoot parameters used in present canopy models are also expected to be light-sensitive, and studies involving shoot morphology should also consider the variability in needle geometry. Needle dimensions and total tree height were not correlated. However, LWA increase with both increasing a(d) and total tree height. When LWA was expressed as the product of ND and needle height (NH, height of the rhomboidal transverse section of a needle), LWA appeared to increase with irradiance, because of changing NH, and with total tree height, because of changing needle density.

Journal Article↗
PubMed1996

Light environment alters ozone uptake per net photosynthetic rate in black cherry trees.

Foliar ozone uptake rates of different-sized black cherry (Prunus serotina Ehrh.) trees were compared within a deciduous forest and adjacent openings in north-central Pennsylvania during one growing season. Study trees included open-grown seedlings and saplings, forest understory seedlings and saplings, and sunlit and shaded portions of mature canopy tree crowns. Instantaneous ozone uptake rates were highest in high-light environments primarily because of higher stomatal conductances. Low ozone uptake rates of seedlings and saplings in the forest understory could be attributed partially to lower average ambient ozone concentrations compared to the canopy and open environments. Among the tree size and light combinations tested, ozone uptake rates were highest in open-grown seedlings and lowest in forest-grown seedlings. Despite lower ozone uptake rates of foliage in shaded environments, ozone uptake per net photosynthesis of foliage in shaded environments was significantly higher than that of foliage in sunlit environments because of weaker coupling between net photosynthesis and stomatal conductance in shaded environments. The potential for greater ozone injury in shaded environments as a result of greater ozone uptake per net photosynthesis is consistent with previous reports of greater ozone injury in shaded foliage than in sunlit foliage.

Journal Article↗
PubMed1996

Canopy development, CO(2) exchange and carbon balance of a modeled agroforestry tree.

We developed a whole-canopy CO(2) exchange simulation model to study effects of pruning on the carbon balance of trees. Model inputs include global short-wave radiation, photosynthetic photon flux density (PFD), air temperature, time series of the development of canopy diameter, height and total leaf area during the simulation period and local geographical and atmospheric parameters. Canopy structure is derived stochastically from the time series of canopy development and growth functions of individual phytoelements. The PFD incident on a phytoelement is computed from the average gap frequency of the canopy and the binary random probability of sunflecks on the phytoelement. Instantaneous CO(2) assimilation rate of each phytoelement is computed from PFD and phytoelement age. Assimilation rates are integrated over space and time to estimate whole-canopy CO(2) assimilation. The model was used to study carbon balance in five sources of the leguminous agroforestry tree Erythrina poeppigiana (Walpers) O.F. Cook during two 6-month pruning intervals. The canopy description appeared to be realistic. According to the simulations, cumulative assimilation did not provide enough carbon for tree growth until two months after pruning, indicating dependence of tree growth on reserve carbohydrates. The two most productive sources, which had the most open canopies, were the most dependent on reserve carbohydrates after pruning.

Journal Article↗
PubMed1997

Effect of crop load on fruiting and leaf photosynthesis of 'Braeburn'/M.26 apple trees.

Four-year-old apple (Malus x domestica Borkh.) trees cv. 'Braeburn' on M.26 rootstock were thinned at full bloom to establish six crop loads ranging from a heavy crop to a deflowered treatment. At harvest, mean yield per tree varied from 0 to 38 kg and mean fruit weight ranged from 225 g in the heaviest cropping treatment to 385 g in the lightest cropping treatment. Light cropping resulted in a significant advance in fruit maturity as indicated by background color, starch/iodine score and soluble solids. There were small differences in leaf photosynthetic rate among the treatments when shoot growth was active. However, in early January, coincident with cessation of shoot growth and maximum rate of accumulation of fruit weight, leaf assimilation rate was reduced by as much as 65% on the deflowered trees compared to the trees carrying the heaviest crop. Leaf assimilation rate showed a curvilinear response to crop load at this time, with little increase in leaf assimilation when crop load exceeded 12 fruit m(-2) leaf area.

Journal Article↗
PubMed1998

Organic and inorganic sulfur transport in the xylem sap and the sulfur budget of Picea abies trees.

