DOCSLIB.ORG

Gene Evolution 1

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Gene Evolution 1 Gene evolution 1 03‐327/727 Lecture 3 Fall 2013 Review of character state analysis Inferring character evolution on a tree –Characters and character states –Ancestral and derived characters –The parsimony criterion – Inferring state changes • Properties of characters – Homoplasy, monophyly, paraphyly, polyphyly • Relatedness: common ancestry, no similarity • Classification, cladistics, and phylogenetics 1 Character •A heritable trait or "well defined feature that … can assume one or more mutually exclusive states“* Gorilla Chimp Human Fur Yes Yes No Wt Heavy Light Light Tool No Yes Yes use * Graur and Li, Molecular Evolution, 2000 Use parsimony to infer • Ancestral character states (states on internal nodes) • Character state transitions (on branches) Parsimony: • Thrifty, stingy • The hypothesis that requires the fewest changes to explain the data is the best Gorilla Chimp Human hypothesis. Fur Yes Yes No Wt Heavy Light Light Tool No Yes Yes use 2 Use parsimony to infer furry, light • Ancestral character states (states on internal nodes) gain: tool use • Character state transitions gain: (on branches) body mass furry, light, tool use loss: fur Parsimony: • Thrifty, stingy • The hypothesis that requires the fewest changes to explain the data is the best Gorilla Chimp Human hypothesis. Fur Yes Yes No Wt Heavy Light Light Tool No Yes Yes use • Ancestral (basal) states: furry, light • Low body mass (~50kg) • Fur • Doesn’t use tools gain: tool use gain: furry, light body mass tool use loss: fur Character state transitions Gorilla Chimp Human • Derived states Fur Yes Yes No • High body mass (~175kg) • No fur Wt Heavy Light Light Tool • Tool use No Yes Yes use 3 Review • Inferring character evolution on a tree –Characters and character states –Ancestral and derived characters –The parsimony criterion – Inferring state changes Properties of characters – Homoplasy, monophyly, paraphyly, polyphyly • Relatedness: common ancestry, no similarity • Classification, cladistics, and phylogenetics Homoplasy: A two‐state character (trait) is homoplastic with respect to a tree, if it cannot be explain by a single state transition. These traits are not homoplastic because only one state change occurred. 4 A two‐state character (trait) is homoplastic, if it cannot be explain by a single state transition. Homoplasy can arise through a reversal. Example: larval form in salamanders Homoplasy: From Detecting Pattern to Determining Process and Mechanism of Evolution, Wake, Wake and Specht. Science 25 February 2011: Vol. 331 no. 6020 pp. 1032‐1035 A two‐state character (trait) is homoplastic, if it cannot be explain by a single state transition. Homoplasy can arise through parallel or convergent evolution. Example: body elongation Homoplasy: From Detecting Pattern to Determining Process and Mechanism of Evolution, Wake, Wake and Specht. Science 25 February 2011: Vol. 331 no. 6020 pp. 1032‐1035 5 A two‐state character (trait) is homoplastic, if it cannot be explain by a single state transition. Homoplasy can arise through parallel or convergent evolution. Example: elongation of individual vertebrae Homoplasy: From Detecting Pattern to Determining Process and Mechanism of Evolution, Wake, Wake and Specht. Science 25 February 2011: Vol. 331 no. 6020 pp. 1032‐1035 Monphyly, paraphyly and polyphyly Monophyly Polyphyly The species possessing the The species possessing the orange orange trait form a monophyletic trait are not monophyletic, group. Note: Orange is the because of homoplasy derived state. Paraphyly The species possessing the orange trait are not monophyletic, because orange is the ancestral state. Data: A single character with two states: orange and blue. 6 Review • Inferring character evolution on a tree –Characters and character states –Ancestral and derived characters –The parsimony criterion – Inferring state changes • Properties of characters – Homoplasy, monophyly, paraphyly, polyphyly Relatedness: common ancestry, no similarity • Classification, cladistics, and phylogenetics Common ancestry versus similarity • Crocodiles are similar to lizards because the share basal characters (green) • Crocodiles differ from birds due to derived characters (pink)unique to birds • Derived characters shared by birds and Similarity due to shared basal crocodiles (yellow) support the characters can be misleading. monophyly of birds and crocodiles. Birds Crocs Lizards Turtles scales, shell, External feathers skin skales, skin skin Body temp warm cold cold cold Legs two four four four Gait upright semi-erect sprawling sprawling Antorbital fenestra yes yes no no Mandibular fenestra yes yes no no Builds/defends nests yes yes no no 7 Review • Inferring character evolution on a tree –Characters and character states –Ancestral and derived characters –The parsimony criterion – Inferring state changes • Properties of characters – Homoplasy, monophyly, paraphyly, polyphyly • Relatedness: common ancestry, no similarity Classification, cladistics, and phylogenetics