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SICLE: A high-throughput tool for extracting evolutionary relationships from phylogenetic trees  [PDF]
Dan DeBlasio,Jennifer Wiscaver
Quantitative Biology , 2013,
Abstract: We present the phylogeny analysis software SICLE (Sister Clade Extractor), an easy to use, adaptable, and high-throughput tool to describe the nearest neighbors to a node of interest in a phylogenetic tree as well as the support value for the relationship. With SICLE it is possible to summarize the phylogenetic information produced by automated phylogenetic pipelines to rapidly identify and quantify the possible evolutionary relationships that merit further investigation. The program is a simple command line utility and is easy to adapt and implement in any phylogenetic pipeline. As a test case, we applied this new tool to published gene phylogenies to identify potential instances of horizontal gene transfer in Salinibacter ruber.
Phylogenetic Incongruence in E. coli O104: Understanding the Evolutionary Relationships of Emerging Pathogens in the Face of Homologous Recombination  [PDF]
Weilong Hao, Vanessa G. Allen, Frances B. Jamieson, Donald E. Low, David C. Alexander
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0033971
Abstract: Escherichia coli O104:H4 was identified as an emerging pathogen during the spring and summer of 2011 and was responsible for a widespread outbreak that resulted in the deaths of 50 people and sickened over 4075. Traditional phenotypic and genotypic assays, such as serotyping, pulsed field gel electrophoresis (PFGE), and multilocus sequence typing (MLST), permit identification and classification of bacterial pathogens, but cannot accurately resolve relationships among genotypically similar but pathotypically different isolates. To understand the evolutionary origins of E. coli O104:H4, we sequenced two strains isolated in Ontario, Canada. One was epidemiologically linked to the 2011 outbreak, and the second, unrelated isolate, was obtained in 2010. MLST analysis indicated that both isolates are of the same sequence type (ST678), but whole-genome sequencing revealed differences in chromosomal and plasmid content. Through comprehensive phylogenetic analysis of five O104:H4 ST678 genomes, we identified 167 genes in three gene clusters that have undergone homologous recombination with distantly related E. coli strains. These recombination events have resulted in unexpectedly high sequence diversity within the same sequence type. Failure to recognize or adjust for homologous recombination can result in phylogenetic incongruence. Understanding the extent of homologous recombination among different strains of the same sequence type may explain the pathotypic differences between the ON2010 and ON2011 strains and help shed new light on the emergence of this new pathogen.
Phylogenetic relationships in the genus Aethomys (Rodentia: Muridae)  [cached]
C.T. Chimimba
African Zoology , 2011,
Abstract: Phylogenetic relationships in the genusAethomys were examined based on qualitative cranial data for all currently recognized species. A cladistic analysis suggested the presence of three clades: 1) A. bocagei, A. thomasi, A. silindensis, A. kaiseri, and A. nyikae; 2) A. chrysophilus, A. ineptus, and A. hindei; 3) A. granti, A. namaquensis, and A. stannarius. These phylogenetic groupings are largely inconsistent with previously postulated supraspecific relationships for the genus. Nonetheless, relationships within each clade broadly correspond with some previously suggested evolutionary hypotheses among some members of the genus, the only notable
Refuting phylogenetic relationships
James Bucknam, Yan Boucher, Eric Bapteste
Biology Direct , 2006, DOI: 10.1186/1745-6150-1-26
