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PubMed2003

Standardized phylogenetic tree: a reference to discover functional evolution.

Functional evolution is often driven by positive natural selection. Although it is thought to be rare in evolution at the molecular level, its effects may be observed as the accelerated evolutionary rates. Therefore one of the effective ways to identify functional evolution is to identify accelerated evolution. Many methods have been developed to test the statistical significance of the accelerated evolutionary rate by comparison with the appropriate reference rate. The rates of synonymous substitution are one of the most useful and popular references, especially for large-scale analyses. On the other hand, these rates are applicable only to a limited evolutionary time period because they saturate quickly--i.e., multiple substitutions happen frequently because of the lower functional constraint. The relative rate test is an alternative method. This technique has an advantage in terms of the saturation effect but is not sufficiently powerful when the evolutionary rate differs considerably among phylogenetic lineages. For the aim to provide a universal reference tree, we propose a method to construct a standardized tree which serves as the reference for accelerated evolutionary rate. The method is based upon multiple molecular phylogenies of single genes with the aim of providing higher reliability. The tree has averaged and normalized branch lengths with standard deviations for statistical neutrality limits. The standard deviation also suggests the reliability level of the branch order. The resulting tree serves as a reference tree for the reliability level of the branch order and the test of evolutionary rate acceleration even when some of the species lineages show an accelerated evolutionary rate for most of their genes due to bottlenecking and other effects.

Animals↗
PubMed2003

Reanalysis of Murphy et al.'s data gives various mammalian phylogenies and suggests overcredibility of Bayesian trees.

Murphy and colleagues reported that the mammalian phylogeny was resolved by Bayesian phylogenetics. However, the DNA sequences they used had many alignment gaps and undetermined nucleotide sites. We therefore reanalyzed their data by minimizing unshared nucleotide sites and retaining as many species as possible (13 species). In constructing phylogenetic trees, we used the Bayesian, maximum likelihood (ML), maximum parsimony (MP), and neighbor-joining (NJ) methods with different substitution models. These trees were constructed by using both protein and DNA sequences. The results showed that the posterior probabilities for Bayesian trees were generally much higher than the bootstrap values for ML, MP, and NJ trees. Two different Bayesian topologies for the same set of species were sometimes supported by high posterior probabilities, implying that two different topologies can be judged to be correct by Bayesian phylogenetics. This suggests that the posterior probability in Bayesian analysis can be excessively high as an indication of statistical confidence and therefore Murphy et al.'s tree, which largely depends on Bayesian posterior probability, may not be correct.

Animals↗
PubMed2006

On the ancestral compatibility of two phylogenetic trees with nested taxa.

Compatibility of phylogenetic trees is the most important concept underlying widely-used methods for assessing the agreement of different phylogenetic trees with overlapping taxa and combining them into common supertrees to reveal the tree of life. The notion of ancestral compatibility of phylogenetic trees with nested taxa was recently introduced. In this paper we analyze in detail the meaning of this compatibility from the points of view of the local structure of the trees, of the existence of embeddings into a common supertree, and of the joint properties of their cluster representations. Our analysis leads to a very simple polynomial-time algorithm for testing this compatibility, which we have implemented and is freely available for download from the BioPerl collection of Perl modules for computational biology.

Algorithms↗
PubMed2002

Vessel distensibility and flow distribution in vascular trees.

In a class of model vascular trees having distensible blood vessels, we prove that flow partitioning throughout the tree remains constant, independent of the nonzero driving flow (or nonzero inlet to terminal outlet pressure difference). Underlying assumptions are: (1) every vessel in the tree exhibits the same distensibility relationship given by D/D(0) = f(P) where D is the diameter which results from distending pressure P and D(0) is the diameter of the individual vessel at zero pressure (each vessel may have its own individual D(0). The choice of f(P) includes distensibilities often used in vessel biomechanics modeling, e.g., f(P) = 1 + alpha P or f(P) = b + (1-b) exp(-c P), as well as f(P) which exhibit autoregulatory behavior. (2) Every terminal vessel in the tree is subjected to the same terminal outlet pressure. (3) Bernoulli effects are ignored. (4) Flow is nonpulsatile. (5) Blood viscosity within any individual vessel is constant. The results imply that for a vascular tree consistent with assumptions 2-5, the flow distribution calculations based on a rigid geometry, e.g., D=D(0), also gives the flow distribution when assuming the common distensibility relationships.

