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PubMed1988

Relationships between gene trees and species trees.

It is well known that a phylogenetic tree (gene tree) constructed from DNA sequences for a genetic locus does not necessarily agree with the tree that represents the actual evolutionary pathway of the species involved (species tree). One of the important factors that cause this difference is genetic polymorphism in the ancestral species. Under the assumption of neutral mutations, this problem can be studied by evaluating the probability (P) that a gene tree has the same topology as that of the species tree. When one gene (allele) is used from each of the species involved, the probability can be expressed as a simple function of Ti = ti/(2N), where ti is the evolutionary time measured in generations for the ith internodal branch of the species tree and N is the effective population size. When any of the Ti's is less than 1, the probability P becomes considerably less than 1.0. This probability cannot be substantially increased by increasing the number of alleles sampled from a locus. To increase the probability, one has to use DNA sequences from many different loci that have evolved independently of each other.

Alleles↗
PubMed2001

Finding the tree of life: matching phylogenetic trees to the fossil record through the 20th century.

Phylogenies, or evolutionary trees, are fundamental to biology. Systematists have laboured since the time of Darwin to discover the tree of life. Recent developments in systematics, such as cladistics and molecular sequencing, have led practitioners to believe that their phylogenies are more testable now than equivalent efforts from the 1960s or earlier. Whole trees, and nodes within trees, may be assessed for their robustness. However, these quantitative approaches cannot be used to demonstrate that one tree is more likely to be correct than another. Congruence assessments may help. Comparison of a sample of 1000 published trees with an essentially independent standard (dates of origin of groups in geological time) shows that the order of branching has improved slightly, but the disparity between estimated times of origination from phylogeny and stratigraphy has, if anything, become worse. Controlled comparisons of phylogenies of four major groups (Agnatha, Sarcopterygii, Sauria and Mammalia) do not show uniform improvement, or decline, of fit to stratigraphy through the twentieth century. Nor do morphological or molecular trees differ uniformly in their performance.

Animals↗
PubMed2005

The concordance of gene trees and species trees at two linked loci.

The gene genealogies of two linked loci in three species are analyzed using a series of Markov chain models. We calculate the probability that the gene tree of one locus is concordant with the species tree, given that the gene tree of the other locus is concordant. We define a threshold value of the recombination rate, r*, to be the rate for which the difference between the conditional probability of concordance and its asymptotic value is reduced to 5% of the initial difference. We find that, although r* depends in a complicated way on the times of speciation and effective population sizes, it is always relatively small, <10/N4, where N4 is the effective size of the species represented by the internal branch of the species tree. Consequently, the concordance of gene trees of neutral loci with the species tree is expected to be on roughly the same length scale on the chromosome as the extent of significant linkage disequilibrium within species unless the effective size of contemporary populations is very different from the effective sizes of their ancestral populations. Both balancing selection and selective sweeps can result in much longer genomic regions having concordant gene trees.

Animals↗
PubMedDate not supplied

Falls from trees and tree associated injuries in rural Melanesians.

Falls from trees and other tree related injuries are the most common cause of trauma in some parts of rural Melanesia. A four year review of all admissions for trauma to the Provincial Hospital at Alotau, Milne Bay Province, Papua New Guinea, showed that 27% were due to falls from trees, and a further 10% were due to related injuries, such as being struck by a falling branch or a coconut. A questionnaire distributed to rural health centres showed that during the study period at least 28 villagers died from falls from trees before reaching hospital. Head and chest trauma were common causes of death. Many injured patients were boys. Forearm fractures were the most common injuries, but more serious injuries were also frequently encountered. Trees responsible for most deaths and injuries included the coconut palm, betel palm, mango, and breadfruit. There are many strategies for preventing such injuries; perhaps the most important is to stop small boys climbing tall trees. Such falls are a serious occupational hazard for many subsistence farmers.

Adolescent↗
PubMed2005

Inferring species phylogenies from multiple genes: concatenated sequence tree versus consensus gene tree.