Cladistic approach to evolutionary trees •Gather data on characters to be used • Establish the character states • Determine which states are ancestral (polarize the characters) • Select outgroup(s) with all ancestral states • Apply the principle of parsimony to obtain a hierarchical organization of taxa that minimizes state transitions 8 Example: Deuterostomes are monophyletic The traits mapped onto the phylogeny were carefully chosen to be derived states that define these groups. Classification, cladistics, and phylogenetics • Classification: traditionally based on similarity •Darwin: Evolution by descent from a common ancestor with modification • Cladistics: Attempts to unify classification and evolution by focusing on shared, derived characters –Construct trees based on shared, derived characters –In a classification based on such a tree, groups will share common ancestry and similar derived characters •Elegant solution, but too restrictive for most cases of interest today – Requires that the data satisfy strict criteria (no homoplasy) –More suited to morphoplogical characters, than sequence data –Not suited to data with conflicting phylogenetic signal – Cannot take advantage of more powerful statistical approaches. 9 Molecular Phylogenetics What are the processes we are trying to reconstruct? • Species evolution – Morphological characters –Molecular characters Gene evolution Outline •A motivating example: Hemoglobin evolution •Gene family evolution: Today – Mechanisms of new gene origination –Models of functional differentiation •Gene trees – Properties of gene trees –What they are good for • More terminology: Homology, orthology, paralogy • Multigene families 10 Vertebrate and globins arose via duplication of an ancestral globin gene in a vertebrate ancestor beta alpha Duplication Differentiation via mutation alpha beta Migration to separate chromosomes Chromosome 11 Chromosome 16 Additional duplication gave rise to the human globin family beta alpha alpha beta 11 Additional duplication gave rise to the human globin family Additional duplication gave rise to the human globin family beta alpha What is the benefit of having several copies of the globins? alpha beta 12 beta alpha Functional roles of the globins alpha beta , 0 wks 8 wks birth Embryo Fetus Adult Sickle cell disease beta alpha alpha beta 13 beta But fetal β globin (γ) can partially compensate for alpha the sickle cell mutation in adult fetal β globin! alpha beta In some individuals, fetal globin continues to , be expressed into adulthood 0 wks 8 wks birth Embryo Fetus Adult Outline •A motivating example: Hemoglobin evolution •Gene family evolution: – Mechanisms of new gene origination –Models of functional differentiation •Gene trees – Properties of gene trees –What they are good for • More terminology: Homology, orthology, paralogy • Multigene families 14 Gene duplication Gene families evolve on a range of scales • Single genes • Chromosomal segments a few genes) • Partial chromosomes • Entire chromosomes • Whole genome duplication Gene duplication Gene families evolve on a range of scales • Recombination • Single genes • Unequal crossing over • Chromosomal segments • Retrotransposition (a few genes) • Transposition • Non‐homologous End • Partial chromosomes Joining • Entire chromosomes • …. • Whole genome duplication 15 Tandem duplication and gene loss via unequal crossing over Tandem duplication and gene loss via unequal crossing over 16 OrthologousExamples relationships of tandem among duplications: the HBZ (A) and HBA (B)The genes globins of anthropoid primates, as inferred from an analysis of 5′ and 3′ flanking sequence. Hoffmann F G et al. Mol Biol Evol 2008;25:591-602 © The Author 2008. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: [email protected] Examples of tandem duplications: The globins 17 Examples of tandem duplications: The HOX cluster Examples of tandem duplications: The HOX cluster 18 Transposable elements Vestigial viruses that reside in the genome Endonuclease Reverse transcriptase •RNA transposons aka Retrotransposons Protease Integrase –Copy and Paste •DNA transposons Long terminal repeats –Cut and Paste TE families vary from genome to genome Retrotransposition integration of cDNA transcription cDNA RNA splicing reverse transcriptase ribosome 19 Transposable elements: Relevance to duplication Duplication by retrotransposition Endonuclease Reverse transcriptase DNA transposons
Load more

Recommended publications
  • Phylogenetics Topic 2: Phylogenetic and Genealogical Homology
