Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “phylogenetic tree”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 37 records · Page 2Linked to original sources
PubMed2004

[Introduction to the methods of constructing phylogenetic trees with DNA sequences].

Construction of phylogenetic trees is a key means in molecular evolutionary studies. The methods of constructing phylogenetic trees include the distance-based methods, parsimony, maximum likelihood, and Bayesian inference methods. To resolve a special problem about phylogeny, several notices are necessary: first, to select the reasonable data at less bias as possible; second, to choose the proper method to reconstruct phylogenetic tree; third, to evaluate the conclusions and explain them on the field of evolution. The present paper provides a brief introduction of the principles of data selection and tree-construction methods, and discusses about their advantage and disadvantage points.

Base Sequence↗
PubMed2004

Visualising very large phylogenetic trees in three dimensional hyperbolic space.

BACKGROUND: Common existing phylogenetic tree visualisation tools are not able to display readable trees with more than a few thousand nodes. These existing methodologies are based in two dimensional space. RESULTS: We introduce the idea of visualising phylogenetic trees in three dimensional hyperbolic space with the Walrus graph visualisation tool and have developed a conversion tool that enables the conversion of standard phylogenetic tree formats to Walrus' format. With Walrus, it becomes possible to visualise and navigate phylogenetic trees with more than 100,000 nodes. CONCLUSION: Walrus enables desktop visualisation of very large phylogenetic trees in 3 dimensional hyperbolic space. This application is potentially useful for visualisation of the tree of life and for functional genomics derivatives, like The Adaptive Evolution Database (TAED).

Animals↗
PubMed1986

Evidence against use of bacterial amino acid sequence data for construction of all-inclusive phylogenetic trees.

It has been proposed that phylogenetic trees, intended to show divergence of eukaryotic protein and nucleic acid sequences, be extended to include those from bacteria. However, we have compared the amino acid sequences of 18 of the most divergent mitochondrial cytochromes c with those of 18 bacterial cytochromes c2 and have found that the average percentage difference between these mitochondrial cytochromes c and cytochromes c2 was not significantly greater than that among the cytochromes c2 alone. The large discontinuities in physical-chemical properties recognized between the prokaryote and eukaryote cytochromes render it highly improbable that members of the two classes should be no more different from one another than members of either class alone, assuming that sequence differences can accurately reveal evolutionary divergence. Instead, we propose that divergent amino acid sequences approach a limit of change considerably less than for comparison of random sequences. This limit of change presumably is determined by the structure/function relationship. When two homologous protein sequences have reached such a limit, convergence or back-mutations and parallel mutations become as frequent as divergent mutations. As two diverging proteins approach this steady-state condition, sequence differences no longer reflect the numbers of mutations resulting in amino acid substitution and therefore species cannot be positioned on a phylogenetic tree. Insertions and deletions are less reversible than are amino acid substitutions and, provided they are well-documented, might be more reliable indicators of bacterial relationships. Nevertheless, we suggest that data available on bacterial protein sequences do not permit construction of all-inclusive phylogenetic trees. Comparisons of protein and rRNA trees suggest that similar restrictions apply to use of rRNA sequence data.

Amino Acid Sequence↗
PubMed1999

Topology selection in unrooted molecular phylogenetic tree by minimum model-based complexity method.

In reconstruction of phylogenetic trees from molecular data, it has been pointed out that multifurcate phylogenetic trees are difficult to be correctly reconstructed by the conventional methods like maximum likelihood method(ML). In order to resolve this problem, we have been engaged in developing a new phylogenetic tree reconstruction method, based on the minimum complexity principle widely used in the inductive inference. Our method, which we call "minimum model-based complexity (MBC) method", has been proved so far to be efficient in estimating multifurcate branching when the tree is described in the form of rooted one. In this study, we make further investigations about the efficiency of MBC method in estimating the multifurcation in unrooted phylogenetic trees. To do so, we conduct computer simulation in which the estimations by MBC method are compared with those by ML, AIC and statistical test approach. The results show that MBC method also provides good estimations even in the case of multifurcate unrooted trees and suggest that it could be generally used for reconstruction of phylogenetic tree having arbitrary multifurcations.