Lung↗
PubMed2006

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

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

Adaptation, Physiological↗
PubMed2003

Effects of habitat disruption on the activity of nectarivorous bats (Chiroptera: Phyllostomidae) in a dry tropical forest: implications for the reproductive success of the neotropical tree Ceiba grandiflora.

In the tropical dry forest of the central Pacific coast of Mexico the pollination and reproductive success of the bombacaceous tree Ceiba grandiflora was negatively affected by habitat disruption. Two of the three bat species that function as effective pollinators for this species ( Glossophaga soricina and Musonycteris harrisoni) visited flowers found in trees in disturbed habitats significantly less than trees found in undisturbed habitats. A similar pattern was observed for the effective bat pollinator, Leptonycteris curasoae; however the difference was not significant. The three nectarivorous bats that functioned as effective pollinators of C. grandiflora also visited flowers to exclusively feed on pollen by biting or pulling off an anther (see Fig. S1 of Electronic Supplementary Material). The number of pollen grains deposited on stigmas from flowers in undisturbed areas was significantly greater than from flowers in disturbed habitats. The greater visitation rate and the greater number of pollen grains deposited on flowers from trees in undisturbed forest resulted in a significantly greater fruit set for trees in these areas. Our study demonstrates the negative effect that habitat disruption has on bat pollinators in tropical dry forest ecosystems and documents the negative consequences for the plants they pollinate.

Animals↗
PubMed2004

Patterns of tree dieback in Queensland, Australia: the importance of drought stress and the role of resistance to cavitation.

During the extreme 1992-1997 El Niño drought event, widespread stem mortality, or tree "dieback", of both mature and juvenile eucalypts occurred within the tropical savannas of northeast Australia. Most of the dieback occurred in individuals of the ironbark species complex ( Eucalyptus crebra- E. xanthoclada) while individuals of the bloodwood species Corymbia erythrophloia, exhibited significantly less stem mortality. Indicative of greater water stress, predawn and midday xylem water potentials of ironbark adults and saplings were significantly more negative than predawn values of bloodwoods. The very negative xylem water potentials in ironbarks suggest that stem mortality in both adult and juvenile ironbarks results from drought-induced embolism and that ironbarks perhaps have a shallower and less extensive root system than bloodwoods. Although predawn and midday water potentials for ironbark adults and saplings were similar, a census of mature and juvenile ironbark trees indicated that mortality was higher in adult trees. Cavitation vulnerability curves indicated that ironbark saplings may be better buffered against cavitation than adult trees. If they possess smaller root systems, saplings are more likely than adults to experience low xylem water potentials, even in non-drought years. Xylem conduits produced in adult trees during periods of normal rainfall, although perhaps more efficient in water conduction, may be more vulnerable to cavitation during infrequent severe droughts.

Adaptation, Physiological↗
PubMed2002

Determining prognostic factors for gastric cancer using the regression tree method.

BACKGROUND: The regression tree method is a useful statistical technique that has been little used in the analysis of prognosis. METHODS: The prognostic factors of gastric cancer were investigated, using the regression tree method, in 555 patients who had undergone curative resection for serosa-negative gastric cancer and who were enrolled in a randomized controlled trial of postoperative adjuvant chemotherapy (JCOG [Japan Clinical Oncology Group] 8801 study). RESULTS: By the regression tree method, the first divided prognostic factor (the most important factor) was lymph node metastasis; in particular, extent of lymphatic spread had the greatest impact on prognosis. In addition, age, tumor size, depth of invasion, and individual dose intensity were found to be significant prognostic factors, whereas sex, tumor location, macroscopic tumor type, and extent of lymph node dissection were not. The resulting tree structure consisted of nine terminal nodes with different prognostic factors, and four clusters were obtained by the merging of terminal nodes that showed a similar prognosis. The cluster which showed the best survival rate (5-year survival rate, 0.986) consisted of two terminal nodes: node 12, which contained N0T1 patients who were younger than 62 years and had a tumor size of less than 7.5 cm, and node 14, which contained N1 patients who were younger than 46 years. CONCLUSION: In serosa-negative gastric cancer, lymph node metastasis was the most important prognostic factor. Utilization of the regression tree method enabled visual interpretation of the results of statistical analyses through the graphic representation of prognostic factors. It allowed the identification of the optimal combination of these prognostic factors that defined several groups of patients with distinct prognoses and may serve as a useful reference for the individualization of treatment strategy.

