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PubMed2000

NOTUNG: a program for dating gene duplications and optimizing gene family trees.

Large scale gene duplication is a major force driving the evolution of genetic functional innovation. Whole genome duplications are widely believed to have played an important role in the evolution of the maize, yeast, and vertebrate genomes. The use of evolutionary trees to analyze the history of gene duplication and estimate duplication times provides a powerful tool for studying this process. Many studies in the molecular evolution literature have used this approach on small data sets, using analyses performed by hand. The rapid growth of genetic sequence data will soon allow similar studies on a genomic scale, but such studies will be limited unless the analysis can be automated. Even existing data sets admit alternative hypotheses that would be too tedious to consider without automation. In this paper, we describe a program called NOTUNG that facilitates large scale analysis, using both rooted and unrooted trees. When tested on trees analyzed in the literature, NOTUNG consistently yielded results that agree with the assessments in the original publications. Thus, NOTUNG provides a basic building block for inferring duplication dates from gene trees automatically and can also be used as an exploratory analysis tool for evaluating alternative hypotheses.

Algorithms↗
PubMed1994

Reconstructing trees when sequence sites evolve at variable rates.

For a sequence of colors independently evolving on a tree under a simple Markov model, we consider conditions under which the tree can be uniquely recovered from the "sequence spectrum"-the expected frequencies of the various leaf colorations. This is relevant for phylogenetic analysis (where colors represent nucleotides or amino acids; leaves represent extant taxa) as the sequence spectrum is estimated directly from a collection of aligned sequences. Allowing the rate of the evolutionary process to vary across sites is an important extension over most previous studies-we show that, given suitable restrictions on the rate distribution, the true tree (up to the placement of its root) is uniquely identified by its sequence spectrum. However, if the rate distribution is unknown and arbitrary, then, for simple models, it is possible for every tree to produce the same sequence spectrum. Hence there is a logical barrier to accurate, consistent phylogenetic inference for these models when assumptions about the rate distribution are not made. This result exploits a novel theorem on the action of polynomials with non-negative coefficients on sequences.

Markov Chains↗
PubMed1997

The deferred path heuristic for the generalized tree alignment problem.

Many multiple alignment methods implicitly or explicitly try to minimize the amount of biological change implied by an alignment. At the level of sequences, biological change is measured along a phylogenetic tree, a structure frequently being predicted only after the multiple alignment instead of together with it. The Generalized Tree Alignment problem addresses both questions simultaneously. It can formally be viewed as a Steiner tree problem in sequence space and our approach merges a path heuristic for the construction of a Steiner tree with a clustering method as usually applied only to distance data. This combination is achieved using sequence graphs, a data structure for efficient representation of similar sequences. Although somewhat slower in practice than an earlier method by Hein (1989) the current approach achieves significantly better results in terms of the underlying scoring function. Furthermore, a variant of the algorithm is introduced that maintains a guaranteed error bound of (2 - 2/n) for n sequences.

Algorithms↗
PubMed2004

Microgeographic genome size differentiation of the carob tree, Ceratonia siliqua, at 'Evolution Canyon', Israel.

BACKGROUND AND AIMS: We tested whether the local differences in genome size recorded earlier in the wild barley, Hordeum spontaneum, at 'Evolution Canyon', Mount Carmel, Israel, can also be found in other organisms. As a model species for our test we chose the evergreen carob tree, Ceratonia siliqua. METHODS: Genome size was measured by means of DAPI flow cytometry. KEY RESULTS: In adults, significantly more DNA was recorded in trees growing on the more illuminated, warmer, drier, microclimatically more fluctuating 'African' south-facing slope than in trees on the opposite, less illuminated, cooler and more humid, 'European' north-facing slope in spite of an interslope distance of only 100 m at the canyon bottom and 400 m at the top. The amount of DNA was significantly negatively correlated with leaf length and tree circumference. In seedlings, interslope differences in the amount of genome DNA were not found. In addition, the first cases of triploidy and tetraploidy were found in C. siliqua. CONCLUSIONS: The data on C. siliqua at 'Evolution Canyon' showed that local variability in the C-value exists in this species and that ecological stress might be a strong evolutionary driving force in shaping the amount of DNA.

Biological Evolution↗
PubMed2004

Root system architecture of Quercus pubescens trees growing on different sloping conditions.

