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PubMed2003

Development of a mathematical method for classifying and comparing tree architecture using parameters from a topological model of a trifurcating botanical tree.

This paper describes a model for the topological mapping of trifurcating botanical trees. The model was based on a system of modular units that represented the interconnectivity of shoot meristems (terminal segments) and internodes (internal segments) within whole plant canopies, organized with increasing centrifugal ordering. The model was capable of describing the dynamics of plant growth as expressed by changes in topological parameters over time. Preliminary calculations for experimental trees indicated that the model represents growth in a biologically sound manner. Methods are described for the calculation of the architecture parameters size, size-complexity, structural complexity, and tree asymmetry index (TAI). Parameter calculations were based on the mathematical principles developed for the classification of bifurcating dendrite trees, and were designed to both extract structural information, and to enable statistical comparison between trees of different size. Parameters were mathematically adjusted for trifurcation, and appeared to be able to represent quantitatively the architectural properties of tree structures. In addition to the calculation of the TAI for trifurcating trees, new methods were developed to enable comparisons to be made of the architectural complexity of trifurcating trees of differing size. These were based on the principle of the pair-wise comparison of the mean centrifugal order number (MCON) with respect to segments against highest order number. We argue and illustrate that this principle can be more informative than that of pair-wise comparison of the MCON against tree degree (topological size). Further improvements to this method were made by examining branching points (vertices) rather than segments (links) to calculate the MCON.

Models, Biological↗
PubMed2006

Optimal gene trees from sequences and species trees using a soft interpretation of parsimony.

Gene duplication and gene loss as well as other biological events can result in multiple copies of genes in a given species. Because of these gene duplication and loss dynamics, in addition to variation in sequence evolution and other sources of uncertainty, different gene trees ultimately present different evolutionary histories. All of this together results in gene trees that give different topologies from each other, making consensus species trees ambiguous in places. Other sources of data to generate species trees are also unable to provide completely resolved binary species trees. However, in addition to gene duplication events, speciation events have provided some underlying phylogenetic signal, enabling development of algorithms to characterize these processes. Therefore, a soft parsimony algorithm has been developed that enables the mapping of gene trees onto species trees and modification of uncertain or weakly supported branches based on minimizing the number of gene duplication and loss events implied by the tree. The algorithm also allows for rooting of unrooted trees and for removal of in-paralogues (lineage-specific duplicates and redundant sequences masquerading as such). The algorithm has also been made available for download as a software package, Softparsmap.

Algorithms↗
PubMed2000

Supercooling Capacity Increases from Sea Level to Tree Line in the Hawaiian Tree Species Metrosideros polymorpha.

Population-specific differences in the freezing resistance of Metrosideros polymorpha leaves were studied along an elevational gradient from sea level to tree line (located at ca. 2500 m above sea level) on the east flank of the Mauna Loa volcano in Hawaii. In addition, we also studied 8-yr-old saplings grown in a common garden from seeds collected from the same field populations. Leaves of low-elevation field plants exhibited damage at -2 degrees C, before the onset of ice formation, which occurred at -5.7 degrees C. Leaves of high-elevation plants exhibited damage at ca. -8.5 degrees C, concurrent with ice formation in the leaf tissue, which is typical of plants that avoid freezing in their natural environment by supercooling. Nuclear magnetic resonance studies revealed that water molecules of both extra- and intracellular leaf water fractions from high-elevation plants had restricted mobility, which is consistent with their low water content and their high levels of osmotically active solutes. Decreased mobility of water molecules may delay ice nucleation and/or ice growth and may therefore enhance the ability of plant tissues to supercool. Leaf traits that correlated with specific differences in supercooling capacity were in part genetically determined and in part environmentally induced. Evidence indicated that lower apoplastic water content and smaller intercellular spaces were associated with the larger supercooling capacity of the plant's foliage at tree line. The irreversible tissue-damage temperature decreased by ca. 7 degrees C from sea level to tree line in leaves of field populations. However, this decrease appears to be only large enough to allow M. polymorpha trees to avoid leaf tissue damage from freezing up to a level of ca. 2500 m elevation, which is also the current tree line location on the east flank of Mauna Loa. The limited freezing resistance of M. polymorpha leaves may be partially responsible for the occurrence of tree line at a relatively low elevation in Hawaii compared with continental tree lines, which can be up to 1500 m higher. If the elevation of tree line is influenced by the inability of M. polymorpha leaves to supercool to lower subzero temperatures, then it will be the first example that freezing damage resulting from limited supercooling capacity can be a factor in tree line formation.