Abstract: We discuss some of the limits of a methodology restricted to verificationism, the philosophy on which gene concatenation practices generally rely. As an alternative, we describe a software which identifies and focuses on impossible or refuted relationships, through a simple analysis of bootstrap bipartitions, followed by multivariate statistical analyses. We show how refuting phylogenetic relationships could in principle facilitate systematics. We also apply our method to the study of two complex phylogenies: the phylogeny of the archaea and the phylogeny of the core of genes shared by all life forms. While many groups are rejected, our results left open a possible proximity of N. equitans and the Methanopyrales, of the Archaea and the Cyanobacteria, and as well the possible grouping of the Methanobacteriales/Methanoccocales and Thermosplasmatales, of the Spirochaetes and the Actinobacteria and of the Proteobacteria and firmicutes.It is sometimes easier (and preferable) to decide which species do not group together than which ones do. When possible topologies are limited, identifying local relationships that are rejected may be a useful alternative to classical concatenation approaches aiming to find a globally resolved tree on the basis of weak phylogenetic markers.This article was reviewed by Mark Ragan, Eugene V Koonin and J Peter Gogarten.Reviewed by Mark Ragan, Eugene V Koonin and J Peter Gogarten. For the full reviews, please go to the Reviewers' comments section.Since the 1960's, molecular phylogeneticists have sought to reconstruct organismal relationships based on gene and protein trees [1]. Generally, successes in this enterprise have been evaluated as a function of the capacity to build unambiguous monophyletic groups, thus reducing the paraphyly of former classifications [2]. Despite such precise goals, tree reconstruction remains notoriously difficult, both for practical and conceptual reasons. Regarding some of the problems of classical phylogenetics,
Taxon ordering in phylogenetic trees by means of evolutionary algorithms
Francesco Cerutti, Luigi Bertolotti, Tony L Goldberg, Mario Giacobini
BioData Mining , 2011, DOI: 10.1186/1756-0381-4-20
Abstract: Starting from a West Nile virus phylogenetic tree, in a (1 + 1)-EA we evolved it by randomly rotating the internal nodes and selecting the tree with better fitness every generation. The fitness is a sum of genetic distances between the considered taxon and the r (radius) next taxa. After having set the radius to the best performance, we evolved the trees with (λ + μ)-EAs to study the influence of population on the algorithm.The (1 + 1)-EA consistently outperformed a random search, and better results were obtained setting the radius to 8. The (λ + μ)-EAs performed as well as the (1 + 1), except the larger population (1000 + 1000).The trees after the evolution showed an improvement both of the fitness (based on a genetic distance matrix, then close taxa are actually genetically close), and of the biological interpretation. Samples collected in the same state or year moved close each other, making the tree easier to interpret. Biological relationships between samples are also easier to observe.A central goal of evolutionary biology is to describe the "Tree of Life", inferring relationships among all living organisms. First appeared in the XIX century, trees were often used to describe relationships among organisms, but only Charles Darwin, in his revolutionary Origin of the Species [1], was the first to define them as evolutionary trees. Instead of using phenotypic characters, as Darwin did first, nowadays such trees are commonly built on genetic information and models of molecular evolution.A phylogenetic tree is a mathematical structure to represent the evolutionary history of sequences or individuals. It consists of nodes connected by branches (or edges). The terminal nodes represent the "leaves" of the tree (or tips of the branches) and are also called taxa. Internal nodes represent ancestors, and can be connected to many branches; in this case the node is a politomy and represents either simultaneous divergence of descendants (hard politomy) or uncertainty about t
Relevant phylogenetic invariants of evolutionary models  [PDF]
Marta Casanellas,Jesus Fernandez-Sanchez
Quantitative Biology , 2009,
Abstract: Recently there have been several attempts to provide a whole set of generators of the ideal of the algebraic variety associated to a phylogenetic tree evolving under an algebraic model. These algebraic varieties have been proven to be useful in phylogenetics. In this paper we prove that, for phylogenetic reconstruction purposes, it is enough to consider generators coming from the edges of the tree, the so-called edge invariants. This is the algebraic analogous to Buneman's Splits Equivalence Theorem. The interest of this result relies on its potential applications in phylogenetics for the widely used evolutionary models such as Jukes-Cantor, Kimura 2 and 3 parameters, and General Markov models.
PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships
Cuong Than, Derek Ruths, Luay Nakhleh
BMC Bioinformatics , 2008, DOI: 10.1186/1471-2105-9-322
Abstract: In this paper, we report on the PhyloNet software package, which is a suite of tools for analyzing reticulate evolutionary relationships, or evolutionary networks, which are rooted, directed, acyclic graphs, leaf-labeled by a set of taxa. These tools can be classified into four categories: (1) evolutionary network representation: reading/writing evolutionary networks in a newly devised compact form; (2) evolutionary network characterization: analyzing evolutionary networks in terms of three basic building blocks – trees, clusters, and tripartitions; (3) evolutionary network comparison: comparing two evolutionary networks in terms of topological dissimilarities, as well as fitness to sequence evolution under a maximum parsimony criterion; and (4) evolutionary network reconstruction: reconstructing an evolutionary network from a species tree and a set of gene trees.The software package, PhyloNet, offers an array of utilities to allow for efficient and accurate analysis of evolutionary networks. The software package will help significantly in analyzing large data sets, as well as in studying the performance of evolutionary network reconstruction methods. Further, the software package supports the proposed eNewick format for compact representation of evolutionary networks, a feature that allows for efficient interoperability of evolutionary network software tools. Currently, all utilities in PhyloNet are invoked on the command line.A phylogenetic tree models the evolutionary history of a set of taxa from their most recent common ancestor. The assumptions of strict divergence and vertical inheritance render trees appropriate for modeling the evolutionary histories of several groups of species or organisms. However, when reticulate evolutionary events such as horizontal gene transfer or interspecific recombination occur, the evolutionary history is more appropriately modeled by an evolutionary network.Evidence of reticulate evolution has been shown in various domains in t
Relationships Among Phylogenetic Networks  [PDF]
Stephen J. Willson
Quantitative Biology , 2010,
Abstract: The underlying reality of a succession of interbreeding populations is a vastly complicated network N. Since Darwin, species trees have been used as a simplified description of the relationships which summarize the overly complicated network N. Recent evidence of hybridization and lateral gene transfer, however, suggest that there are situations where trees are inadequate. Consequently it is important to determine properties that characterize networks closely related to N and possibly more complicated than trees but lacking the full complexity of N. A connected surjective digraph map (CSD) is a map f from one network N to another network M which either collapses an arc to a single point or takes an arc to an arc, which is surjective, and such that the inverse image of a point is always connected. CSD maps are shown to behave well under composition. If there is such a CSD map, the network M is shown to arise naturally as a quotient structure from N. It is proved that if there is a CSD map from N to M, then there is in a way to lift an undirected version of M into N, possibly with added resolution. A CSD map from N to M puts strong constraints on N; if the map were not connected, there would be minimal constraints. A procedure is defined, given N, to construct a standard successively cluster-distinct network from N. In general, it may be useful to study classes of networks such that, for any N, there exists a CSD map from N to some standard member of that class.
Comparison of phylogenetic trees through alignment of embedded evolutionary distances
Kwangbom Choi, Shawn M Gomez
BMC Bioinformatics , 2009, DOI: 10.1186/1471-2105-10-423
Abstract: We describe a novel approach for the comparison of phylogenetic distance information based on the alignment of representative high-dimensional embeddings (xCEED: Comparison of Embedded Evolutionary Distances). The xCEED methodology, which utilizes multidimensional scaling and Procrustes-related superimposition approaches, provides the ability to measure the global similarity between trees as well as incongruities between them. We demonstrate the application of this approach to the prediction of coevolving protein interactions and demonstrate its improved performance over the mirrortree, tol-mirrortree, phylogenetic vector projection, and partial correlation approaches. Furthermore, we show its applicability to both the detection of horizontal gene transfer events as well as its potential use in the prediction of interaction specificity between a pair of multigene families.These approaches provide additional tools for the study of phylogenetic trees and associated evolutionary processes. Source code is available at http://gomezlab.bme.unc.edu/tools webcite.Understanding historical relationships between genes, proteins and species is a core aspect of evolutionary biology, with the phylogenetic tree playing a fundamental role in analysis and visualization. However, major challenges still exist in the representation and analysis of the information encoded within phylogenetic trees. For instance, inferring the "true" tree is fundamentally a difficult problem, leading to continuous refinement of reconstruction methods [1]. Similarly, methodologies for tree comparison are also undergoing significant development [2]. In this instance, the typical goal is to compare trees in order to determine their degree of similarity, providing one mechanism to test a variety of hypotheses regarding evolutionary associations. For example, comparison of gene trees with organismal trees allows the detection of non-standard events such as horizontal gene transfer [3,4]. Comparison of species
Phylogenetic relationships among members of the Pachydactylus capensis group of southern African geckos
Aaron M. Bauer,Trip Lamb
African Zoology , 2011,
Abstract: ThePachydactylus capensis group is a phenetically-defined assemblage of five small-bodied geckos broadly distributed in eastern southern Africa. Several additional small-bodied Pachydactylus have been historically considered subspecies of P. capensis or members of this group. To assess evolutionary relationships among these taxa, we conducted a molecular phylogenetic analysis of the members of the P. capensis group using sequence data from the mitochondrial cytochrome b and 16S ribosomal RNA genes (1081 nt). Maximum parsimony and maximum likelihood analyses recovered a well-supported clade comprising all five species of the currently-recognized P. capensis
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