BACKGROUND AND AIMS: Plant roots' growth direction has important implications for plant development and survival; moreover it plays an effective and vital role in stabilizing weathered soil on a steep slope. The aim of this work was to assess the influence of slope on the architecture of woody root systems. METHODS: Five mature, single-stemmed Quercus pubescens trees growing on a steep slope and five on a shallow slope were excavated to a root diameter of 1 cm. A very precise numeric representation of the geometry and topology of structural root architecture was gained using a low-magnetic-field digitizing device (Fastrak, Polhemus). Several characteristics of root architecture were extracted by macros, including root volume, diameter, length, number, spatial position and branching order. KEY RESULTS: The diameter at breast height (dbh) was the best predictor of the root volume but had no correlation with length and number of roots. The slope affected the root volume for each branching order, and the basal cross-sectional area (CSA), number and length of the first-order roots. Number and length of the second- and third-order laterals were closely related in both conditions, although this relationship was closer in the shallow trees, suggesting the influence of a genetic control. Sloping trees showed a clustering tendency of the first- and second-order lateral roots in the up-slope direction, suggesting that the laterals rather than the taproots provide much of the anchorage. In a steep-slope condition, the taproot tapering was positively correlated with the asymmetry magnitude of first-order roots, indicating compensation between taproot and main lateral roots' clustering tendency. CONCLUSIONS: These results suggest that on a slope, on clayey soils, root asymmetry appears to be a consequence of several environmental factors such as inclination, shallow-slides and soil compactness. In addition, this adaptive growth seems to counteract the turning moment induced by the self-loading forces acting in slope conditions, and as a consequence improves the tree stability.

Environment↗
PubMed2006

Stomatal oscillations in orange trees under natural climatic conditions.

BACKGROUND AND AIMS: Stomatal oscillations have been reported in many plant species, but they are usually induced by sudden step changes in the environment when plants are grown under constant conditions. This study shows that in navel orange trees (Citrus sinensis) pronounced stomatal oscillations occur and persist under natural climatic conditions. METHODS: Oscillations in stomatal conductance were measured, and related to simultaneous measurements of leaf water potential, and flow rate of sap in the stems of young, potted plants. Cycling was also observed in soil-grown, mature orchard trees, as indicated by sap flow in stem and branches. KEY RESULTS: Oscillations in stomatal conductance were caused by the rapid propagation and synchronization of changes in xylem water potential throughout the tree, without rapid changes in atmospheric conditions. CONCLUSIONS: The results show marked stomatal oscillations persisting under natural climatic conditions and underscore the need to discover why this phenomenon is so pronounced in orange trees.

Biological Clocks↗
PubMed2006

Physiological effects of kaolin applications in well-irrigated and water-stressed walnut and almond trees.

BACKGROUND AND AIMS: Kaolin applications have been used to mitigate the negative effects of water and heat stress on plant physiology and productivity with variable results, ranging from increased to decreased yields and photosynthetic rates. The mechanisms of action of kaolin applications are not clear: although the increased albedo reduces leaf temperature and the consequent heat stress, it also reduces the light available for photosynthesis, possibly offsetting benefits of lower temperature. The objective of this study was to investigate which of these effects are prevalent and under which conditions. METHODS: A 6% kaolin suspension was applied on well-irrigated and water-stressed walnut (Juglans regia) and almond (Prunus dulcis) trees. Water status (i.e. stem water potential, psi(s)), gas exchange (i.e. light-saturated CO2 assimilation rate, Amax; stomatal conductance, g(s)), leaf temperature (T(l)) and physiological relationships in treated and control trees were then measured and compared. KEY RESULTS: In both species, kaolin did not affect the daily course of psi(s) whereas it reduced Amax by 1-4 micromol CO2 m(-2) s(-1) throughout the day in all combinations of species and irrigation treatments. Kaolin did not reduce g(s) in any situation. Consequently, intercellular CO2 concentration (C(i)) was always greater in treated trees than in controls, suggesting that the reduction of Amax with kaolin was not due to stomatal limitations. Kaolin reduced leaf temperature (T(l)) by about 1-3 degrees C and leaf-to-air vapour pressure difference (VPD(l)) by about 0.1-0.7 kPa. Amax was lower at all values of g(s), T(l) and VPD(l) in kaolin-treated trees. Kaolin affected the photosynthetic response to the photosynthetically active radiation (PAR) in almond leaves: kaolin-coated leaves had similar dark respiration rates and light-saturated photosynthesis, but a higher light compensation point and lower apparent quantum yield, while the photosynthetic light-response curve saturated at higher PAR. When these parameters were used to model the photosynthetic response curve to PAR, it was estimated that the kaolin film allowed 63% of the incident PAR to reach the leaf. CONCLUSIONS: The main effect of kaolin application was the reduction, albeit minor, of photosynthesis, which appeared to be related to the shading of the leaves. The reduction in T(l) and VPD(l) with kaolin did not suffice to mitigate the adverse effects of heat and water stress on Amax.