Journal Article↗
PubMed2003

Exploring within-tree architectural development of two apple tree cultivars over 6 years.

The present study addresses the prediction of apple tree development, taking into account both the number and within-tree position of tree components. The architectural development of two trees per scion cultivar, 'Fuji' and 'Braeburn', was studied by describing all shoots over 6 years. Flowering and fruiting were observed over 3 years. The description included different scales [entire trees, axes, growth units (GUs) and metamers], and the analysis compared all axes of the trees as a function of their branching order and age. Three main aspects of vegetative development were investigated: the quantity of primary growth; the number and nature of developing axillary shoots; and meristem death. Results confirm the existence of within-tree morphological gradients, and show that the decrease in growth was comparable in magnitude for all axes and GUs, irrespective of their position. This decrease results from a reduction in the number of metamers per GU, which was modelled by an exponential function. The decrease in growth involved changes in the number and nature of the axillary shoots, which could be described by simple functions. The probability of spur death was constant over the years but differed according to cultivar and type of bearing shoot. The within-tree probability of flowering and fruiting was predictable for 'Braeburn' because axes, regardless of their position and type, had a high probability of flowering and a low probability of fruit set which led to a regular bearing habit. In contrast, 'Fuji' had an alternating bearing behaviour that was more complex to predict. This appeared to result from a synchronized increase in the probability that all GUs at tree scale are floral, combined with a high probability of fruit set. The consequences of these results for both yield prediction and architectural simulations are discussed.

Flowers↗
PubMed1997

Trees within trees: genes and species, molecules and morphology.

The construction and interpretation of gene trees is fundamental in molecular systematics. If the gene is defined in a historical (coalescent) sense, there can be multiple gene trees within the single contiguous set of nucleotides, and attempts to construct a single tree for such a sequence must deal with homoplasy created by conflict among divergent histories. On a larger scale, incongruence is expected among gene tree topologies at different loci of individuals within sexually reproducing species, and it has been suggested that this discordance can be used to delimit species. A practical concern for such topological methods is that polymorphisms may be maintained through numerous cladogenic events; this polymorphism problem is less of a concern for nontopological approaches to species delimitation using molecular data. Although a central theoretical concern in molecular systematics is discordance between a given gene tree and the true "species tree," the primary empirical problem faced in reconstructing taxic phylogeny is incongruence among the trees inferred from different sequences. Linkage relationships limit character independence and thus have important implications for handling multiple data sets in phylogenetic analysis, particularly at the species level, where incongruence among different historically associated loci is expected. Gene trees can also be reconstructed for loci that influence phenotypic characters, but there is at best a tenuous relationship between phenotypic homoplasy and homoplasy in such gene trees. Nevertheless, expression patterns and orthology relationships of genes involved in the expression of phenotypes can in theory provide criteria for homology assessment of morphological characters.

Anatomy, Comparative↗
PubMed2005

Relating tree growth to rainfall in Bolivian rain forests: a test for six species using tree ring analysis.

Many tropical regions show one distinct dry season. Often, this seasonality induces cambial dormancy of trees, particularly if these belong to deciduous species. This will often lead to the formation of annual rings. The aim of this study was to determine whether tree species in the Bolivian Amazon region form annual rings and to study the influence of the total amount and seasonal distribution of rainfall on diameter growth. Ring widths were measured on stem discs of a total of 154 trees belonging to six rain forest species. By correlating ring width and monthly rainfall data we proved the annual character of the tree rings for four of our study species. For two other species the annual character was proved by counting rings on trees of known age and by radiocarbon dating. The results of the climate-growth analysis show a positive relationship between tree growth and rainfall in certain periods of the year, indicating that rainfall plays a major role in tree growth. Three species showed a strong relationship with rainfall at the beginning of the rainy season, while one species is most sensitive to the rainfall at the end of the previous growing season. These results clearly demonstrate that tree ring analysis can be successfully applied in the tropics and that it is a promising method for various research disciplines.

