Computational Methods for Phylogenetic Analysis
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Reticulate Evolution and Phylogenetic Networks 6
CHAPTER Reticulate Evolution and Phylogenetic Networks 6 So far, we have modeled the evolutionary process as a bifurcating treelike process. The main feature of trees is that the flow of information in one lineage is independent of that in another lineage. In real life, however, many process- es—including recombination, hybridization, polyploidy, introgression, genome fusion, endosymbiosis, and horizontal gene transfer—do not abide by lineage independence and cannot be modeled by trees. Reticulate evolution refers to the origination of lineages through the com- plete or partial merging of two or more ancestor lineages. The nonvertical con- nections between lineages are referred to as reticulations. In this chapter, we introduce the language of networks and explain how networks can be used to study non-treelike phylogenetic processes. A substantial part of this chapter will be dedicated to the evolutionary relationships among prokaryotes and the very intriguing question of the origin of the eukaryotic cell. Networks Networks were briefly introduced in Chapter 4 in the context of protein-protein interactions. Here, we provide a more formal description of networks and their use in phylogenetics. As mentioned in Chapter 5, trees are connected graphs in which any two nodes are connected by a single path. In phylogenetics, a network is a connected graph in which at least two nodes are connected by two or more pathways. In other words, a network is a connected graph that is not a tree. All networks contain at least one cycle, i.e., a path of branches that can be followed in one direction from any starting point back to the starting point. -
Phylogenetic Comparative Methods: a User's Guide for Paleontologists
Phylogenetic Comparative Methods: A User’s Guide for Paleontologists Laura C. Soul - Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA David F. Wright - Division of Paleontology, American Museum of Natural History, Central Park West at 79th Street, New York, New York 10024, USA and Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA Abstract. Recent advances in statistical approaches called Phylogenetic Comparative Methods (PCMs) have provided paleontologists with a powerful set of analytical tools for investigating evolutionary tempo and mode in fossil lineages. However, attempts to integrate PCMs with fossil data often present workers with practical challenges or unfamiliar literature. In this paper, we present guides to the theory behind, and application of, PCMs with fossil taxa. Based on an empirical dataset of Paleozoic crinoids, we present example analyses to illustrate common applications of PCMs to fossil data, including investigating patterns of correlated trait evolution, and macroevolutionary models of morphological change. We emphasize the importance of accounting for sources of uncertainty, and discuss how to evaluate model fit and adequacy. Finally, we discuss several promising methods for modelling heterogenous evolutionary dynamics with fossil phylogenies. Integrating phylogeny-based approaches with the fossil record provides a rigorous, quantitative perspective to understanding key patterns in the history of life. 1. Introduction A fundamental prediction of biological evolution is that a species will most commonly share many characteristics with lineages from which it has recently diverged, and fewer characteristics with lineages from which it diverged further in the past. This principle, which results from descent with modification, is one of the most basic in biology (Darwin 1859). -
Splits and Phylogenetic Networks
SplitsSplits andand PhylogeneticPhylogenetic NetworksNetworks DanielDaniel H.H. HusonHuson Paris, June 21, 2005 1 ContentsContents 1.1. PhylogeneticPhylogenetic treestrees 2.2. SplitsSplits networksnetworks 3.3. ConsensusConsensus networksnetworks 4.4. HybridizationHybridization andand reticulatereticulate networksnetworks 5.5. RecombinationRecombination networksnetworks 2 PhylogeneticPhylogenetic NetworksNetworks Bandelt (1991): Network displaying evolutionary relationships Other types of Splits Phylogenetic Reticulate phylogenetic networks trees networks networks Median Consensus Hybridization Recombination Augmented networks (super) networks networks trees networks Special case: “Galled trees” Any graph Ancestor Split decomposition, representing