Introduction to Phylogenetics Using
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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). -
Phylogeny Codon Models • Last Lecture: Poor Man’S Way of Calculating Dn/Ds (Ka/Ks) • Tabulate Synonymous/Non-Synonymous Substitutions • Normalize by the Possibilities
Phylogeny Codon models • Last lecture: poor man’s way of calculating dN/dS (Ka/Ks) • Tabulate synonymous/non-synonymous substitutions • Normalize by the possibilities • Transform to genetic distance KJC or Kk2p • In reality we use codon model • Amino acid substitution rates meet nucleotide models • Codon(nucleotide triplet) Codon model parameterization Stop codons are not allowed, reducing the matrix from 64x64 to 61x61 The entire codon matrix can be parameterized using: κ kappa, the transition/transversionratio ω omega, the dN/dS ratio – optimizing this parameter gives the an estimate of selection force πj the equilibrium codon frequency of codon j (Goldman and Yang. MBE 1994) Empirical codon substitution matrix Observations: Instantaneous rates of double nucleotide changes seem to be non-zero There should be a mechanism for mutating 2 adjacent nucleotides at once! (Kosiol and Goldman) • • Phylogeny • • Last lecture: Inferring distance from Phylogenetic trees given an alignment How to infer trees and distance distance How do we infer trees given an alignment • • Branch length Topology d 6-p E 6'B o F P Edo 3 vvi"oH!.- !fi*+nYolF r66HiH- .) Od-:oXP m a^--'*A ]9; E F: i ts X o Q I E itl Fl xo_-+,<Po r! UoaQrj*l.AP-^PA NJ o - +p-5 H .lXei:i'tH 'i,x+<ox;+x"'o 4 + = '" I = 9o FF^' ^X i! .poxHo dF*x€;. lqEgrE x< f <QrDGYa u5l =.ID * c 3 < 6+6_ y+ltl+5<->-^Hry ni F.O+O* E 3E E-f e= FaFO;o E rH y hl o < H ! E Y P /-)^\-B 91 X-6p-a' 6J. -
Family Classification
1.0 GENERAL INTRODUCTION 1.1 Henckelia sect. Loxocarpus Loxocarpus R.Br., a taxon characterised by flowers with two stamens and plagiocarpic (held at an angle of 90–135° with pedicel) capsular fruit that splits dorsally has been treated as a section within Henckelia Spreng. (Weber & Burtt, 1998 [1997]). Loxocarpus as a genus was established based on L. incanus (Brown, 1839). It is principally recognised by its conical, short capsule with a broader base often with a hump-like swelling at the upper side (Banka & Kiew, 2009). It was reduced to sectional level within the genus Didymocarpus (Bentham, 1876; Clarke, 1883; Ridley, 1896) but again raised to generic level several times by different authors (Ridley, 1905; Burtt, 1958). In 1998, Weber & Burtt (1998 ['1997']) re-modelled Didymocarpus. Didymocarpus s.s. was redefined to a natural group, while most of the rest Malesian Didymocarpus s.l. and a few others morphologically close genera including Loxocarpus were transferred to Henckelia within which it was recognised as a section within. See Section 4.1 for its full taxonomic history. Molecular data now suggests that Henckelia sect. Loxocarpus is nested within ‗Twisted-fruited Asian and Malesian genera‘ group and distinct from other didymocarpoid genera (Möller et al. 2009; 2011). 1.2 State of knowledge and problem statements Henckelia sect. Loxocarpus includes 10 species in Peninsular Malaysia (with one species extending into Peninsular Thailand), 12 in Borneo, two in Sumatra and one in Lingga (Banka & Kiew, 2009). The genus Loxocarpus has never been monographed. Peninsular Malaysian taxa are well studied (Ridley, 1923; Banka, 1996; Banka & Kiew, 2009) but the Bornean and Sumatran taxa are poorly known. -
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. -
A Comparative Phenetic and Cladistic Analysis of the Genus Holcaspis Chaudoir (Coleoptera: .Carabidae)
Lincoln University Digital Thesis Copyright Statement The digital copy of this thesis is protected by the Copyright Act 1994 (New Zealand). This thesis may be consulted by you, provided you comply with the provisions of the Act and the following conditions of use: you will use the copy only for the purposes of research or private study you will recognise the author's right to be identified as the author of the thesis and due acknowledgement will be made to the author where appropriate you will obtain the author's permission before publishing any material from the thesis. A COMPARATIVE PHENETIC AND CLADISTIC ANALYSIS OF THE GENUS HOLCASPIS CHAUDOIR (COLEOPTERA: CARABIDAE) ********* A thesis submitted in partial fulfilment of the requirements for the degree of Doctor of Philosophy at Lincoln University by Yupa Hanboonsong ********* Lincoln University 1994 Abstract of a thesis submitted in partial fulfilment of the requirements for the degree of Ph.D. A comparative phenetic and cladistic analysis of the genus Holcaspis Chaudoir (Coleoptera: .Carabidae) by Yupa Hanboonsong The systematics of the endemic New Zealand carabid genus Holcaspis are