Phylogenetic trees from multiple genes can be obtained in two fundamentally different ways. In one, gene sequences are concatenated into a super-gene alignment, which is then analyzed to generate the species tree. In the other, phylogenies are inferred separately from each gene, and a consensus of these gene phylogenies is used to represent the species tree. Here, we have compared these two approaches by means of computer simulation, using 448 parameter sets, including evolutionary rate, sequence length, base composition, and transition/transversion rate bias. In these simulations, we emphasized a worst-case scenario analysis in which 100 replicate datasets for each evolutionary parameter set (gene) were generated, and the replicate dataset that produced a tree topology showing the largest number of phylogenetic errors was selected to represent that parameter set. Both randomly selected and worst-case replicates were utilized to compare the consensus and concatenation approaches primarily using the neighbor-joining (NJ) method. We find that the concatenation approach yields more accurate trees, even when the sequences concatenated have evolved with very different substitution patterns and no attempts are made to accommodate these differences while inferring phylogenies. These results appear to hold true for parsimony and likelihood methods as well. The concatenation approach shows >95% accuracy with only 10 genes. However, this gain in accuracy is sometimes accompanied by reinforcement of certain systematic biases, resulting in spuriously high bootstrap support for incorrect partitions, whether we employ site, gene, or a combined bootstrap resampling approach. Therefore, it will be prudent to report the number of individual genes supporting an inferred clade in the concatenated sequence tree, in addition to the bootstrap support.

Animals↗
PubMed2000

Suitability of process-based tree growth models for addressing tree response to climate change.

Empirical models of tree growth have been used for many years to predict timber yields and other properties of trees. However, such models rely on measured relationships between tree growth and historic environmental conditions. As anthropogenic actions alter the environment, especially atmospheric composition, empirical models become less reliable and process-based models become more useful. Process-based models are challenged to simulate growth of structurally and physiologically complex organisms using explicit mathematical expressions to capture growth response to environmental conditions. In this review we summarize the physiological requirements of process-based models and examine the capabilities of six published models (CARBON, ECOPHYS, PGSM, TREE-BGC, TREGRO, W91) for simulating tree response to changes in environmental conditions (elevated temperature, increased CO(2) concentration, and enhanced concentrations of tropospheric ozone). These analyses indicate that current models are reliable integrators of environmental effects on individual processes (e.g. photosynthesis), but may be less reliable where physiological acclimation occurs or when extrapolated to growth of specific tree compartments.

Journal Article↗
PubMed1998

In-vitro activity of essential oils, in particular Melaleuca alternifolia (tea tree) oil and tea tree oil products, against Candida spp.

The in-vitro activity of a range of essential oils, including tea tree oil, against the yeast candida was examined. Of the 24 essential oils tested by the agar dilution method against Candida albicans ATCC 10231, three did not inhibit C. albicans at the highest concentration tested, which was 2.0% (v/v) oil. Sandalwood oil had the lowest MIC, inhibiting C. albicans at 0.06%. Melaleuca alternifolia (tea tree) oil was investigated for activity against 81 C. albicans isolates and 33 non-albicans Candida isolates. By the broth microdilution method, the minimum concentration of oil inhibiting 90% of isolates for both C. albicans and non-albicans Candida species was 0.25% (v/v). The minimum concentration of oil killing 90% of isolates was 0.25% for C. albicans and 0.5% for non-albicans Candida species. Fifty-seven Candida isolates were tested for sensitivity to tea tree oil by the agar dilution method; the minimum concentration of oil inhibiting 90% of isolates was 0.5%. Tests on three intra-vaginal tea tree oil products showed these products to have MICs and minimum fungicidal concentrations comparable to those of non-formulated tea tree oil, indicating that the tea tree oil contained in these products has retained its anticandidal activity. These data indicate that some essential oils are active against Candida spp., suggesting that they may be useful in the topical treatment of superficial candida infections.

Antifungal Agents↗
PubMed1993

Sulfate concentrations in Norway spruce needles in relation to atmospheric SO(2): a comparison of trees from various forests in Germany with trees fumigated with SO(2) in growth chambers.