Bolivia↗
PubMed1992

Tree asymmetry--a sensitive and practical measure for binary topological trees.

The topological structure of a binary tree is characterized by a measure called tree asymmetry, defined as the mean value of the asymmetry of its partitions. The statistical properties of this tree-asymmetry measure have been studied using a growth model for binary trees. The tree-asymmetry measure appears to be sensitive for topological differences and the tree-asymmetry expectation for the growth model that we used appears to be almost independent of the size of the trees. These properties and the simple definition make the measure suitable for practical use, for instance for characterizing, comparing and interpreting sets of branching patterns. Examples are given of the analysis of three sets of neuronal branching patterns. It is shown that the variance in tree-asymmetry values for these observed branching patterns corresponds perfectly with the variance predicted by the used growth model.

Animals↗
PubMed2004

Stable carbon isotopic composition of tree rings from a pine tree from Augustów Wilderness, Poland, as a temperature and local environment conditions indicator.

Tree rings can be used as archives of climatic and environmental data with annual resolution. Tree rings widths, maximum late wood density and other parameters as stable composition in tree rings can be used for the reconstruction of past climatic and environmental changes. Stable carbon isotope ratios in tree rings may provide valuable information on past climatic conditions. 13C/12C ratios of plant organic matter can reflect corresponding 13C/12C ratio of atmospheric CO2 during formation of the rings. Investigations of isotopic carbon composition in tree rings from in the ecologically clean the Augustów Wilderness region in the north-eastern part of Poland (22 degrees 58'E, 53 degrees 51'N) (nowadays a sanctuary) were undertaken. Series of delta13C in alpha-cellulose and in wholewood were acquired. Those measurements constituted a part of more complex investigations of carbon isotope composition in tree rings including the measurements of radiocarbon concentration and tree ring widths. This article presents preliminary results. It is argued that contrary to the tree ring widths and delta13C in wholewood that do not reveal significant correlation with temperature, the variation of delta13C in the latewood alpha-cellulose is correlated with combined July and August temperatures.

Carbon Isotopes↗
PubMed2005

Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases.

MOTIVATION: Comparative sequence analysis is widely used to study genome function and evolution. This approach first requires the identification of homologous genes and then the interpretation of their homology relationships (orthology or paralogy). To provide help in this complex task, we developed three databases of homologous genes containing sequences, multiple alignments and phylogenetic trees: HOBACGEN, HOVERGEN and HOGENOM. In this paper, we present two new tools for automating the search for orthologs or paralogs in these databases. RESULTS: First, we have developed and implemented an algorithm to infer speciation and duplication events by comparison of gene and species trees (tree reconciliation). Second, we have developed a general method to search in our databases the gene families for which the tree topology matches a peculiar tree pattern. This algorithm of unordered tree pattern matching has been implemented in the FamFetch graphical interface. With the help of a graphical editor, the user can specify the topology of the tree pattern, and set constraints on its nodes and leaves. Then, this pattern is compared with all the phylogenetic trees of the database, to retrieve the families in which one or several occurrences of this pattern are found. By specifying ad hoc patterns, it is therefore possible to identify orthologs in our databases.

Algorithms↗
PubMed2006

Discordance of species trees with their most likely gene trees.

Because of the stochastic way in which lineages sort during speciation, gene trees may differ in topology from each other and from species trees. Surprisingly, assuming that genetic lineages follow a coalescent model of within-species evolution, we find that for any species tree topology with five or more species, there exist branch lengths for which gene tree discordance is so common that the most likely gene tree topology to evolve along the branches of a species tree differs from the species phylogeny. This counterintuitive result implies that in combining data on multiple loci, the straightforward procedure of using the most frequently observed gene tree topology as an estimate of the species tree topology can be asymptotically guaranteed to produce an incorrect estimate. We conclude with suggestions that can aid in overcoming this new obstacle to accurate genomic inference of species phylogenies.

Algorithms↗
PubMed2001

S-TREE: self-organizing trees for data clustering and online vector quantization.