Split decomposition, recombination evolutionary Neighbor-net graphs data 3 PhylogeneticPhylogenetic NetworksNetworks 22 11 Other types of Splits Phylogenetic Reticulate phylogenetic networks trees networks networks 33 44 55 Median Consensus Hybridization Recombination Augmented networks (super) networks networks trees networks from sequences Special case: “Galled trees” from trees Any graph Ancestor Split decomposition, representing Split decomposition, recombination evolutionary Neighbor-net graphs data from distances 4 PhylogeneticPhylogenetic NetworksNetworksDan Gusfield: “Phylogenetic network” 22 11 “Generalized Other types of Splits Phylogenetic Reticulate phylogeneticphylogenetic networks trees networks network”networks 33 44 \ 55 Median Consensus Hybridization Recombination“More generalizedAugmented -
The Probability of Monophyly of a Sample of Gene Lineages on a Species Tree
PAPER The probability of monophyly of a sample of gene COLLOQUIUM lineages on a species tree Rohan S. Mehtaa,1, David Bryantb, and Noah A. Rosenberga aDepartment of Biology, Stanford University, Stanford, CA 94305; and bDepartment of Mathematics and Statistics, University of Otago, Dunedin 9054, New Zealand Edited by John C. Avise, University of California, Irvine, CA, and approved April 18, 2016 (received for review February 5, 2016) Monophyletic groups—groups that consist of all of the descendants loci that are reciprocally monophyletic is informative about the of a most recent common ancestor—arise naturally as a conse- time since species divergence and can assist in representing the quence of descent processes that result in meaningful distinctions level of differentiation between groups (4, 18). between organisms. Aspects of monophyly are therefore central to Many empirical investigations of genealogical phenomena have fields that examine and use genealogical descent. In particular, stud- made use of conceptual and statistical properties of monophyly ies in conservation genetics, phylogeography, population genetics, (19). Comparisons of observed monophyly levels to model pre- species delimitation, and systematics can all make use of mathemat- dictions have been used to provide information about species di- ical predictions under evolutionary models about features of mono- vergence times (20, 21). Model-based monophyly computations phyly. One important calculation, the probability that a set of gene have been used alongside DNA sequence differences between and lineages is monophyletic under a two-species neutral coalescent within proposed clades to argue for the existence of the clades model, has been used in many studies. Here, we extend this calcu- (22), and tests involving reciprocal monophyly have been used to lation for a species tree model that contains arbitrarily many species. -
Constructing a Phylogenetic Tree (Cladogram) K.L
Constructing a Phylogenetic Tree (Cladogram) K.L. Wennstrom, Shoreline Community College Biologists use phylogenetic trees to express the evolutionary relationships among groups of organisms. Such trees are constructed by comparing the anatomical structures, embryology, and genetic sequences of different species. Species that are more similar to one another are interpreted as being more closely related to one another. Before you continue, you should carefully read BioSkills 2, “Reading a Phylogenetic Tree” in your textbook. The BioSkills units can be found at the back of the book. BioSkills 2 begins on page B-3. Steps in creating a phylogenetic tree 1. Obtain a list of characters for the species you are interested in comparing. 2. Construct a character table or Venn diagram that illustrates which characters the groups have in common. a. In a character table, the columns represent characters, beginning with the most common and ending with the least common. The rows represent organisms, beginning with the organism with the fewest derived characters and ending with the organism with the most derived characters. Place an X in the boxes in the table to represent which characters are present in each organism. b. In a Venn diagram, the circles represent the characters, and the contents of each circle represent the organisms that have those characters. Organism Characters Rose Leaves, flowers, thorns Grass Leaves Daisy Leaves, flowers Character Table Venn Diagram leaves thorns flowers Grass X Daisy X X Rose X X X 3. Using the information in your character table or Venn diagram, construct a cladogram that represents the relationship of the organisms through evolutionary time. -