Biological Evolution↗
PubMed1983

Accuracy of estimated phylogenetic trees from molecular data. II. Gene frequency data.

The accuracies and efficiencies of three different methods of making phylogenetic trees from gene frequency data were examined by using computer simulation. The methods examined are UPGMA, Farris' (1972) method, and Tateno et al.'s (1982) modified Farris method. In the computer simulation eight species (or populations) were assumed to evolve according to a given model tree, and the evolutionary changes of allele frequencies were followed by using the infinite-allele model. At the end of the simulated evolution five genetic distance measures (Nei's standard and minimum distances, Rogers' distance, Cavalli-Sforza's f theta, and the modified Cavalli-Sforza distance) were computed for all pairs of species, and the distance matrix obtained for each distance measure was used for reconstructing a phylogenetic tree. The phylogenetic tree obtained was then compared with the model tree. The results obtained indicate that in all tree-making methods examined the accuracies of both the topology and branch lengths of a reconstructed tree (rooted tree) are very low when the number of loci used is less than 20 but gradually increase with increasing number of loci. When the expected number of gene substitutions (M) for the shortest branch is 0.1 or more per locus and 30 or more loci are used, the topological error as measured by the distortion index (dT) is not great, but the probability of obtaining the correct topology (P) is less than 0.5 even with 60 loci. When M is as small as 0.004, P is substantially lower. In obtaining a good topology (small dT and high P) UPGMA and the modified Farris method generally show a better performance than the Farris method. The poor performance of the Farris method is observed even when Rogers' distance which obeys the triangle inequality is used. The main reason for this seems to be that the Farris method often gives overestimates of branch lengths. For estimating the expected branch lengths of the true tree UPGMA shows the best performance. For this purpose Nei's standard distance gives a better result than the others because of its linear relationship with the number of gene substitutions. Rogers' or Cavalli-Sforza's distance gives a phylogenetic tree in which the parts near the root are condensed and the other parts are elongated. It is recommended that more than 30 loci, including both polymorphic and monomorphic loci, be used for making phylogenetic trees. The conclusions from this study seem to apply also to data on nucleotide differences obtained by the restriction enzyme techniques.

Algorithms↗
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↗
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

Reconstruction of large phylogenetic trees: a parallel approach.

Reconstruction of phylogenetic trees for very large datasets is a known example of a computationally hard problem. In this paper, we present a parallel computing model for the widely used Multiple Instruction Multiple Data (MIMD) architecture. Following the idea of divide-and-conquer, our model adapts the recursive-DCM3 decomposition method [Roshan, U., Moret, B.M.E., Williams, T.L., Warnow, T, 2004a. Performance of suptertree methods on various dataset decompositions. In: Binida-Emonds, O.R.P. (Eds.), Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life, vol. 3 of Computational Biology, Kluwer Academics, pp. 301-328; Roshan, U., Moret, B.M.E., Williams, T.L., Warnow, T., 2004b. Rec-I-DCM3: A Fast Algorithmic Technique for reconstructing large phylogenetic trees, Proceedings of the IEEE Computational Systems Bioinformatics Conference (ICSB)] to divide datasets into smaller subproblems. It distributes computation load over multiple processors so that each processor constructs subtrees on each subproblem within a batch in parallel. It finally collects the resulting trees and merges them into a supertree. The proposed model is flexible as far as methods for dividing and merging datasets are concerned. We show that our method greatly reduces the computational time of the sequential version of the program. As a case study, our parallel approach only takes 22.1h on four processors to outperform the best score to date (Found at 123.7h by the Rec-I-DCM3 program [Roshan, U., Moret, B.M.E., Williams, T.L., Warnow, T, 2004a. Performance of suptertree methods on various dataset decompositions. In: Binida-Emonds, O.R.P. (Eds.), Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life, vol. 3 of Computational Biology, Kluwer Academics, pp. 301-328; Roshan, U., Moret, B.M.E., Williams, T.L., Warnow, T., 2004b. Rec-I-DCM3: A Fast Algorithmic Technique for reconstructing large phylogenetic trees, Proceedings of the IEEE Computational Systems Bioinformatics Conference (ICSB)] on one dataset. Developed with the standard message-passing library, MPI, the program can be recompiled and run on any MIMD systems.