This paper introduces S-TREE (Self-Organizing Tree), a family of models that use unsupervised learning to construct hierarchical representations of data and online tree-structured vector quantizers. The S-TREE1 model, which features a new tree-building algorithm, can be implemented with various cost functions. An alternative implementation, S-TREE2, which uses a new double-path search procedure, is also developed. The performance of the S-TREE algorithms is illustrated with data clustering and vector quantization examples, including a Gauss-Markov source benchmark and an image compression application. S-TREE performance on these tasks is compared with the standard tree-structured vector quantizer (TSVQ) and the generalized Lloyd algorithm (GLA). The image reconstruction quality with S-TREE2 approaches that of GLA while taking less than 10% of computer time. S-TREE1 and S-TREE2 also compare favorably with the standard TSVQ in both the time needed to create the codebook and the quality of image reconstruction.

Algorithms↗
PubMed2005

Ontogenetic transition of leaf physiology and anatomy from seedlings to mature trees of a rain forest pioneer tree, Macaranga gigantea.

In a field study, we compared anatomy and diurnal gas exchange and chlorophyll fluorescence in sunlit mature leaves of Macaranga gigantea (Reichb. f. and Zoll.) Muell. seedlings, saplings, an adult tree and suckers originating from stumps. We tested the hypothesis that the pattern of resource use shifts across various life stages with ontogenetic changes in leaf anatomy and physiology. Among leaves of different developmental stages, seedling leaves were the smallest and thinnest, whereas adult tree leaves were the largest and thickest, and the air space within the lamina was largest in seedling leaves and smallest in adult tree leaves. Photosynthetic nitrogen-use efficiency (PNUE) was higher in seedling and sapling leaves than in adult tree leaves. Mean PNUE in seedling leaves was 1.6 times that in adult tree leaves. Nevertheless, among the developmental stages, net photosynthetic rate (Pn) per unit leaf area was lowest in seedling leaves because they have the lowest nitrogen (N) content per unit leaf area. In situ water vapor stomatal conductance (g(s) at a given leaf-to-air vapor pressure deficit was highest in sapling leaves, suggesting that they have a high hydraulic efficiency per unit leaf area. Among developmental stages, intrinsic water-use efficiency (Pn/g(s)) and photochemical capacity of photosystem II were lowest in seedling leaves. Sapling leaves had the highest N concentration and Pn per unit dry mass and the highest g(s), indicating that the gradual transition from the seedling stage to the sapling stage is accompanied by an accumulation of N in plant bodies and the development of hydraulic systems to counteract unfavorable environmental stresses. The properties of adult tree leaves (low PNUE, high carbon:N ratio, small and dense cells and thick lamina) indicate that, during the transition from the sapling stage to the adult tree stage, the priority of resource use in leaves gradually shifts from enhancement of photosynthetic performance to defense against herbivory and mechanical damage. Leaf morphology and physiology were coordinated with the differences in resource use at each life stage.

Carbon Dioxide↗
PubMed1984

Tree pollen allergy. II. Sensitization to various tree pollen allergens in Sweden. A multi-centre study.

In a multi-centre study, comprising 16 clinics, 871 adult hay fever patients were studied. Most patients included had springtime hay fever. Skin prick tests were performed with 20 different tree or bush pollen (lignoses) allergens. RAST determinations were done with eight different tree pollen allergens in 590 patients. Birch pollen (BP) allergen gave the highest frequency of positive test results. The test results with the various tree pollen allergens in patients with BP allergy were compared with those in patients without BP allergy. With all the allergens a significantly higher frequency of positive test results was found in those with BP allergy than in those without. Only very small differences were noted between various parts of the country, and sensitization against various tree pollens was common even in regions where the corresponding trees do not grow. It was concluded that a high degree of cross-sensitization exists among tree pollens, and testing with BP allergen is sufficient for the diagnostic screening of tree pollen allergy.

Humans↗
PubMed1995

Contents of free amino acids in needles of Norway Spruce trees in relation to novel forest decline. Studies on trees from a site in the northern Black Forest.