Stochastic Models in Phylogenetic Comparative Methods: Analytical Properties and Parameter Estimation
Thesis for the Degree of Doctor of Philosophy Stochastic models in phylogenetic comparative methods: analytical properties and parameter estimation Krzysztof Bartoszek Division of Mathematical Statistics Department of Mathematical Sciences Chalmers University of Technology and University of Gothenburg G¨oteborg, Sweden 2013 Stochastic models in phylogenetic comparative methods: analytical properties and parameter estimation Krzysztof Bartoszek Copyright c Krzysztof Bartoszek, 2013. ISBN 978–91–628–8740–7 Department of Mathematical Sciences Division of Mathematical Statistics Chalmers University of Technology and University of Gothenburg SE-412 96 GOTEBORG,¨ Sweden Phone: +46 (0)31-772 10 00 Author e-mail: [email protected] Typeset with LATEX. Department of Mathematical Sciences Printed in G¨oteborg, Sweden 2013 Stochastic models in phylogenetic comparative methods: analytical properties and parameter estimation Krzysztof Bartoszek Abstract Phylogenetic comparative methods are well established tools for using inter–species variation to analyse phenotypic evolution and adaptation. They are generally hampered, however, by predominantly univariate ap- proaches and failure to include uncertainty and measurement error in the phylogeny as well as the measured traits. This thesis addresses all these three issues. First, by investigating the effects of correlated measurement errors on a phylogenetic regression. Second, by developing a multivariate Ornstein– Uhlenbeck model combined with a maximum–likelihood estimation pack- age in R. This model allows, uniquely, a direct way of testing adaptive coevolution. Third, accounting for the often substantial phylogenetic uncertainty in comparative studies requires an explicit model for the tree. Based on recently developed conditioned branching processes, with Brownian and Ornstein–Uhlenbeck evolution on top, expected species similarities are derived, together with phylogenetic confidence intervals for the optimal trait value. -
Application of Phylogenetic Networks in Evolutionary Studies
Application of Phylogenetic Networks in Evolutionary Studies Daniel H. Huson* and David Bryant *Center for Bioinformatics (ZBIT), Tu¨bingen University, Tu¨bingen, Germany; and Department of Mathematics, Auckland University, Auckland, New Zealand The evolutionary history of a set of taxa is usually represented by a phylogenetic tree, and this model has greatly facilitated the discussion and testing of hypotheses. However, it is well known that more complex evolutionary scenarios are poorly described by such models. Further, even when evolution proceeds in a tree-like manner, analysis of the data may not be best served by using methods that enforce a tree structure but rather by a richer visualization of the data to evaluate its properties, at least as an essential first step. Thus, phylogenetic networks should be employed when reticulate events such as hybridization, horizontal gene transfer, recombination, or gene duplication and loss are believed to be involved, and, even in the absence of such events, phylogenetic networks have a useful role to play. This article reviews the terminology used for phylogenetic networks and covers both split networks and reticulate networks, how they are defined, and how they can be interpreted. Additionally, the article outlines the beginnings of a comprehensive statistical framework for applying split network methods. We show how split networks can represent confidence sets of trees and introduce a conservative statistical test for whether the conflicting signal in a network is treelike. Finally, this article describes a new program, SplitsTree4, an interactive and comprehensive tool for inferring different types of phylogenetic networks from sequences, distances, and trees. Introduction The familiar evolutionary model assumes a tree, a Finally, we present our new program SplitsTree4, model that has greatly facilitated the discussion and testing which provides a comprehensive and interactive frame- of hypotheses. -
Collecting Reliable Clades Using the Greedy Strict Consensus Merger