Adult↗
PubMed2005

Thyroid function in nestling tree swallows and eastern bluebirds exposed to non-persistent pesticides and p, p'-DDE in apple orchards of southern Ontario, Canada.

This study examined the associated effects of pesticides and persistent residues of p,p'-DDE on thyroid function in 16-day-old tree swallows (Tachycineta bicolor) and 12-day-old eastern bluebirds (Sialia sialis). Apple orchards sprayed with pesticides in current use and reference sites were chosen for study in southern Ontario, Canada, during 2000-2001. We assessed thyroid hormone concentrations (plasma and muscle thyroxine [T4], and triiodothyronine [T3]) and the response to a challenge with thyroid stimulating hormone (TSH) as well as parameters of thyroid histology. Individual nests were exposed to as many as seven individual pesticide applications and up to five pesticide mixtures. Concentrations of p,p'-DDE in eggs from both species were highest in orchard sites, and ranged from 0.05 to 5.44 mg/kg wet weight for tree swallows, and from 0.17 to 95.4 mg/kg for eastern bluebirds. In 2000, tree swallows from sprayed orchards had elevated plasma T4 concentrations, and thyroid glands with collapsed follicles, hypertrophic epithelia, and higher follicular epithelial cells relative to chicks from reference sites. Plasma T4 concentration was positively correlated with the total number of pesticide mixtures applied during egg incubation through chick rearing. In 2001, basal plasma T3 concentration in tree swallow chicks did not differ between orchard and reference sites, though there were differences among orchards; T3 was positively correlated with total number of individual sprays applied during egg incubation through chick rearing. Tree swallows challenged with TSH showed no significant difference in thyroid hormone concentration or follicular epithelial cell height between exposure groups; however, a significantly greater proportion of chicks from reference sites were found to have thyroids with focal or diffuse hypertrophic epithelia relative to orchard chicks. In 2001, bluebirds from sprayed orchards had significantly higher T3 concentrations in response to TSH challenge; this response was positively correlated with the total number of pesticides applied during egg incubation through chick rearing.

Animals↗
PubMed2006

Trace element concentrations and bioindicator responses in tree swallows from northwestern Minnesota.

Extremely high concentrations of cadmium (3.5 microg/g dry wgt.) and elevated concentrations of chromium (>10 microg/g dry wgt.) and mercury (1.6 microg/g dry wgt.) were reported in waterbird tissues at Agassiz National Wildlife Refuge in northwestern Minnesota in 1994. Tree swallows (Tachycineta bicolor) were studied during 1998-2001 at three drainages into the Refuge, two pools on the Refuge, and at a nearby reference location to document whether high levels of contaminants were still present, and if so to quantify the source and severity of the contamination. Trace elements were measured in tree swallow eggs, livers, and diet. Reproductive success and bioindicator responses were monitored. In 2000, water was drawn down on Agassiz Pool, one of the main pools on the Refuge. This presented an opportunity to evaluate the response of trace element concentrations in the diet and tissues of tree swallows after reflooding. High concentrations of trace elements were not detected in swallow tissues, nor were there differences among locations. Less than 20% of swallow samples had detectable concentrations of cadmium or chromium. Mercury concentrations were low and averaged <0.25 microg/g dry wgt. in swallow tissues. Trace elements, including mercury, did not increase in tree swallows following the 2000 drawdown at Agassiz Pool. Hatching success and survival of nestlings to 12 days-of-age for tree swallows on the Refuge were similar to the national average and consistent with background trace element concentrations. Bioindicator measurements were within the normal ranges as well.

Animals↗
PubMed1988

Network analysis of an arterial tree.