investigated, using phenetic and cladistic methods, to construct phenetic and phylogenetic relationships. Three different character data sets: morphological, allozyme and random amplified polymorphic DNA (RAPD) based on the polymerase chain reaction (PCR), are used to estimate the relationships. Cladistic and morphometric analyses are undertaken on adult morphological characters. Twenty six external morphological characters, including male and female genitalia, are used for cladistic analysis. The results from the cladistic analysis are strongly congruent with previous publications. The morphometric analysis uses multivariate discriminant functions, with 18 morphometric variables, to derive a phenogram by clustering from Mahalanobis distances (D2) of the discrimination analysis using the unweighted pair-group method with arithmetical averages (UPGMA). -
Solution Sheet
Solution sheet Sequence Alignments and Phylogeny Bioinformatics Leipzig WS 13/14 Solution sheet 1 Biological Background 1.1 Which of the following are pyrimidines? Cytosine and Thymine are pyrimidines (number 2) 1.2 Which of the following contain phosphorus atoms? DNA and RNA contain phosphorus atoms (number 2). 1.3 Which of the following contain sulfur atoms? Methionine contains sulfur atoms (number 3). 1.4 Which of the following is not a valid amino acid sequence? There is no amino acid with the one letter code 'O', such that there is no valid amino acid sequence 'WATSON' (number 4). 1.5 Which of the following 'one-letter' amino acid sequence corresponds to the se- quence Tyr-Phe-Lys-Thr-Glu-Gly? The amino acid sequence corresponds to the one letter code sequence YFKTEG (number 1). 1.6 Consider the following DNA oligomers. Which to are complementary to one an- other? All are written in the 5' to 3' direction (i.TTAGGC ii.CGGATT iii.AATCCG iv.CCGAAT) CGGATT (ii) and AATCCG (iii) are complementary (number 2). 2 Pairwise Alignments 2.1 Needleman-Wunsch Algorithm Given the alphabet B = fA; C; G; T g, the sequences s = ACGCA and p = ACCG and the following scoring matrix D: A C T G - A 3 -1 -1 -1 -2 C -1 3 -1 -1 -2 T -1 -1 3 -1 -2 G -1 -1 -1 3 -2 - -2 -2 -2 -2 0 1. What kind of scoring function is given by the matrix D, similarity or distance score? 2. Use the Needleman-Wunsch algorithm to compute the pairwise alignment of s and p. -
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. -
A Fréchet Tree Distance Measure to Compare Phylogeographic Spread Paths Across Trees Received: 24 July 2018 Susanne Reimering1, Sebastian Muñoz1 & Alice C
www.nature.com/scientificreports OPEN A Fréchet tree distance measure to compare phylogeographic spread paths across trees Received: 24 July 2018 Susanne Reimering1, Sebastian Muñoz1 & Alice C. McHardy 1,2 Accepted: 1 November 2018 Phylogeographic methods reconstruct the origin and spread of taxa by inferring locations for internal Published: xx xx xxxx nodes of the phylogenetic tree from sampling locations of genetic sequences. This is commonly applied to study pathogen outbreaks and spread. To evaluate such reconstructions, the inferred spread paths from root to leaf nodes should be compared to other methods or references. Usually, ancestral state reconstructions are evaluated by node-wise comparisons, therefore requiring the same tree topology, which is usually unknown. Here, we present a method for comparing phylogeographies across diferent trees inferred from the same taxa. We compare paths of locations by calculating discrete Fréchet distances. By correcting the distances by the number of paths going through a node, we defne the Fréchet tree distance as a distance measure between phylogeographies. As an application, we compare phylogeographic spread patterns on trees inferred with diferent methods from hemagglutinin sequences of H5N1 infuenza viruses, fnding that both tree inference and ancestral reconstruction cause variation in phylogeographic spread that is not directly refected by topological diferences. The method is suitable for comparing phylogeographies inferred with diferent tree or phylogeographic inference methods to each other or to a known ground truth, thus enabling a quality assessment of such techniques. Phylogeography combines phylogenetic information describing the evolutionary relationships among species or members of a population with geographic information to study migration patterns. -
Phylogenetics