Collecting reliable clades using the Greedy Strict Consensus Merger Markus Fleischauer and Sebastian Böcker Lehrstuhl für Bioinformatik, Friedrich-Schiller Universität, Jena, Thüringen, Germany ABSTRACT Supertree methods combine a set of phylogenetic trees into a single supertree. Similar to supermatrix methods, these methods provide a way to reconstruct larger parts of the Tree of Life, potentially evading the computational complexity of phylogenetic inference methods such as maximum likelihood. The supertree problem can be formalized in different ways, to cope with contradictory information in the input. Many supertree methods have been developed. Some of them solve NP-hard optimization problems like the well-known Matrix Representation with Parsimony, while others have polynomial worst-case running time but work in a greedy fashion (FlipCut). Both can profit from a set of clades that are already known to be part of the supertree. The Superfine approach shows how the Greedy Strict Consensus Merger (GSCM) can be used as preprocessing to find these clades. We introduce different scoring functions for the GSCM, a randomization, as well as a combination thereof to improve the GSCM to find more clades. This helps, in turn, to improve the resolution of the GSCM supertree. We find this modifications to increase the number of true positive clades by 18% compared to the currently used Overlap scoring. Subjects Bioinformatics, Computational Biology, Evolutionary Studies, Genetics, Taxonomy Keywords Consensus, Supertree, Supermatrix, Divide and Conquer, FlipCut, Phylogeny INTRODUCTION Submitted 14 September 2015 Supertree methods are used to combine a set of phylogenetic trees with non-identical but Accepted 3 June 2016 Published 28 June 2016 overlapping taxon sets, into a larger supertree that contains all the taxa of every input tree. -
Supertree Construction: Opportunities and Challenges
Supertree Construction: Opportunities and Challenges Tandy Warnow Abstract Supertree construction is the process by which a set of phylogenetic trees, each on a subset of the overall set S of species, is combined into a tree on the full set S. The traditional use of supertree methods is the assembly of a large species tree from previously computed smaller species trees; however, supertree methods are also used to address large-scale tree estimation using divide-and-conquer (i.e., a dataset is divided into overlapping subsets, trees are constructed on the subsets, and then combined using the supertree method). Because most supertree methods are heuristics for NP-hard optimization problems, the use of supertree estimation on large datasets is challenging, both in terms of scalability and accuracy. In this chap- ter, we describe the current state of the art in supertree construction and the use of supertree methods in divide-and-conquer strategies. Finally, we identify directions where future research could lead to improved supertree methods. Key words: supertrees, phylogenetics, species trees, divide-and-conquer, incom- plete lineage sorting, Tree of Life 1 Introduction The estimation of phylogenetic trees, whether gene trees (that is, the phylogeny re- lating the sequences found at a specific locus in different species) or species trees, is a precursor to many downstream analyses, including protein structure and func- arXiv:1805.03530v1 [q-bio.PE] 9 May 2018 tion prediction, the detection of positive selection, co-evolution, human population genetics, etc. (see [58] for just some of these applications). Indeed, as Dobzhanksy said, “Nothing in biology makes sense except in the light of evolution” [44]. -
Reading Phylogenetic Trees: a Quick Review (Adapted from Evolution.Berkeley.Edu)
Biological Trees Gloria Rendon SC11 Education June, 2011 Biological trees • Biological trees are used for the purpose of classification, i.e. grouping and categorization of organisms by biological type such as genus or species. Types of Biological trees • Taxonomy trees, like the one hosted at NCBI, are hierarchies; thus classification is determined by position or rank within the hierarchy. It goes from kingdom to species. • Phylogenetic trees represent evolutionary relationships, or genealogy, among species. Nowadays, these trees are usually constructed by comparing 16s/18s ribosomal RNA. • Gene trees represent evolutionary relationships of a particular biological molecule (gene or protein product) among species. They may or may not match the species genealogy. Examples: hemoglobin tree, kinase tree, etc. TAXONOMY TREES Exercise 1: Exploring the Species Tree at NCBI •There exist many taxonomies. •In this exercise, we will examine the taxonomy at NCBI. •NCBI has a taxonomy database where each category in the tree (from the root to the species level) has a unique identifier called taxid. •The lineage of a species is the full path you take in that tree from the root to the point where that species is located. •The (NCBI) taxonomy common tree is therefore the tree that results from adding together the full lineages of each species in a particular list of your choice. Exercise 1: Exploring the Species Tree at NCBI • Open a web browser on NCBI’s Taxonomy page http://www.ncbi.nlm.n ih.gov/Taxonomy/ • Click on each one of the names here to look up the taxonomy id (taxid) of each one of the five categories of the taxonomy browser: Archaea, bacteria, Eukaryotes, Viroids and Viruses. -