The arterial tree of a Sprague-Dawley rat was casted and carefully mapped with the aim of comparing its network characteristics with those suggested by the classical model of an arterial tree. It is shown that if the tree is to be measured accurately, the concept of 'whole vessels' on which the classical model is based must be abandoned since such vessels do not actually exist in the network, nor can they be accurately defined. The concept of 'vessel segments' is proposed instead and its use is demonstrated. A total of 1313 vessel segments in the arterial tree of the rat are mapped and divided into well defined 'levels'. The length and diameter of each segment are measured and the distribution and averages of these at different levels are presented as indicators of the branching characteristics of the tree.

Animals↗
PubMed1990

Minimally colored trees.

Each edge in a weighted colored tree has a nonnegative weight corresponding to the colors of its incident vertices. The sum of these weights is the weight of the tree. Algorithms of O(n) are known to find minimal colorings, that is, to assign colors from a given finite set to the vertices of a tree so as to minimize the weight of the tree. In this paper generating functions are used to find the number of minimal colorings and the average weight of each edge over such colorings, also using O(n) operations. Applications to evolutionary trees are given.

Algorithms↗
PubMed1995

A fast 3-dimensional neuronal tree reconstruction system that uses cubic polynomials to estimate dendritic curvature.

The main goal of this work was to develop and test the accuracy of our 3DARBOR neuronal tree reconstruction system by comparing it with a very precise but time-consuming method of reconstruction (NEUTRACE). Comparison was performed by reconstructing 18 dendritic trees of frog spinal motoneurons from serial sections with both methods and comparing several morphological summaries of the two reconstructions. In 3DARBOR the planar projection of the dendritic trees was drawn and fed into an IBM-compatible PC through a graphic tablet. Dendritic coordinates along the perpendicular (focus) axis on the plane of drawing were estimated by an interpolation method. The interpolation was based on the lengths of projected dendrites and the coordinates of points where dendrites entered the next section. Focus axis coordinates of these points could automatically be calculated from the serial numbers and thicknesses of sections. 3DARBOR was tested by comparison of the distributions of characteristic points of dendritic trees, segment lengths and branching angles. Product moment analysis on dendritic trees was also performed. It was concluded that 3DARBOR is a fast enough reconstruction system without any systematical error of interpolation that can correctly supply the most morphological parameters and visualize the natural arborizations.

Animals↗
PubMed1995

Construction of molecular evolutionary phylogenetic trees from DNA sequences based on minimum complexity principle.

Ever since the discovery of a molecular clock, many methods have been developed to reconstruct the molecular evolutionary phylogenetic trees. In this paper, we deal with the problem from the viewpoint of an inductive inference and apply Rissanen's minimum description length principle to extract the minimum complexity phylogenetic tree. Our method describes the complexity of the molecular phylogenetic tree by three terms which are related to the tree topology, the sum of the branch lengths and the difference between the model and the data measured by logarithmic likelihood. Five mitochondrial DNA sequences, from the human, the common chimpanzee, the pygmy chimpanzee, the gorilla and the orangutan, are used for investigating the validity of this method. It is suggested that this method might be superior to the traditional method in that it still shows good accuracy even near the root of phylogenetic trees.

Algorithms↗
PubMed1994

Does (K+Mg+Ca+P) fertilization lead to recovery of tree health in a nitrogen stressed Quercus rubra L. stand?

In The Netherlands atmospheric deposition of nitrogen compounds to forest ecosystems has been very high for some decades and has led to severe nutritional imbalances in soils as well as in trees. At this moment legislation is not fully in effect with respect to lowering emission/deposition fluxes, particularly of nitrogen. The trees suffer mainly from severe magnesium, potassium and calcium and sometimes phosphorus deficiencies. In this study it was investigated whether fertilization with potassium, magnesium, calcium and phosphorus could prevent a Quercus rubra stand from further decline by restoring the nutritional balance, though the detrimental input of nitrogen compounds still continues. Three fertilization treatments were applied: (i) a standard dose of 1250 kg.ha(-1) containing 60 kg P.ha(-1) (as P2O5), 100 kg K.ha(-1) (as K2O), 80 kg Mg.ha(-1) (as MgO) and 340 kg Ca.ha(-1) (as CaCO3); (ii) two times the standard dose; and (iii) three times the standard dose. Soil solution chemistry showed that the highest dose led to the most significant results: an improved nutrient balance and an increased availability of nutrients. After one growing season following fertilization, the trees looked much healthier and crown density had increased. This revitalization lasted for at least four years. For tree health the mid dose seemed appropriate. After the first growing season potassium is the most mobile nutrient, in the soil and also in the trees, but tended to decrease in the fourth year after fertilization. Magnesium and calcium reached normal values in the leaves after four growing seasons. No obvious effects of phosphorus were found.