Phylogenetics What is phylogenetics? • Study of branching patterns of descent among lineages • Lineages – Populations – Species – Molecules • Shift between population genetics and phylogenetics is often the species boundary – Distantly related populations also show patterning – Patterning across geography What is phylogenetics? • Goal: Determine and describe the evolutionary relationships among lineages – Order of events – Timing of events • Visualization: Phylogenetic trees – Graph – No cycles Phylogenetic trees • Nodes – Terminal – Internal – Degree • Branches • Topology Phylogenetic trees • Rooted or unrooted – Rooted: Precisely 1 internal node of degree 2 • Node that represents the common ancestor of all taxa – Unrooted: All internal nodes with degree 3+ Stephan Steigele Phylogenetic trees • Rooted or unrooted – Rooted: Precisely 1 internal node of degree 2 • Node that represents the common ancestor of all taxa – Unrooted: All internal nodes with degree 3+ Phylogenetic trees • Rooted or unrooted – Rooted: Precisely 1 internal node of degree 2 • Node that represents the common ancestor of all taxa – Unrooted: All internal nodes with degree 3+ • Binary: all speciation events produce two lineages from one • Cladogram: Topology only • Phylogram: Topology with edge lengths representing time or distance • Ultrametric: Rooted tree with time-based edge lengths (all leaves equidistant from root) Phylogenetic trees • Clade: Group of ancestral and descendant lineages • Monophyly: All of the descendants of a unique common ancestor • Polyphyly: -
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. -
Reconstructing Phylogenetic Trees September 18Th, 2008 Systematic Methods 2 Through Time
Reconstructing Phylogenetic Trees September 18th, 2008 Systematic Methods 2 Through Time Linneaus Darwin Carolus Linneaus Charles Darwin Systematic Methods 3 Through Time PhylogenyLinneaus by ExpertDarwin Opinion & Gestalt Carolus Linneaus Charles Darwin 4 Computing Revolution • Late 1950s & 60s. • Growing availability of core computing facilities. http://www-03.ibm.com/ibm/history/ http://www1.istockphoto.com/ exhibits/vintage/vintage_4506VV4002.html 5 Robert R. Sokal Charles D. Michener 6 Robert R. Sokal Charles D. Michener Tree Reconstruction I: Intro. & Distance Measures • The challenge of tree reconstruction. • Phenetics and an introduction to tree reconstruction methods. • Discrete v. distance measures. • Clustering v. optimality searches. • Tree building algorithms. How Many Trees? Taxa Unrooted Rooted Trees Trees 4 3 15 8 10,395 135,135 10 2,027,025 34,459,425 22 3x10^23 50 3x10^74* * More trees than there are atoms in the universe. Reconstructing Trees • The challenge of tree reconstruction. • Lots of possibilities. • Phenetics and an introduction to tree reconstruction methods. • Discrete v. distance measures. • Clustering v. optimality searches. • Tree building algorithms. Discrete Data discrete Discrete Data Discrete v. Distance Trees Clustering Methods Optimality Criterion NP-Completeness • Non-deterministic polynomial. • Impossible to guarantee optimal tree for even relatively modest number of sequences. • Use of heuristic methods. Available Methods Distance Clustering Methods • The phenetic approach. • Two common algorithms for tree reconstruction. • UPGMA & Neighbor joining. Phenetics • Also called numerical taxonomy because of emphasis on data. • Relationships inferred based on overall similarity. Phenetics UPGMA • UPGMA - Unweighted pair group method with arithmetic means (Sokal & Michener 1958). • Remarkably simple and straightforward. • Can be used with many types of distances (molecular, morphological, etc.). -
Molecular Evolution and Phylogenetic Tree Reconstruction
1 4 Molecular Evolution and 3 2 5 Phylogenetic Tree Reconstruction 1 4 2 3 5 Orthology, Paralogy, Inparalogs, Outparalogs Phylogenetic Trees • Nodes: species • Edges: time of independent evolution • Edge length represents evolution time § AKA genetic distance § Not necessarily chronological time Inferring Phylogenetic Trees Trees can be inferred by several criteria: § Morphology of the organisms • Can lead to mistakes § Sequence comparison Example: Mouse: ACAGTGACGCCCCAAACGT Rat: ACAGTGACGCTACAAACGT Baboon: CCTGTGACGTAACAAACGA Chimp: CCTGTGACGTAGCAAACGA Human: CCTGTGACGTAGCAAACGA Distance Between Two Sequences Basic principle: • Distance proportional to degree of independent sequence evolution Given sequences xi, xj, dij = distance between the two sequences One possible definition: i j dij = fraction f of sites u where x [u] ≠ x [u] Better scores are derived by modeling evolution as a continuous change process Molecular Evolution Modeling sequence substitution: Consider what happens at a position for time Δt, • P(t) = vector of probabilities of {A,C,G,T} at time t • µAC = rate of transition from A to C per unit time • µA = µAC + µAG + µAT rate of transition out of A • pA(t+Δt) = pA(t) – pA(t) µA Δt + pC(t) µCA Δt + pG(t) µGA Δt + pT(t) µTA Δt Molecular Evolution In matrix/vector notation, we get P(t+Δt) = P(t) + Q P(t) Δt where Q is the substitution rate matrix Molecular Evolution • This is a differential equation: P’(t) = Q P(t) • Q => prob. distribution over {A,C,G,T} at each position, stationary (equilibrium) frequencies πA, πC, πG,