Stylophoran Supertrees Revisited
Stylophoran supertrees revisited BERTRAND LEFEBVRE Lefebvre, B. 2005. Stylophoran supertrees revisited. Acta Palaeontologica Polonica 50 (3): 477–486. Supertree analysis is a recent exploratory method that involves the simultaneous combination of two or more charac− ter−based source trees into a single consensus supertree. This method was recently applied by Ruta to a fossil group of enigmatic Palaeozoic forms, the stylophoran echinoderms. Ruta’s supertree suggested that mitrates are polyphyletic and originated from paraphyletic cornutes. Re−examination of Ruta’s data matrix strongly suggests that most source trees were based on dubious homologies resulting from theory−laden assumptions (calcichordate model) or superficial similar− ities (ankyroid scenario). A new supertree analysis was performed using a slightly corrected version of Ruta’s original combined matrix; the 70% majority−rule consensus of 24,168 most parsimonious supertrees suggests that mitrates are monophyletic and derived from paraphyletic cornutes. A second new supertree analysis was generated to test the influ− ence of the pruning of three taxa in some calcichordate source trees; the 70% majority−rule consensus of 3,720 shortest supertrees indicates that both cornutes and mitrates are monophyletic and derived from a Ceratocystis−like ancestor. The two new supertree analyses demonstrate the dramatic influence of the relative contributions of each initial assumption of plate homologies (and underlying anatomical interpretations), in original source trees, on the final topology of supertrees. Key words: Echinodermata, Stylophora, Cornuta, Mitrata, Ankyroida, Calcichordata, supertree, Palaeozoic. Bertrand Lefebvre [bertrand.lefebvre@u−bourgogne.fr], Biogéosciences, Université de Bourgogne, 6 boulevard Ga− briel, F−21000 Dijon, France. Introduction disparate, character−derived trees (Purvis 1995; Bininda− Emonds et al. -
Phylogenetic Supertree Reveals Detailed Evolution of SARS-Cov-2
www.nature.com/scientificreports OPEN Phylogenetic supertree reveals detailed evolution of SARS‑CoV‑2 Tingting Li1, Dongxia Liu2, Yadi Yang1, Jiali Guo3, Yujie Feng3, Xinmo Zhang3, Shilong Cheng4 & Jie Feng2* Corona Virus Disease 2019 (COVID‑19) caused by the emerged coronavirus SARS‑CoV‑2 is spreading globally. The origin of SARS‑Cov‑2 and its evolutionary relationship is still ambiguous. Several reports attempted to fgure out this critical issue by genome‑based phylogenetic analysis, yet limited progress was obtained, principally owing to the disability of these methods to reasonably integrate phylogenetic information from all genes of SARS‑CoV‑2. Supertree method based on multiple trees can produce the overall reasonable phylogenetic tree. However, the supertree method has been barely used for phylogenetic analysis of viruses. Here we applied the matrix representation with parsimony (MRP) pseudo‑sequence supertree analysis to study the origin and evolution of SARS‑CoV‑2. Compared with other phylogenetic analysis methods, the supertree method showed more resolution power for phylogenetic analysis of coronaviruses. In particular, the MRP pseudo‑sequence supertree analysis frmly disputes bat coronavirus RaTG13 be the last common ancestor of SARS‑CoV‑2, which was implied by other phylogenetic tree analysis based on viral genome sequences. Furthermore, the discovery of evolution and mutation in SARS‑CoV‑2 was achieved by MRP pseudo‑sequence supertree analysis. Taken together, the MRP pseudo‑sequence supertree provided more information on the SARS‑CoV‑2 evolution inference relative to the normal phylogenetic tree based on full‑length genomic sequences. Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), a novel coronavirus emerged in December 2019, causes an ongoing outbreak of Corona Virus Disease 2019 (COVID-19).