Journal Article↗
PubMed1993

Measurement from arteriograms of regional myocardial bed size distal to any point in the coronary vascular tree for assessing anatomic area at risk.

OBJECTIVES: To obtain the size of regional myocardial mass for individual coronary arteries in vivo. BACKGROUND: The anatomic site of occlusion in a coronary artery does not predict the size of the risk area because location of the occlusion does not account for the size of the artery or of its dependent myocardial bed. METHODS: Intracoronary radiolabeled microspheres were injected and coronary arteriograms were quantitatively analyzed by semiautomated methods. The coronary artery lumen areas and the sum of epicardial coronary artery branch lengths distal to the points where radiomicrospheres had been injected were determined from both in vivo and postmortem coronary arteriograms. Regional myocardial mass distal to the point of each microsphere injection was correlated with corresponding distal summed coronary branch lengths and with coronary artery lumen areas. RESULTS: 1) Regional myocardial mass was closely and linearly related to sum of coronary artery branch lengths distal to any point in the coronary artery tree and therefore could be determined for any location on a coronary arteriogram. 2) The fraction of total left ventricular mass at risk distal to a stenosis could be determined from the corresponding fraction of total coronary artery tree length independently of the scale or X-ray magnification used to measure absolute branch lengths. 3) Cross-sectional lumen area at any point in the left coronary artery tree was closely related to the size of the dependent vascular bed with a curvilinear relation similar to that observed in humans with normal coronary arteriograms. CONCLUSIONS: On coronary arteriograms, the anatomic area at risk for myocardial infarction distal to any point in the coronary artery tree can be determined from the sum of distal coronary artery branch lengths. There is a curvilinear relation between coronary artery lumen area and dependent regional myocardial mass comparable to that in humans, reflecting fundamental physical principles underlying the structure of the coronary vascular tree.

Animals↗
PubMed2004

Seasonal variations of monoterpene emissions from coniferous trees of different ages in Korea.

Seasonal variations of emission rates and compositions from coniferous species were measured under controlled conditions using a vegetation enclosure method. Total emission rates and compositions of monoterpene compounds from young and adult trees in different seasons were compared. It was found that the total emission rates and the components of monoterpene varied significantly with tree species, age, and season. Total emissions from C. japonica and P. koraiensis were higher for older trees than for younger trees; however, significantly higher emissions were found from younger trees for C. obtusa. Higher monoterpene emission rates from each plant were found in spring and summer compared with autumn and winter emissions.

Korea↗
PubMedDate not supplied

MR cholangiography 3D biliary tree automatic reconstruction system.

An algorithm for reconstructing magnetic resonance cholangiography (MRC) biliary structure is proposed. The processing of MRC data can be divided into four phases. In the first phase, the region of interest (ROI) containing the liver and biliary ducts is extracted from the original volume data based on human anatomy and B-spline curve. The second phase involves segmenting the biliary ducts from the region identified in the previous phase. Because the image of biliary portion is brighter than the liver, the segmentation is started by choosing the brightest pixel in the ROI as the seed for 3D region growing. This procedure could be executed many times, depending on the provided stopping condition. In the third phase, the segmented biliary duct regions are traced to construct the biliary tree. An automated 3D tracking algorithm is proposed for this phase. This 3D tracking algorithm estimates the coordinates of the points along the medial axis of each biliary duct branch. The cross sections associated with the points along the medial axis are also calculated approximately during the tracking process. The biliary tree data structure is constructed in this phase. The biliary tree is reconstructed and rendered in the last phase. Although the proposed algorithm takes a longer time compared with the conventional approach, the reconstructed biliary tree 3D structure can provide more clearly image. A concise representation for the biliary tree can be achieved with the proposed method and provide both quantitative and structural information for clinical reference.

Algorithms↗