Carbon Dioxide↗
PubMed1994

fastDNAmL: a tool for construction of phylogenetic trees of DNA sequences using maximum likelihood.

We have developed a new tool, called fastDNAml, for constructing phylogenetic trees from DNA sequences. The program can be run on a wide variety of computers ranging from Unix workstations to massively parallel systems, and is available from the Ribosomal Database Project (RDP) by anonymous FTP. Our program uses a maximum likelihood approach and is based on version 3.3 of Felsenstein's dnaml program. Several enhancements, including algorithmic changes, significantly improve performance and reduce memory usage, making it feasible to construct even very large trees. Trees containing 40-100 taxa have been easily generated, and phylogenetic estimates are possible even when hundreds of sequences exist. We are currently using the tool to construct a phylogenetic tree based on 473 small subunit rRNA sequences from prokaryotes.

Algorithms↗
PubMed2002

TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing.

SUMMARY: TREE-PUZZLE is a program package for quartet-based maximum-likelihood phylogenetic analysis (formerly PUZZLE, Strimmer and von Haeseler, Mol. Biol. Evol., 13, 964-969, 1996) that provides methods for reconstruction, comparison, and testing of trees and models on DNA as well as protein sequences. To reduce waiting time for larger datasets the tree reconstruction part of the software has been parallelized using message passing that runs on clusters of workstations as well as parallel computers. AVAILABILITY: http://www.tree-puzzle.de. The program is written in ANSI C. TREE-PUZZLE can be run on UNIX, Windows and Mac systems, including Mac OS X. To run the parallel version of PUZZLE, a Message Passing Interface (MPI) library has to be installed on the system. Free MPI implementations are available on the Web (cf. http://www.lam-mpi.org/mpi/implementations/).

Algorithms↗
PubMed2002

A tree kernel to analyse phylogenetic profiles.

MOTIVATION: The phylogenetic profile of a protein is a string that encodes the presence or absence of the protein in every fully sequenced genome. Because proteins that participate in a common structural complex or metabolic pathway are likely to evolve in a correlated fashion, the phylogenetic profiles of such proteins are often 'similar' or at least 'related' to each other. The question we address in this paper is the following: how to measure the 'similarity' between two profiles, in an evolutionarily relevant way, in order to develop efficient function prediction methods? RESULTS: We show how the profiles can be mapped to a high-dimensional vector space which incorporates evolutionarily relevant information, and we provide an algorithm to compute efficiently the inner product in that space, which we call the tree kernel. The tree kernel can be used by any kernel-based analysis method for classification or data mining of phylogenetic profiles. As an application a Support Vector Machine (SVM) trained to predict the functional class of a gene from its phylogenetic profile is shown to perform better with the tree kernel than with a naive kernel that does not include any information about the phylogenetic relationships among species. Moreover a kernel principal component analysis (KPCA) of the phylogenetic profiles illustrates the sensitivity of the tree kernel to evolutionarily relevant variations.

Algorithms↗
PubMed1990

Comparing multiple RNA secondary structures using tree comparisons.

In a previous paper, an algorithm was presented for analyzing multiple RNA secondary structures utilizing a multiple string alignment algorithm. In this paper we present another approach to the problem of comparing many secondary structures by utilizing a very efficient tree-matching algorithm that will compare two trees in O([T1] X [T2] X L1 X L2) in the worst case and very close to O([T1] X [T2]) for average trees representing secondary structures. The result of the pairwise comparison algorithm is then used with a cluster algorithm to produce a multiple structure clustering which can be displayed in a taxonomy tree to show related structures.

Algorithms↗
PubMed2025

Bayesian inference of fitness landscapes via tree-structured branching processes.