    Phylogenetics Topic 2: Phylogenetic and genealogical homology Phylogenies distinguish homology from similarity Previously, we examined how rooted phylogenies provide a framework for distinguishing similarity due to common ancestry (HOMOLOGY) from non-phylogenetic similarity (ANALOGY). Here we extend the concept of phylogenetic homology by making a further distinction between a HOMOLOGOUS CHARACTER and a HOMOLOGOUS CHARACTER STATE. This distinction is important to molecular evolution, as we often deal with data comprised of homologous characters with non-homologous character states. The figure below shows three hypothetical protein-coding nucleotide sequences (for simplicity, only three codons long) that are related to each other according to a phylogenetic tree. In the figure the nucleotide sequences are aligned to each other; in so doing we are making the implicit assumption that the characters aligned vertically are homologous characters. In the specific case of nucleotide and amino acid alignments this assumption is called POSITIONAL HOMOLOGY. Under positional homology it is implicit that a given position, say the first position in the gene sequence, was the same in the gene sequence of the common ancestor. In the figure below it is clear that some positions do not have identical character states (see red characters in figure below). In such a case the involved position is considered to be a homologous character, while the state of that character will be non-homologous where there are differences. Phylogenetic perspective on homologous characters and homologous character states ACG TAC TAA SYNAPOMORPHY: a shared derived character state in C two or more lineages. ACG TAT TAA These must be homologous in state.
    [Show full text]
  • An Introduction to Phylogenetic Analysis
    This article reprinted from: Kosinski, R.J. 2006. An introduction to phylogenetic analysis. Pages 57-106, in Tested Studies for Laboratory Teaching, Volume 27 (M.A. O'Donnell, Editor). Proceedings of the 27th Workshop/Conference of the Association for Biology Laboratory Education (ABLE), 383 pages. Compilation copyright © 2006 by the Association for Biology Laboratory Education (ABLE) ISBN 1-890444-09-X All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted, in any form or by any means, electronic, mechanical, photocopying, recording, or otherwise, without the prior written permission of the copyright owner. Use solely at one’s own institution with no intent for profit is excluded from the preceding copyright restriction, unless otherwise noted on the copyright notice of the individual chapter in this volume. Proper credit to this publication must be included in your laboratory outline for each use; a sample citation is given above. Upon obtaining permission or with the “sole use at one’s own institution” exclusion, ABLE strongly encourages individuals to use the exercises in this proceedings volume in their teaching program. Although the laboratory exercises in this proceedings volume have been tested and due consideration has been given to safety, individuals performing these exercises must assume all responsibilities for risk. The Association for Biology Laboratory Education (ABLE) disclaims any liability with regards to safety in connection with the use of the exercises in this volume. The focus of ABLE is to improve the undergraduate biology laboratory experience by promoting the development and dissemination of interesting, innovative, and reliable laboratory exercises.
    [Show full text]
  • II. a Cladistic Analysis of Rbcl Sequences and Morphology
    Systematic Botany (2003), 28(2): pp. 270±292 q Copyright 2003 by the American Society of Plant Taxonomists Phylogenetic Relationships in the Commelinaceae: II. A Cladistic Analysis of rbcL Sequences and Morphology TIMOTHY M. EVANS,1,3 KENNETH J. SYTSMA,1 ROBERT B. FADEN,2 and THOMAS J. GIVNISH1 1Department of Botany, University of Wisconsin, 430 Lincoln Drive, Madison, Wisconsin 53706; 2Department of Systematic Biology-Botany, MRC 166, National Museum of Natural History, Smithsonian Institution, P.O. Box 37012, Washington, DC 20013-7012; 3Present address, author for correspondence: Department of Biology, Hope College, 35 East 12th Street, Holland, Michigan 49423-9000 ([email protected]) Communicating Editor: John V. Freudenstein ABSTRACT. The chloroplast-encoded gene rbcL was sequenced in 30 genera of Commelinaceae to evaluate intergeneric relationships within the family. The Australian Cartonema was consistently placed as sister to the rest of the family. The Commelineae is monophyletic, while the monophyly of Tradescantieae is in question, due to the position of Palisota as sister to all other Tradescantieae plus Commelineae. The phylogeny supports the most recent classi®cation of the family with monophyletic tribes Tradescantieae (minus Palisota) and Commelineae, but is highly incongruent with a morphology-based phylogeny. This incongruence is attributed to convergent evolution of morphological characters associated with pollination strategies, especially those of the androecium and in¯orescence. Analysis of the combined data sets produced a phylogeny similar to the rbcL phylogeny. The combined analysis differed from the molecular one, however, in supporting the monophyly of Dichorisandrinae. The family appears to have arisen in the Old World, with one or possibly two movements to the New World in the Tradescantieae, and two (or possibly one) subsequent movements back to the Old World; the latter are required to account for the Old World distribution of Coleotrypinae and Cyanotinae, which are nested within a New World clade.
