oalib
Search Results: 1 - 10 of 100 matches for " "
All listed articles are free for downloading (OA Articles)
Page 1 /100
Display every page Item
The generalized Robinson-Foulds metric  [PDF]
Sebastian B?cker,Stefan Canzar,Gunnar W. Klau
Computer Science , 2013,
Abstract: The Robinson-Foulds (RF) metric is arguably the most widely used measure of phylogenetic tree similarity, despite its well-known shortcomings: For example, moving a single taxon in a tree can result in a tree that has maximum distance to the original one; but the two trees are identical if we remove the single taxon. To this end, we propose a natural extension of the RF metric that does not simply count identical clades but instead, also takes similar clades into consideration. In contrast to previous approaches, our model requires the matching between clades to respect the structure of the two trees, a property that the classical RF metric exhibits, too. We show that computing this generalized RF metric is, unfortunately, NP-hard. We then present a simple Integer Linear Program for its computation, and evaluate it by an all-against-all comparison of 100 trees from a benchmark data set. We find that matchings that respect the tree structure differ significantly from those that do not, underlining the importance of this natural condition.
Inferring Species Trees from Incongruent Multi-Copy Gene Trees Using the Robinson-Foulds Distance  [PDF]
Ruchi Chaudhary,J. Gordon Burleigh,David Fernández-Baca
Computer Science , 2012,
Abstract: We present a new method for inferring species trees from multi-copy gene trees. Our method is based on a generalization of the Robinson-Foulds (RF) distance to multi-labeled trees (mul-trees), i.e., gene trees in which multiple leaves can have the same label. Unlike most previous phylogenetic methods using gene trees, this method does not assume that gene tree incongruence is caused by a single, specific biological process, such as gene duplication and loss, deep coalescence, or lateral gene transfer. We prove that it is NP-hard to compute the RF distance between two mul-trees, but it is easy to calculate the generalized RF distance between a mul-tree and a singly-labeled tree. Motivated by this observation, we formulate the RF supertree problem for mul-trees (MulRF), which takes a collection of mul-trees and constructs a species tree that minimizes the total RF distance from the input mul-trees. We present a fast heuristic algorithm for the MulRF supertree problem. Simulation experiments demonstrate that the MulRF method produces more accurate species trees than gene tree parsimony methods when incongruence is caused by gene tree error, duplications and losses, and/or lateral gene transfer. Furthermore, the MulRF heuristic runs quickly on data sets containing hundreds of trees with up to a hundred taxa.
Supertrees based on the subtree prune-and-regraft distance  [PDF]
Chris Whidden,Norbert Zeh,Robert G Beiko
PeerJ , 2015, DOI: 10.7287/peerj.preprints.18v1
Abstract: Supertree methods reconcile a set of phylogenetic trees into a single structure that is often interpreted as a branching history of species. A key challenge is combining conflicting evolutionary histories that are due to artifacts of phylogenetic reconstruction and phenomena such as lateral gene transfer (LGT). Although they often work well in practice, existing supertree approaches use optimality criteria that do not reflect underlying processes, have known biases and may be unduly influenced by LGT. We present the first method to construct supertrees by using the subtree prune-and-regraft (SPR) distance as an optimality criterion. Although calculating the rooted SPR distance between a pair of trees is NP-hard, our new maximum agreement forest-based methods can reconcile trees with hundreds of taxa and > 50 transfers in fractions of a second, which enables repeated calculations during the course of an iterative search. Our approach can accommodate trees in which uncertain relationships have been collapsed to multifurcating nodes. Using a series of simulated benchmark datasets, we show that SPR supertrees are more similar to correct species histories under plausible rates of LGT than supertrees based on parsimony or Robinson-Foulds distance criteria. We successfully constructed an SPR supertree from a phylogenomic dataset of 40,631 gene trees that covered 244 genomes representing several major bacterial phyla. Our SPR-based approach also allowed direct inference of highways of gene transfer between bacterial classes and genera; a small number of these highways connect genera in different phyla and can highlight specific genes implicated in long-distance LGT.