MOTIVATION: The complex dynamics of cancer evolution, driven by mutation and selection, underlies the molecular heterogeneity observed in tumors. The evolutionary histories of tumors of different patients can be encoded as mutation trees and reconstructed in high resolution from single-cell sequencing data, offering crucial insights for studying fitness effects of and epistasis among mutations. Existing models, however, either fail to separate mutation and selection or neglect the evolutionary histories encoded by the tumor phylogenetic trees. RESULTS: We introduce FiTree, a tree-structured multi-type branching process model with epistatic fitness parameterization and a Bayesian inference scheme to learn fitness landscapes from single-cell tumor mutation trees. Through simulations, we demonstrate that FiTree outperforms state-of-the-art methods in inferring the fitness landscape underlying tumor evolution. Applying FiTree to a single-cell acute myeloid leukemia dataset, we identify epistatic fitness effects consistent with known biological findings and quantify uncertainty in predicting future mutational events. The new model unifies probabilistic graphical models of cancer progression with population genetics, offering a principled framework for understanding tumor evolution and informing therapeutic strategies. AVAILABILITY AND IMPLEMENTATION: The Python package FiTree and the analysis workflows are available at https://github.com/cbg-ethz/FiTree.

Bayes Theorem↗
PubMed2005

Mining SARS-CoV protease cleavage data using non-orthogonal decision trees: a novel method for decisive template selection.

MOTIVATION: Although the outbreak of the severe acute respiratory syndrome (SARS) is currently over, it is expected that it will return to attack human beings. A critical challenge to scientists from various disciplines worldwide is to study the specificity of cleavage activity of SARS-related coronavirus (SARS-CoV) and use the knowledge obtained from the study for effective inhibitor design to fight the disease. The most commonly used inductive programming methods for knowledge discovery from data assume that the elements of input patterns are orthogonal to each other. Suppose a sub-sequence is denoted as P2-P1-P1'-P2', the conventional inductive programming method may result in a rule like 'if P1 = Q, then the sub-sequence is cleaved, otherwise non-cleaved'. If the site P1 is not orthogonal to the others (for instance, P2, P1' and P2'), the prediction power of these kind of rules may be limited. Therefore this study is aimed at developing a novel method for constructing non-orthogonal decision trees for mining protease data. RESULT: Eighteen sequences of coronavirus polyprotein were downloaded from NCBI (http://www.ncbi.nlm.nih.gov). Among these sequences, 252 cleavage sites were experimentally determined. These sequences were scanned using a sliding window with size k to generate about 50,000 k-mer sub-sequences (for short, k-mers). The value of k varies from 4 to 12 with a gap of two. The bio-basis function proposed by Thomson et al. is used to transform the k-mers to a high-dimensional numerical space on which an inductive programming method is applied for the purpose of deriving a decision tree for decision-making. The process of this transform is referred to as a bio-mapping. The constructed decision trees select about 10 out of 50,000 k-mers. This small set of selected k-mers is regarded as a set of decisive templates. By doing so, non-orthogonal decision trees are constructed using the selected templates and the prediction accuracy is significantly improved.

Algorithms↗
PubMed1996

Contingency tests of neutrality using intra/interspecific gene trees: the rejection of neutrality for the evolution of the mitochondrial cytochrome oxidase II gene in the hominoid primates.

Contingency tests of neutrality are performed using mitochondrial cytochrome oxidase II (COII) DNA sequences from hominoid primates, including humans. An intra-/interspecific haplotype tree is estimated, including a statistical assessment of ambiguities in tree topology and branch lengths. Four functional mutational categories are considered: silent and replacement substitutions in the transmembrane portion of the COII molecule, and silent and replacement substitutions in the cytosolic portion. Three tree topological mutational categories are used: intraspecific tips, intraspecific interiors, and interspecific fixed mutations. A full contingency analysis is performed, followed by nested contingency analyses. The analyses indicate that replacement mutations in the cytosolic portion are deleterious, and replacement mutations in the transmembrane portion and silent mutations throughout tend to be neutral. These conclusions are robust to ambiguities in tree topology and branch lengths. These inferences would have been impossible with an analysis that only contrasts silent and replacement vs. polymorphic and fixed. Also, intraspecific interior mutations have similar evolutionary dynamics to fixed mutations, so pooling tip and interior mutations into a single "polymorphic" class reduces power. Finally, the detected deleterious selection causes lowered inbreeding effective sizes, so arguments for small effective sizes in recent human evolutionary history based upon mitochondrial DNA may be invalid.