    [Show full text]
  • Hemiplasy and Homoplasy in the Karyotypic Phylogenies of Mammals
    Hemiplasy and homoplasy in the karyotypic phylogenies of mammals Terence J. Robinson*†, Aurora Ruiz-Herrera‡, and John C. Avise†§ *Evolutionary Genomics Group, Department of Botany and Zoology, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa; ‡Laboratorio di Biologia Cellulare e Molecolare, Dipartimento di Genetica e Microbiologia, Universita`degli Studi di Pavia, via Ferrata 1, 27100 Pavia, Italy; and §Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697 Contributed by John C. Avise, July 31, 2008 (sent for review May 28, 2008) Phylogenetic reconstructions are often plagued by difficulties in (2). These syntenic blocks, sometimes shared across even dis- distinguishing phylogenetic signal (due to shared ancestry) from tantly related species, may involve entire chromosomes, chro- phylogenetic noise or homoplasy (due to character-state conver- mosomal arms, or chromosomal segments. Based on the premise gences or reversals). We use a new interpretive hypothesis, termed that each syntenic assemblage in extant species is of monophy- hemiplasy, to show how random lineage sorting might account for letic origin, researchers have reconstructed phylogenies and specific instances of seeming ‘‘phylogenetic discordance’’ among ancestral karyotypes for numerous mammalian taxa (ref. 3 and different chromosomal traits, or between karyotypic features and references therein). Normally, the phylogenetic inferences from probable species phylogenies. We posit that hemiplasy is generally these cladistic appraisals are self-consistent (across syntenic less likely for underdominant chromosomal polymorphisms (i.e., blocks) and taxonomically reasonable, and they have helped those with heterozygous disadvantage) than for neutral polymor- greatly to identify particular mammalian clades. However, in a phisms or especially for overdominant rearrangements (which few cases problematic phylogenetic patterns of the sort described should tend to be longer-lived), and we illustrate this concept by above have emerged.
    [Show full text]
  • Phylogenetic Analysis
    Phylogenetic Analysis Aristotle • Through classification, one might discover the essence and purpose of species. Nelson & Platnick (1981) Systematics and Biogeography Carl Linnaeus • Swedish botanist (1700s) • Listed all known species • Developed scheme of classification to discover the plan of the Creator 1 Linnaeus’ Main Contributions 1) Hierarchical classification scheme Kingdom: Phylum: Class: Order: Family: Genus: Species 2) Binomial nomenclature Before Linnaeus physalis amno ramosissime ramis angulosis glabris foliis dentoserratis After Linnaeus Physalis angulata (aka Cutleaf groundcherry) 3) Originated the practice of using the ♂ - (shield and arrow) Mars and ♀ - (hand mirror) Venus glyphs as the symbol for male and female. Charles Darwin • Species evolved from common ancestors. • Concept of closely related species being more recently diverged from a common ancestor. Therefore taxonomy might actually represent phylogeny! The phylogeny and classification of life a proposed by Haeckel (1866). 2 Trees - Rooted and Unrooted 3 Trees - Rooted and Unrooted ABCDEFGHIJ A BCDEH I J F G ROOT ROOT D E ROOT A F B H J G C I 4 Monophyletic: A group composed of a collection of organisms, including the most recent common ancestor of all those organisms and all the descendants of that most recent common ancestor. A monophyletic taxon is also called a clade. Paraphyletic: A group composed of a collection of organisms, including the most recent common ancestor of all those organisms. Unlike a monophyletic group, a paraphyletic group does not include all the descendants of the most recent common ancestor. Polyphyletic: A group composed of a collection of organisms in which the most recent common ancestor of all the included organisms is not included, usually because the common ancestor lacks the characteristics of the group.