Ordering uniform supertrees by their spectral radii  [PDF]
Xiying Yuan
Mathematics , 2015,
Abstract: A connected and acyclic hypergraph is called a supertree. In this paper we mainly focus on the spectral radii of uniform supertrees. Li, Shao and Qi determined the first two $k$-uniform supertrees with large spectral radii among all the $k$-uniform supertrees on $n$ vertices [H. Li, J. Shao, L. Qi, The extremal spectral radii of $k$-uniform supertrees, arXiv:1405.7257v1, May 2014]. By applying the operation of moving edges on hypergraphs and using the weighted incidence matrix method we extend the above order to the fourth $k$-uniform supertree.
Maximum Likelihood Supertrees  [PDF]
Mike Steel,Allen Rodrigo
Quantitative Biology , 2007,
Abstract: We analyse a maximum-likelihood approach for combining phylogenetic trees into a larger `supertree'. This is based on a simple exponential model of phylogenetic error, which ensures that ML supertrees have a simple combinatorial description (as a median tree, minimising a weighted sum of distances to the input trees). We show that this approach to ML supertree reconstruction is statistically consistent (it converges on the true species supertree as more input trees are combined), in contrast to the widely-used MRP method, which we show can be statistically inconsistent under the exponential error model. We also show that this statistical consistency extends to an ML approach for constructing species supertrees from gene trees. In this setting, incomplete lineage sorting (due to coalescence rates of homologous genes being lower than speciation rates) has been shown to lead to gene trees that are frequently different from species trees, and this can confound efforts to reconstruct the species phylogeny correctly.
Constructing majority-rule supertrees
Jianrong Dong, David Fernández-Baca, FR McMorris
Algorithms for Molecular Biology , 2010, DOI: 10.1186/1748-7188-5-2
Abstract: We study a variant of one of Cotton and Wilkinson's methods, called majority-rule (+) supertrees. After proving that a key underlying problem for constructing majority-rule (+) supertrees is NP-hard, we develop a polynomial-size exact integer linear programming formulation of the problem. We then present a data reduction heuristic that identifies smaller subproblems that can be solved independently. While this technique is not guaranteed to produce optimal solutions, it can achieve substantial problem-size reduction. Finally, we report on a computational study of our approach on various real data sets, including the 121-taxon, 7-tree Seabirds data set of Kennedy and Page.The results indicate that our exact method is computationally feasible for moderately large inputs. For larger inputs, our data reduction heuristic makes it feasible to tackle problems that are well beyond the range of the basic integer programming approach. Comparisons between the results obtained by our heuristic and exact solutions indicate that the heuristic produces good answers. Our results also suggest that the majority-rule (+) approach, in both its basic form and with data reduction, yields biologically meaningful phylogenies.A supertree method begins with a collection of phylogenetic trees with possibly different leaf (taxon) sets, and assembles them into a larger phylogenetic tree, a supertree, whose taxon set is the union of the taxon sets of the input trees. Interest in supertrees was sparked by Gordon's paper [1]. Since then, particularly during the past decade, there has been a flurry of activity with many supertree methods proposed and studied from the algorithmic, theoretical, and biological points of view. The appeal of supertree synthesis is that it can combine disparate data to provide a high-level perspective that is harder to attain from individual trees. A recent example of the use of this approach is the species-level phylogeny of nearly all extant Mammalia constructed by Bin
PhySIC_IST: cleaning source trees to infer more informative supertrees
Celine Scornavacca, Vincent Berry, Vincent Lefort, Emmanuel JP Douzery, Vincent Ranwez
BMC Bioinformatics , 2008, DOI: 10.1186/1471-2105-9-413
Abstract: To overcome this problem, we propose to infer non-plenary supertrees, i.e. supertrees that do not necessarily contain all the taxa present in the source trees, discarding those whose position greatly differs among source trees or for which insufficient information is provided. We detail a variant of the PhySIC veto method called PhySIC_IST that can infer non-plenary supertrees. PhySIC_IST aims at inferring supertrees that satisfy the same appealing theoretical properties as with PhySIC, while being as informative as possible under this constraint. The informativeness of a supertree is estimated using a variation of the CIC (Cladistic Information Content) criterion, that takes into account both the presence of multifurcations and the absence of some taxa. Additionally, we propose a statistical preprocessing step called STC (Source Trees Correction) to correct the source trees prior to the supertree inference. STC is a liberal step that removes the parts of each source tree that significantly conflict with other source trees. Combining STC with a veto method allows an explicit trade-off between veto and liberal approaches, tuned by a single parameter.Performing large-scale simulations, we observe that STC+PhySIC_IST infers much more informative supertrees than PhySIC, while preserving low type I error compared to the well-known MRP method. Two biological case studies on animals confirm that the STC preprocess successfully detects anomalies in the source trees while STC+PhySIC_IST provides well-resolved supertrees agreeing with current knowledge in systematics.The paper introduces and tests two new methodologies, PhySIC_IST and STC, that demonstrate the interest in inferring non-plenary supertrees as well as preprocessing the source trees. An implementation of the methods is available at: http://www.atgc-montpellier.fr/physic_ist/ webcite.A phylogeny, or phylogenetic tree, is a representation of the evolutionary relationships among species. A well-known problem in biol
Optimizing Phylogenetic Supertrees Using Answer Set Programming  [PDF]
Laura Koponen,Emilia Oikarinen,Tomi Janhunen,Laura S?il?