Journal Article↗
PubMed1988

[Evolution of RNA-dependent RNA-polymerases from positive RNA viruses: comparison of phylogenetic trees constructed by different methods].

Presumptive phylogenetic trees of evolutionary conserved fragments of RNA-dependent RNA polymerases of 26 positive strand RNA viruses were generated using a simple clustering procedure or a novel approach based on the so-called maximal topologic similarity principle. The latter methodology involves a quantitative measure of the degree of correspondence between the topology of generated trees and structure of the initial distance matrix. The algorithm for tree construction based on the maximal topologic similarity principle does not include the assumption of evolutionary rate constancy, as opposed to the clustering procedure. Nevertheless, it is demonstrated that the trees generated by the two methods are topologically similar, indicating that no drastic change of evolutionary rate had occurred in evolution of the positive strand RNA virus RNA polymerases. This in turn suggests that RNA-dependent RNA polymerases (or at least their evolutionary conserved core domains used for construction of the phylogenetic trees) are principally functionally equivalent in all positive strand RNA viruses.

Algorithms↗
PubMed2002

A web-based Tree View (TV) program for the visualization of phylogenetic trees.

We designed a web-based program, Tree View (TV), which uses a dynamic data structure algorithm to draw the phylogenetic tree for a family of homologous proteins. This program has a user-friendly interface and can be easily implemented into other programs for convenient protein sequence analysis. It is available at our web site: http://www.biology.ucsd.edu-yzhai/biotools.html.

Algorithms↗
PubMed2006

Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation.

UNLABELLED: Interactive Tree Of Life (iTOL) is a web-based tool for the display, manipulation and annotation of phylogenetic trees. Trees can be interactively pruned and re-rooted. Various types of data such as genome sizes or protein domain repertoires can be mapped onto the tree. Export to several bitmap and vector graphics formats is supported. AVAILABILITY: iTOL is available at http://itol.embl.de

Algorithms↗
PubMed2004

From a phylogenetic tree to a reticulated network.

In many phylogenetic problems, assuming that species have evolved from a common ancestor by a simple branching process is unrealistic. Reticulate phylogenetic models, however, have been largely neglected because the concept of reticulate evolution have not been supported by using appropriate analytical tools and software. The reticulate model can adequately describe such complicated mechanisms as hybridization between species or lateral gene transfer in bacteria. In this paper, we describe a new algorithm for inferring reticulate phylogenies from evolutionary distances among species. The algorithm is capable of detecting contradictory signals encompassed in a phylogenetic tree and identifying possible reticulate events that may have occurred during evolution. The algorithm produces a reticulate phylogeny by gradually improving upon the initial solution provided by a phylogenetic tree model. The new algorithm is compared to the popular SplitsGraph method in a reanalysis of the evolution of photosynthetic organisms. A computer program to construct and visualize reticulate phylogenies, called T-Rex (Tree and Reticulogram Reconstruction), is available to researchers at the following URL: www.fas.umontreal.ca/biol/casgrain/en/labo/t-rex.

Algorithms↗
PubMed2006

PTreeRec: Phylogenetic Tree Reconstruction based on genome BLAST distance.

Phylogenetic Tree Reconstruction (PTreeRec) is a web-based tool for automatic phylogeny inferences from whole-genome sequences, which accepts files of DNA sequences in the FASTA format and allows users to save the output tree file, and displays the inferred tree through an applet in a web browser. PTreeRec involves three basic steps. First, regions of maximal segment pairs (MSPs) based on an all-against-all pairwise comparison of genomes are located. Second, a distance matrix is calculated from MSP scores or coverage. Finally, a phylogenetic tree is reconstructed by the neighbor-joining method.