Temporal changes in inorganic and organic sulfur compounds (sulfate, glutathione, cysteine, methionine) were analyzed in xylem sap of 40-year-old Norway spruce (Picea abies (L.) Karst.) trees growing on acidic soils at a healthy and a declining stand in the Fichtelgebirge (North Bavaria, Germany). Studies were carried out (1) to quantify glutathione (GSH) transport in the xylem of spruce, (2) to study the significance of reduced sulfur versus sulfate (SO(4) (2-)) transport in the xylem, and (3) to compare total sulfur (S) transport in the xylem with the amount of foliar uptake of SO(2) in an air-polluted environment. Glutathione was the main reduced S compound in the xylem ranging in concentration from 0.5 to 5 &mgr;mol l(-1). Concentrations of inorganic SO(4) (2-) in the xylem sap were up to 50 times higher than those of GSH ranging from 60 to 230 &mgr;mol l(-1). During the growing season, concentrations of all S compounds in the xylem were highest in May (up to 246 &mgr;mol l(-1)) and decreased during summer and fall (up to 21 &mgr;mol l(-1)). On average, SO(4) (2-) concentrations in xylem sap were 30% higher at the declining site compared with the healthy site. Diurnal changes in organic S compounds were significant for GSH and cysteine with high concentrations during the night and low concentrations during the day. Diurnal changes in inorganic concentrations were not significant. Xylem sap concentrations of SO(4) (2-) and cysteine were twice as high and GSH concentrations were tenfold higher in surface roots than in branches. At both sites, transport of organic S was low (up to 3% of total S) compared to transport of SO(4) (2-). Annual transport of total S in the xylem (SO(4) (2-) was the main component) ranged from 60 to 197 mmol tree(-1) year(-1) at the healthy site and from 123 to 239 mmol tree(-1) year(-1) at the declining site. Although gaseous uptake of SO(2) was estimated to be similar at both sites (38 mmol tree(-1) year(-1); Horn et al. 1989), the ratio between annual gaseous uptake of SO(2) and transport of S in the xylem was 1:4 and 1:5 at the healthy and declining sites, respectively.

Journal Article↗
PubMed1999

Transpiration increases during the dry season: patterns of tree water use in eucalypt open-forests of northern Australia.

Australian savannas exhibit marked seasonality in precipitation, with more than 90% of the annual total falling between October and May. The dry season is characterized by declining soil water availability and high vapor pressure deficits (up to 2.5 kPa). We used heat pulse technology to measure whole-tree transpiration rates on a daily and seasonal basis for the two dominant eucalypts at a site near Darwin, Australia. Contrary to expectations, transpiration rates were higher during the dry season than during the wet season, largely because of increased evaporative demand and the exploitation of groundwater reserves by the trees. Transpiration rates exhibited a marked hysteresis in relation to vapor pressure deficit, which was more marked in the dry season than in the wet season. This result may be attributable to low soil hydraulic conductivity, or the use of stored stem water, or both. Tree water use was strongly correlated with leaf area and diameter at breast height and there were no differences in transpiration between the species studied. These results are discussed in relation to scaling tree water use to stand water use.

Journal Article↗
PubMed1986

Experimental approaches to the study of the effects of nutrients and water on carbon assimilation by trees.

This paper outlines the experiemental approaches needed to provide detailed information about the effects of nutrients and water on carbon assimilation, and hence growth of trees. Data from a large multidisciplinary experiment being conducted in Australia illustrate important aspects of the approach advocated. The system model consists of a series of submodels describing the main physiological processes considered to govern the growth of trees. It is argued that field experiments designed to investigate physiological processes and their interactions should involve treatments that cause large differences in the growth rates of trees and in the condition of the trees at any time. The biomass of experimental stands should be defined. Measurements of stem and leaf growth, litterfall, leaf photosynthetic characteristics, plant water status and soil water content, plant nutrient status and nutrient mineralization rates in the soil provide the information needed to explain observed differences in growth and to refine the models underlying the research.

Journal Article↗
PubMed2001

Effects of irrigation deprivation during the harvest period on yield determinants in mature almond trees.

Effects of irrigation deprivation during the harvest period on yield determinants in mature almond (Prunus dulcis (Mill.) D.A. Webb cv. Nonpareil) trees were investigated during a 3-year field experiment. Return bloom and fruit set were measured on 2185 individually tagged spurs. Water stress resulting from irrigation deprivation during the harvest period, which purportedly coincides with the time of flower initiation, had no effect on the percentage of spurs that flowered or set fruit during subsequent years. Although water stress had no apparent effect on spur mortality, 66% of the tagged spurs died within 3 years. In addition, many spurs were vegetative by the third year, indicating the importance of spur renewal for sustained fruit production. Reductions in nut yield were evident after two successive years of irrigation deprivation during the harvest period. Regression analysis indicated a loss in yield of 7.7 kg tree(-1) in response to each 1 MPa decrease in stem water potential below -1.2 MPa during the previous seasons. The number of fruiting positions per tree (estimated indirectly for whole trees based on weight of current-year shoots > 5 cm in length) was negatively associated with water stress. Yield reduction in response to water stress during harvest appears to be a compound, multiyear effect, associated with reduced annual growth and renewal of fruiting positions.

Agriculture↗