The free amino acid content in needles of Norway spruce trees (about 45-year-old) was determined by means of HPLC. The studied trees have been growing at a forestry site in the Black Forest which is characterized by a high impact of ozone and magnesium deficiency. Measurements were carried out on visibly healthy and on damaged trees on several dates during two vegetation periods and during the course of a day. The amino acids occurring at the highest concentrations were glutamate, arginine, aspartate, and glutamine. The typical seasonal changes in the content of free amino acids, with their minimum during summer, were disturbed in the needles of the damaged trees. Particularly in summer and autumn the damaged trees showed increased levels of total amino acids and of most single amino acids. During the course of a day, the needles of the damaged trees showed a reduced amplitude in diurnal variations with the absolute level almost always higher in comparison to that of the undamaged trees. The results suggest that a shift in protein turnover towards enhanced degradation has taken place.

Journal Article↗
PubMed2002

Genome trees and the tree of life.

Genome comparisons indicate that horizontal gene transfer and differential gene loss are major evolutionary phenomena that, at least in prokaryotes, involve a large fraction, if not the majority, of genes. The extent of these events casts doubt on the feasibility of constructing a 'Tree of Life', because the trees for different genes often tell different stories. However, alternative approaches to tree construction that attempt to determine tree topology on the basis of comparisons of complete gene sets seem to reveal a phylogenetic signal that supports the three-domain evolutionary scenario and suggests the possibility of delineation of previously undetected major clades of prokaryotes. If the validity of these whole-genome approaches to tree building is confirmed by analyses of numerous new genomes, which are currently being sequenced at an increasing rate, it would seem that the concept of a universal 'species' tree is still appropriate. However, this tree should be reinterpreted as a prevailing trend in the evolution of genome-scale gene sets rather than as a complete picture of evolution.

Animals↗
PubMedDate not supplied

Structure trees and species trees: what they say about morphological development and evolution.

The evolutionary history of morphological structures generally is equated with that of the taxa that carry them. It is argued here that, analogous to genes, developmental genetic pathways underlying morphological structures may be subject to developmental evolutionary changes that result, for instance, in duplication (serial homology analogous to gene duplication and paralogy). Entities that undergo evolution are expected to be related to each other as a tree. Just as with molecular evolution, "structure trees" and species trees sometimes may be incongruent, with implications for morphological homology concepts. Detection of structure trees through morphological evolutionary analyses may point to an entity that is maintained through evolution, possibly in part because it is a developmentally integrated structure ("individualized"). This idea is illustrated in a morphological evolutionary analysis of leaf primordia. These analyses suggest that leaf primordia in monocots and close relatives are related to each other as a tree and, therefore, are developmentally integrated, evolving entities. Among monocot primordia this tree structure breaks down, and it is concluded that there is no entity, the "monocot leaf primordium." However, one group of primordia is identified within monocots that have uniform characteristics and that are well represented by model species maize and rice. Such analyses of structure trees can facilitate the extrapolation and interpretation of results from molecular developmental and other comparative studies.

Flowers↗
PubMed2005

Assessment of protein distance measures and tree-building methods for phylogenetic tree reconstruction.

Distance-based methods are popular for reconstructing evolutionary trees of protein sequences, mainly because of their speed and generality. A number of variants of the classical neighbor-joining (NJ) algorithm have been proposed, as well as a number of methods to estimate protein distances. We here present a large-scale assessment of performance in reconstructing the correct tree topology for the most popular algorithms. The programs BIONJ, FastME, Weighbor, and standard NJ were run using 12 distance estimators, producing 48 tree-building/distance estimation method combinations. These were evaluated on a test set based on real trees taken from 100 Pfam families. Each tree was used to generate multiple sequence alignments with the ROSE program using three evolutionary models. The accuracy of each method was analyzed as a function of both sequence divergence and location in the tree. We found that BIONJ produced the overall best results, although the average accuracy differed little between the tree-building methods (normally less than 1%). A noticeable trend was that FastME performed poorer than the rest on long branches. Weighbor was several orders of magnitude slower than the other programs. Larger differences were observed when using different distance estimators. Protein-adapted Jukes-Cantor and Kimura distance correction produced clearly poorer results than the other methods, even worse than uncorrected distances. We also assessed the recently developed Scoredist measure, which performed equally well as more complex methods.

Base Sequence↗