Algorithms↗
PubMed1979

A graph theoretic approach to the development of minimal phylogenetic trees.

The problem of determining the minimal phylogenetic tree is discussed in relation to graph theory. It is shown that this problem is an example of the Steiner problem in graphs which is to connect a set of points by a minimal length network where new points can be added. There is no reported method of solving realistically-sized Steiner problems in reasonable computing time. A heuristic method of approaching the phylogenetic problem is presented, together with a worked example with 7 mammalian cytochrome c sequences. It is shown in this case that the method develops a phylogenetic tree that has the smallest possible number of amino acid replacements. The potential and limitations of the method are discussed. It is stressed that objective methods must be used for comparing different trees. In particular it should be determined how close a given tree is to a mathematically determined lower bound. A theorem is proved which is used to establish a lower bound on the lenghtof any tree and if a tree is found with a length equal to the lower bound, then no shorter tree can exist.

Mathematics↗
PubMed2006

Orthonormal transform to decompose the variance of a life-history trait across a phylogenetic tree.

In recent years, there has been an increased interest in studying the variability of a quantitative life-history trait across a set of species sharing a common phylogeny. However, such studies have suffered from an insufficient development of statistical methods aimed at decomposing the trait variance with respect to the topological structure of the tree. Here we propose a new and generic approach that expresses the topological properties of the phylogenetic tree via an orthonormal basis, which is further used to decompose the trait variance. Such a decomposition provides a structure function, referred to as an "orthogram," which is relevant to characterize in both graphical and statistical aspects the dependence of trait values on the topology of the tree ("phylogenetic dependence"). We also propose four complementary test statistics to be computed from orthogram values that help to diagnose both the intensity and the nature of phylogenetic dependence. The relevance of the method is illustrated by the analysis of three phylogenetic data sets, drawn from the literature and typifying contrasted levels and aspects of phylogenetic dependence. Freely available routines which have been programmed in the R framework are also proposed.

Analysis of Variance↗
PubMed2005

apTreeshape: statistical analysis of phylogenetic tree shape.

apTreeshape is a R package dedicated to simulation and analysis of phylogenetic tree topologies using statistical imbalance measures. It is a companion library of the R package 'ape', which provides additional functions for reading, plotting, manipulating phylogenetic trees and for connecting to public phylogenetic tree databases. One strength of the package is to include appropriate corrections of classical shape statistics as well as new tests based on the statistical theory of likelihood ratios.

Algorithms↗
PubMed1990

A simple graphic method for reconstructing phylogenetic trees from molecular data.

A simple graphic method is proposed for reconstructing phylogenetic trees from molecular data. This method is similar to the unweighted pair-group method with arithmetic mean, but the process of computation of average distances and reconstruction of new matrices, required in the latter method, is eliminated from this new method, so that one can reconstruct a phylogenetic tree without using a computer, unless the number of operational taxonomic units is very large. Furthermore, this method allows a phylogenetic tree to have multifurcating branches whenever there is ambiguity with bifurcation.

Algorithms↗
PubMed2004

[Cloning and sequencing of the introns of UCP gene and construction of molecular phylogenetic tree in chicken].

The UCP genes were the newly discovered genes that can increase the energy expenditure and involve in the metabolism of fat and regulation of energy. Four pairs of primers in chicken UCP exon region were designed to amplify the introns of chicken UCP gene according to the splice ways of the mouse UCP2 gene (Accession No.AF096288). The sequence results showed that the chicken UCP gene also had five GT-AG type introns. The molecular phylogenetic tree was constructed based on the sequence of cds, intron 2 and intron 3 region, respectively. The phylogenetic tree based on the UCP cds region was consistent with the species phylogenetic tree. This result implicated that UCP gene can be regarded as the useful gene for the study of animal phylogenesis. On the contrast, the phylogenetic tree based on the intron 2 and intron 3 region was different from the species phylogenetic tree, which showed that the evolution of intron and cds region is different.

Animals↗