    [Show full text]
  • Quantifying the Risk of Hemiplasy in Phylogenetic Inference
    Quantifying the risk of hemiplasy in phylogenetic inference Rafael F. Guerreroa,b,1 and Matthew W. Hahna,b aDepartment of Biology, Indiana University, Bloomington, IN 47405; and bDepartment of Computer Science, Indiana University, Bloomington, IN 47405 Edited by David M. Hillis, The University of Texas at Austin, Austin, TX, and approved November 5, 2018 (received for review June 29, 2018) Convergent evolution—the appearance of the same character paralogs as orthologs, and a lack of fit between the sequence state in apparently unrelated organisms—is often inferred when a data and the substitution model used to infer the tree. The bi- trait is incongruent with the species tree. However, trait incongru- ological causes of gene-tree discordance are incomplete lineage ence can also arise from changes that occur on discordant gene sorting (ILS) and introgression/hybridization (18), although trees, a process referred to as hemiplasy. Hemiplasy is rarely taken natural selection can sometimes result in discordance (e.g., ref. into account in studies of convergent evolution, despite the fact 19). In the presence of any of these biological processes, indi- that phylogenomic studies have revealed rampant discordance. vidual loci can have different histories from the species tree; Here, we study the relative probabilities of homoplasy (including discordance due to either introgression or ILS in the history of convergence and reversal) and hemiplasy for an incongruent trait. extant lineages does not go away over time, so studies of both We derive expressions for the probabilities of the two events, ancient and recent divergences can be affected. showing that they depend on many of the same parameters.
    [Show full text]
  • "Homology and Homoplasy: a Philosophical Perspective"
    Homology and Introductory article Homoplasy: A Article Contents . The Concept of Homology up to Darwin . Adaptationist, Taxic and Developmental Concepts of Philosophical Perspective Homology . Developmental Homology Ron Amundson, University of Hawaii at Hilo, Hawaii, USA . Character Identity Networks Online posting date: 15th October 2012 Homology refers to the underlying sameness of distinct Homology is sameness, judged by various kinds of body parts or other organic features. The concept became similarity. The recognition of body parts that are shared by crucial to the understanding of relationships among different kinds of organisms dates at least back to Aristotle, organisms during the early nineteenth century. Its but acceptance of this fact as scientifically important to biology developed during the first half of the nineteenth importance has vacillated during the years between the century. In an influential definition published in 1843, publication of Darwin’s Origin of Species and recent times. Richard Owen defined homologues as ‘the same organ in For much of the twentieth century, homology was different animals under every variety of form and function’ regarded as nothing more than evidence of common (Owen, 1843). Owen had a very particular kind of struc- descent. In recent times, however, it has regained its for- tural sameness in mind. It was not to be confused with mer importance. It is regarded by advocates of evo- similarities that are due to shared function, which were lutionary developmental biology as a source of evidence termed ‘analogy.’ Bird wings are not homologous to insect for developmental constraint, and evidence for biases in wings, even though they look similar and perform the same phenotypic variation and the commonalities in organic function.
    [Show full text]
  • Parsimony, Synapomorphy, and Explanatory Power: a Reply to Duncan
    Saether, O. A. 1983. The canalized evolutionary potential. Inconsistencies in phylogenetic reasoning. Syst. Zoo!. 32(4): 343-359. Sober, E. 1975. Simplicity. Clarendon Press, Oxford. Thomas, W. W. 1984. The systematics of Rhynchospora section Dichromena. Mem. N. Y. Bot. Gard. 37: 1-116. Wagner, W. H., Jr. 1961. Problems in the classification of ferns. In: Recent advances in botany, vol. 1, pp. 841-844. Univ. Toronto Press, Toronto. --. 1980. Origin and philosophy ofthe groundplan-divergence method ofcladistics. Syst. Bot. 5: 173-193. Wiley, E. O. 1981. Phylogenetics. The theory and practice ofphylogenetic systematics. John Wiley & Sons, New York. Steven P. Churchill, New York Botanical Garden. Bronx, NY 10458, U.S.A.: E. O. Wiley, Museum ofNatural History and Department ofSystematics and Ecology. University ofKansas, Lawrence. KS 66045. U.S.A.; and Larry A. Hauser. Department ofBotany, University ofIllinois. Urbana. IL 61801. U.S.A. PARSIMONY, SYNAPOMORPHY, AND EXPLANATORY POWER: A REPLY TO DUNCAN According to Duncan (1984), "directed character compatibility [clique] analysis is equivalent to Hennig's method," because Hennig restricts the term synapomorphy "to shared apornorphies that are postulated to be uniquely derived." The connection between Hennig's method and parsimony analysis, Duncan maintains, is a misconception that arose because "Farris, [Kluge and Eckardt] (1970) redefine synapomorphy to include shared non-uniquely derived characters, abandon Hennig's criterion that monophyly be based on shared uniquely derived character states, and arbitrarily impose the criterion of parsimony on Hennig's method." The crux of Duncan's argument, then, is his claim concerning Hennig's definition of synapomorphy. In the usual conception, if an apomorphic trait shared by two taxa is inherited from a common ancestor, then this constitutes synapomorphy.