Concentrations of inorganic sulfur, organic sulfur and water-soluble cations and anions were determined in needles of young Norway spruce trees (Picea abies L. (Karst.)) that had been fumigated in growth chambers for weeks or months with different concentrations of SO(2), SO(2) plus ozone, or SO(2) plus NO(2). Measurements were also made on needles from older trees growing in forests in various regions of Germany with different mean annual atmospheric SO(2) emissions. In the fumigated young trees, sulfate accumulation in the needles was a linear function of atmospheric SO(2) concentration. Little or no sulfur was incorporated into the organic sulfur fraction. The mean accumulation rate of sulfate in needles of fumigated trees was about 0.4 nmol g(dw) (-1) (nl l(-1))(-1) h(-1), which is very similar to the estimated rate of uptake of atmospheric SO(2) calculated from mean stomatal conductances (15 mmol m(-2) s(-1)) and the external SO(2) concentration (the calculated rate of uptake was 0.37 nmol g(dw) (-1) (nl l(-1))(-1) h(-1)). Concentrations of organic acids and other inorganic ions did not change much in response to SO(2) fumigation. In needles collected from trees in south and southeast Germany, large differences in sulfate concentrations were observed that probably reflect SO(2) emissions in the different regions. The highest foliar sulfate concentrations, and the highest annual increase in sulfate concentration with needle age were observed in material collected from the heavily polluted Erzgebirge (up to 12 micro mol g(dw) (-1) year(-1)), followed by material from the Fichtelgebirge (up to 6 micro mol g(dw) (-1) year(-1)). If it is assumed that this annual increase is the result of uptake of SO(2) from the atmosphere, mean annual atmospheric SO(2) concentrations can be calculated. The calculated values were somewhat below the measured values in the Fichtelgebirge and in the heavily polluted Erzgebirge. Norway spruce trees can cope with high concentrations of atmospheric SO(2), provided that they can neutralize the sulfuric acid formed from SO(2). It appears that, in the field, the acid load is decreased by H(+) translocation to the roots and subsequent H(+)/K(+) exchange. However, this may be a very slow process, because it was not observed in the short-term fumigation experiments.

Journal Article↗
PubMed2000

Use of a single-tree simulation model to predict effects of ozone and drought on growth of a white fir tree.

A physiologically based, single-tree simulation model, TREGRO, was parameterized with existing phenological, allometric, and growth data and used to predict effects of ozone and drought on growth of a 53-year-old white fir (Abies concolor (Gord. & Glend.) Lindl. ex Hildebr.) tree following a 3-year model simulation. Multiple experimental simulations were conducted to assess the individual and interactive effects of ozone (O(3)) exposure and drought on growth of white fir. The effects of O(3) were imposed as reductions in carbon (C) assimilation of 0, 2.5, 5, 10, and 20%. Drought was imposed as 0, 10, 25, and 50% reductions in total annual precipitation. The results of the simulations were compared with the effects of O(3) on white fir seedlings grown in the presence and absence of ozone in open-top chambers and with a field survey of white fir trees subjected to a gradient of O(3). In the O(3) simulations, an O(3)-induced reduction in C assimilation of 2.5% reduced total tree biomass and branch total nonstructural carbohydrate (TNC) content by < 7%. Although quantifiable in simulation experiments, such small reductions would probably not be detectable in the field. Results from both an open-top chamber experiment and a field survey indicated that reductions in C assimilation of white fir growing in elevated O(3) were much greater than 2.5%, but were not statistically different from control values. A simulated O(3) reduction in C assimilation of >/= 10% reduced total tree biomass by 7% and branch TNC by 55%. Results from the field survey indicated that branch elongation was reduced in response to increased O(3) concentration, corroborating the simulated response of reduced C allocation to the branches of white fir. Although simulated reductions in total annual precipitation of >/= 25% reduced final tree biomass, the simulated reductions also reduced O(3) uptake and therefore reduced the O(3) response of white fir. However, a combination of low amounts of O(3) (2.5% reduction in C assimilation) and drought (25% reduction in annual precipitation) synergistically reduced C gain of white fir more than either stress individually. Our simulations predict that moderate drought (no more than a 25% reduction in total annual precipitation) may not ameliorate the response of white fir to O(3) and that moderate amounts of atmospheric O(3) and drought could be more detrimental to white fir than either stress singly.

Journal Article↗
PubMed2006

Widespread discordance of gene trees with species tree in Drosophila: evidence for incomplete lineage sorting.