Animals↗
PubMed2004

Annual and seasonal variation of sap flow and conductance of pine trees grown in elevated carbon dioxide and temperature.

Measurements of sap flow, crown structure, and microclimate were used to estimate the transpiration of individual 30-year-old Pinus sylvestris L. trees grown in elevated temperature and CO2. The trees were enclosed in closed-top chambers and exposed either to current ambient conditions (CON), or elevated CO2 (+350 micromol mol(-1); EC), or elevated temperature (+2 to +6 degrees C; ET) or a combination of EC and ET (ECT) since 1996, and the measurements were made from 1999 to 2001. EC significantly increased annual sap flow per tree (Ft.m) by 14% in 1999, but reduced it by 13% in 2000 and 16% in 2001. The CO2-induced increase in Ft.m in 1999 was due to a large increase in foliage area of trees, which more than compensated for a small decrease in crown conductance (Gc). The CO2-induced decreases in Ft.m in 2000 and 2001 resulted from a pronounced decline in Gc, which was much greater than the increase in foliage area. The CO2-induced increase in sensitivity of Gc at high vapour pressure deficit (VPD) did not alter the general response of sap flow to CO2 enrichment, but it did affect the diurnal courses of sap flow on some days during the main growing season (days 150-240). ET increased Ft.m by 53%, 45%, and 57% in 1999, 2000, and 2001, respectively, attributable to the combined effects of greater foliage area and maximum crown conductance, lower stomatal sensitivity to high VPD, and higher transpiration demand relative to the control treatments. There was no significant interaction between CO2 and temperature on sap flow, because ECT entailed approximately similar patterns of sap flow to ET, suggesting that the temperature played a dominate role in the case of ECT under boreal climate conditions.

Carbon Dioxide↗
PubMed2005

The rubber tree (Hevea brasiliensis Muell. Arg.) homologue of the LEAFY/FLORICAULA gene is preferentially expressed in both male and female floral meristems.

The rubber tree (Hevea brasiliensis Muell. Arg.) is an important source of natural rubber in tropical regions and, as with many woody species, shows a long juvenile phase. To understand the genetic and molecular mechanisms underlying the reproductive process in rubber trees, H. brasiliensis RRIM600 flower and inflorescence development have been characterized, the rubber tree FLORICAULA/LEAFY (FLO/LFY) orthologue, HbLFY, cloned, and its expression patterns were analysed during vegetative and reproductive development. The rubber tree, similar to other Euphorbiaceae species, produces lateral inflorescences containing male, female, and bisexual flowers. HbLFY is expressed in lateral meristems that give rise to inflorescences and in all flower meristems, consistent with a role in reproductive development. Complementation studies using Arabidopsis lfy mutants indicated that the biological function of LFY might be conserved among Brassicaceae and Euphorbiaceae species.

Arabidopsis↗
PubMed2006

Test a clade in phylogenetic trees.

We develop a new method for testing a portion of a tree (called a clade) based on multiple tests of many 4-taxon trees in this paper. This is particularly useful when the phylogenetic tree constructed by other methods have a clade that is difficult to explain from a biological point of view. The statement about the test of the clade can be made through the multiple P values from these individual tests. By controlling the familywise error rate or the false discovery rate (FDR), 4 different tree test methods are evaluated through simulation methods. It shows that the combination of the approximately unbiased (AU) test and the FDR-controlling procedure provides strong power along with reasonable type I error rate and less heavy computation.

Animals↗
PubMed2006

Paleontological evidence to date the tree of life.

The role of fossils in dating the tree of life has been misunderstood. Fossils can provide good "minimum" age estimates for branches in the tree, but "maximum" constraints on those ages are poorer. Current debates about which are the "best" fossil dates for calibration move to consideration of the most appropriate constraints on the ages of tree nodes. Because fossil-based dates are constraints, and because molecular evolution is not perfectly clock-like, analysts should use more rather than fewer dates, but there has to be a balance between many genes and few dates versus many dates and few genes. We provide "hard" minimum and "soft" maximum age constraints for 30 divergences among key genome model organisms; these should contribute to better understanding of the dating of the animal tree of life.

Animals↗