Computer Science , 2015, DOI: 10.1017/S1471068415000265
Abstract: The supertree construction problem is about combining several phylogenetic trees with possibly conflicting information into a single tree that has all the leaves of the source trees as its leaves and the relationships between the leaves are as consistent with the source trees as possible. This leads to an optimization problem that is computationally challenging and typically heuristic methods, such as matrix representation with parsimony (MRP), are used. In this paper we consider the use of answer set programming to solve the supertree construction problem in terms of two alternative encodings. The first is based on an existing encoding of trees using substructures known as quartets, while the other novel encoding captures the relationships present in trees through direct projections. We use these encodings to compute a genus-level supertree for the family of cats (Felidae). Furthermore, we compare our results to recent supertrees obtained by the MRP method.
Future trypanosomatid phylogenies: refined homologies, supertrees and networks
Stothard, JR;
Memórias do Instituto Oswaldo Cruz , 2000, DOI: 10.1590/S0074-02762000000400014
Abstract: there has been good progress in inferring the evolutionary relationships within trypanosomes from dna data as until relatively recently, many relationships have remained rather speculative. ongoing molecular studies have provided data that have adequately shown trypanosoma to be monophyletic and, rather surprisingly, that there are sharply contrasting levels of genetic variation within and between the major trypanosomatid groups. there are still, however, areas of research that could benefit from further development and resolution that broadly fall upon three questions. are the current statements of evolutionary homology within ribosomal small sub-unit genes in need of refinement? can the published phylograms be expanded upon to form `supertrees' depicting further relationships? does a bifurcating tree structure impose an untenable dogma upon trypanosomatid phylogeny where hybridisation or reticulate evolutionary steps have played a part? this article briefly addresses these three questions and, in so doing, hopes to stimulate further interest in the molecular evolution of the group.
Future trypanosomatid phylogenies: refined homologies, supertrees and networks  [cached]
Stothard JR
Memórias do Instituto Oswaldo Cruz , 2000,
Abstract: There has been good progress in inferring the evolutionary relationships within trypanosomes from DNA data as until relatively recently, many relationships have remained rather speculative. Ongoing molecular studies have provided data that have adequately shown Trypanosoma to be monophyletic and, rather surprisingly, that there are sharply contrasting levels of genetic variation within and between the major trypanosomatid groups. There are still, however, areas of research that could benefit from further development and resolution that broadly fall upon three questions. Are the current statements of evolutionary homology within ribosomal small sub-unit genes in need of refinement? Can the published phylograms be expanded upon to form `supertrees' depicting further relationships? Does a bifurcating tree structure impose an untenable dogma upon trypanosomatid phylogeny where hybridisation or reticulate evolutionary steps have played a part? This article briefly addresses these three questions and, in so doing, hopes to stimulate further interest in the molecular evolution of the group.
Page 1 /100
Display every page Item


Home
Copyright © 2008-2017 Open Access Library. All rights reserved.