The phylogenetic relationship of the now fully sequenced species Drosophila erecta and D. yakuba with respect to the D. melanogaster species complex has been a subject of controversy. All three possible groupings of the species have been reported in the past, though recent multi-gene studies suggest that D. erecta and D. yakuba are sister species. Using the whole genomes of each of these species as well as the four other fully sequenced species in the subgenus Sophophora, we set out to investigate the placement of D. erecta and D. yakuba in the D. melanogaster species group and to understand the cause of the past incongruence. Though we find that the phylogeny grouping D. erecta and D. yakuba together is the best supported, we also find widespread incongruence in nucleotide and amino acid substitutions, insertions and deletions, and gene trees. The time inferred to span the two key speciation events is short enough that under the coalescent model, the incongruence could be the result of incomplete lineage sorting. Consistent with the lineage-sorting hypothesis, substitutions supporting the same tree were spatially clustered. Support for the different trees was found to be linked to recombination such that adjacent genes support the same tree most often in regions of low recombination and substitutions supporting the same tree are most enriched roughly on the same scale as linkage disequilibrium, also consistent with lineage sorting. The incongruence was found to be statistically significant and robust to model and species choice. No systematic biases were found. We conclude that phylogenetic incongruence in the D. melanogaster species complex is the result, at least in part, of incomplete lineage sorting. Incomplete lineage sorting will likely cause phylogenetic incongruence in many comparative genomics datasets. Methods to infer the correct species tree, the history of every base in the genome, and comparative methods that control for and/or utilize this information will be valuable advancements for the field of comparative genomics.

Animals↗
PubMedDate not supplied

[Tree reconciliation: reconstruction of species evolution by phylogenetic gene trees].

It is well known that phylogenetic trees derived from different protein families are often incongruent. This is explained by mapping errors and by the essential processes of gene duplication, loss, and horizontal transfer. Therefore, the problem is to derive a "consensus" tree best fitting the given set of gene trees. This work presents a new method of deriving this tree. The method is different from the existing ones, since it considers not only the topology of the initial gene trees, but also the reliability of their branches. Thereby one can explicitly take into account the possible errors in the gene trees caused by the absence of reliable models of sequence evolution, by uneven evolution of different gene families and taxonomic groups, etc.

Algorithms↗
PubMed2004

Use of modeled photosynthesis and decomposition to describe tree growth at the northern tree line.

Growth of subarctic Scots pine (Pinus sylvestris L.) trees was investigated by a combination of process-based models and dendroecological approaches. Tree ring width indices were strongly autocorrelated and correlated with simulated photosynthetic production of the previous year and with organic matter N mineralization of the current year. An autoregressive model, with photosynthesis and N mineralization as external inputs, explained growth of the trees well. However, relationships for the period 1950-1992 differed significantly from relationships for the period 1876-1949; the slope of the regression of tree ring width index and photosynthesis was lower for the 1950-1992 period. Also, the autocorrelation structure of the data changed. First-order autocorrelation decreased and second-order autocorrelation increased from the earlier to the later period. This means that growth is becoming less sensitive to variations in photosynthetic production, whereas the relationships between growth and N mineralization are remaining fairly constant. We postulate that, although photosynthesis has increased in response to increasing CO2 concentrations, tree growth rate cannot parallel the increase in photosynthesis because potential growth rate is limited directly by temperature.

Carbon Dioxide↗
PubMed1998

Tea tree oil allergy: what is the offending agent? Report of three cases of tea tree oil allergy and review of the literature.

Tea tree oil is currently enjoying popularity as a 'cure-all' for a variety of skin conditions, from infections to psoriasis, and many household and personal products containing Melaleuca oil are available. However, despite its chemical complexities and enthusiastic use, there have been only a few reports of allergic reactions to tea tree oil. At the Skin and Cancer Foundation (Sydney, NSW, Australia), three of 28 normal volunteers tested strongly positive to patch testing with tea tree oil. Following further patch testing with tea tree oil constituents, all three patients reacted strongly to two preparations containing sesquiterpenoid fractions of the oil. Because patients often neglect to mention that they have used 'natural' remedies, it is important that physicians are aware of the potential adverse effects of these products. Furthermore, identification of the allergenic ingredients in tea tree oil may assist the growing industry to produce safer products.

Adult↗
PubMed1998

Feature trees: a new molecular similarity measure based on tree matching.

In this paper we present a new method for evaluating molecular similarity between small organic compounds. Instead of a linear representation like fingerprints, a more complex description, a feature tree, is calculated for a molecule. A feature tree represents hydrophobic fragments and functional groups of the molecule and the way these groups are linked together. Each node in the tree is labeled with a set of features representing chemical properties of the part of the molecule corresponding to the node. The comparison of feature trees is based on matching subtrees of two feature trees onto each other. Two algorithms for tackling the matching problem are described throughout this paper. On a dataset of about 1000 molecules, we demonstrate the ability of our approach to identify molecules belonging to the same class of inhibitors. With a second dataset of 58 molecules with known binding modes taken from the Brookhaven Protein Data Bank, we show that the matchings produced by our algorithms are compatible with the relative orientation of the molecules in the active site in 61% of the test cases. The average computation time for a pair comparison is about 50 ms on a current workstation.

Algorithms↗
PubMed1996

Measuring tree-ring increments on tree bole sections with a video-based robotic positioner.

We report on the design and performance of a system that speeds measurement of radial tree-ring increments on tree stem disks; this method replaces the usual binocular microscope with a video image, and automates the measuring and recording processes. The system was used to measure bole sections cut from stems at various heights to determine volume growth of representative trees in an old-growth ponderosa pine stand. The objective of the measurement system was to speed acquisition of annual growth increments from a large number of disks. A personal computer controls the location of a video camera in a 3-axis positioning system. The operator views the sample on a video monitor and positions the camera over each ring by selecting it with a computer-driven mouse. The computer measures and records the distance that the camera moves between each ring. Task selection is facilitated by menu-driven software that also formats, checks and organizes data files. Measurements have a resolution of 0.026 mm; however, finer resolution could be obtained with a different camera lens. Tests of measurement variability (repeated measurements by individual operators on a single radius) indicated standard errors of 0.006 mm or less for the first measurement sets for four operators. Correlation coefficients among four radii per bole section were as low as 0.66 for a whole tree, suggesting that measurements on single radii may provide poor estimates of radial growth for old trees. This system also offers the potential for automatic ring detection and measurement.

Journal Article↗
PubMed1991

Tree allometry, leaf size and adult tree size in old-growth forests of western Oregon.

Relationships between tree height and crown dimensions and trunk diameter were determined for shade-tolerant species of old-growth forests of western Oregon. The study included both understory and overstory species, deciduous and evergreen angiosperms and evergreen conifers. A comparison of adult understory species with sapling overstory species of similar height showed greater crown width and trunk diameter in the former, whether the comparison is made among conifers or deciduous trees. Conifer saplings had wider crowns than deciduous saplings, but the crown widths of the two groups converged with increase in tree height. Conifer saplings had thicker trunks than deciduous saplings of similar crown width, possibly because of selection for resistance to stem bending under snow loads. The results suggest that understory species have morphologies that increase light interception and persistence in the understory, whereas overstory species allocate their biomass for efficient height growth, thereby attaining the high-light environment of the canopy. The greater crown widths and the additional strength requirements imposed by snow loads on conifer saplings result in less height growth per biomass increment in conifer saplings than in deciduous saplings. However, the convergence in crown width of the two groups at heights greater than 20 m, and the proportionately smaller effect of snow loads on large trees, may result in older conifers equalling or surpassing deciduous trees in biomass allocation to height growth.

Journal Article↗
PubMed1984

Pulse-radiolysis studies on the interaction of one-electron reduced species with blue oxidases. Reduction of native and type-2-copper-depleted Vietnamese-lacquer-tree and Japanese-lacquer-tree laccases.

The interactions of one-electron reduced metronidazole (ArNO2.-) and O2.- with native and Type-2-copper-depleted Vietnamese- and Japanese-lacquer-tree laccases were studied in aqueous solution at pH 6.0 and 7.4 by using the technique of pulse radiolysis. On reaction with ArNO2.-, in the absence of O2, the holo- and the Type-2-copper-depleted proteins accept, with reduction of Type 1 copper, 2 and 1 reducing equivalents respectively. On reaction with O2.- of both holo- and Type-2-copper-depleted Vietnamese-lacquer-tree laccase, almost complete reduction of Type 1 copper was observed and, after completion of the reaction, some (less than 20%) reoxidation of Type 1 copper occurs. Reduction of Type 1 copper of the laccases by these one-electron donors occurs via a bimolecular step; however, the rate of reduction of Vietnamese-lacquer-tree laccase is over 10 times that of Japanese-lacquer-tree laccase. It is inferred that electrons enter the protein via Type 1 copper with, in the case of the holoprotein, subsequent rapid intramolecular transfer of 1 reducing equivalent within the protein. Furthermore it is suggested that intra-molecular electron transfer to Type 3 copper atoms is slow and, in the case of Type-2-copper-depleted protein, may not occur. This slow process may partially account for the variation of the catalytic activities of 'blue' oxidases.

Copper↗