    [Show full text]
  • Phylogeny of Angiosperms
    Unit 8: Phylogeny of Angiosperms • Terms and concepts ❖ primitive and advanced ❖ homology and analogy ❖ parallelism and convergence ❖ monophyly, Paraphyly, polyphyly ❖ clades • origin& evolution of angiosperms; • co-evolution of angiosperms and animals; • methods of illustrating evolutionary relationship (phylogenetic tree, cladogram). TAXONOMY & SYSTEMATICS • Nomenclature = the naming of organisms • Classification = the assignment of taxa to groups of organisms • Phylogeny = Evolutionary history of a group (Evolutionary patterns & relationships among organisms) Taxonomy = Nomenclature + Classification Systematics = Taxonomy + Phylogenetics Phylogeny-Terms • Phylogeny- the evolutionary history of a group of organisms/ study of the genealogy and evolutionary history of a taxonomic group. • Genealogy- study of ancestral relationships and lineages. • Lineage- A continuous line of descent; a series of organisms or genes connected by ancestor/ descendent relationships. • Relationships are depicted through a diagram better known as a phylogram Evolution • Changes in the genetic makeup of populations- evolution, may occur in lineages over time. • Descent with modification • Evolution may be recognized as a change from a pre-existing or ancestral character state (plesiomorphic) to a new character state, derived character state (apomorphy). • 2 mechanisms of evolutionary change- 1. Natural selection – non-random, directed by survival of the fittest and reproductive ability-through Adaptation 2. Genetic Drift- random, directed by chance events
    [Show full text]
  • Phylogenetic Analysis Aristotle • Through Classification, One Might Discover the Essence and Purpose of Species
    Phylogenetic Analysis Aristotle • Through classification, one might discover the essence and purpose of species. Nelson & Platnick (1981) Systematics and Biogeography Carl Linnaeus • Swedish botanist (1700s) • Listed all known species • Developed scheme of classification to discover the plan of the Creator Linnaeus’ Main Contributions 1) Hierarchical classification scheme Kingdom: Phylum: Class: Order: Family: Genus: Species 2) Binomial nomenclature Before Linnaeus physalis amno ramosissime ramis angulosis glabris foliis dentoserratis After Linnaeus Physalis angulata (aka Cutleaf groundcherry) 3) Originated the practice of using the ♂ - (shield and arrow) Mars and ♀ - (hand mirror) Venus glyphs as the symbol for male and female. Charles Darwin • Species evolved from common ancestors. • Concept of closely related species being more recently diverged from a common ancestor. Therefore taxonomy might actually represent phylogeny! The phylogeny and classification of life a proposed by Haeckel (1866). Trees - Rooted and Unrooted Trees - Rooted and Unrooted ABCDEFGHIJ A BCDEH I J F G ROOT ROOT D E ROOT A F B H J G C I Monophyletic: A group composed of a collection of organisms, including the most recent common ancestor of all those organisms and all the descendants of that most recent common ancestor. A monophyletic taxon is also called a clade. Paraphyletic: A group composed of a collection of organisms, including the most recent common ancestor of all those organisms. Unlike a monophyletic group, a paraphyletic group does not include all the descendants of the most recent common ancestor. Polyphyletic: A group composed of a collection of organisms in which the most recent common ancestor of all the included •right organisms is not included, usually because the •left common ancestor lacks the characteristics of the group.
    [Show full text]
  • Basics of Cladistic Analysis
    Basics of Cladistic Analysis Diana Lipscomb George Washington University Washington D.C. Copywrite (c) 1998 Preface This guide is designed to acquaint students with the basic principles and methods of cladistic analysis. The first part briefly reviews basic cladistic methods and terminology. The remaining chapters describe how to diagnose cladograms, carry out character analysis, and deal with multiple trees. Each of these topics has worked examples. I hope this guide makes using cladistic methods more accessible for you and your students. Report any errors or omissions you find to me and if you copy this guide for others, please include this page so that they too can contact me. Diana Lipscomb Weintraub Program in Systematics & Department of Biological Sciences George Washington University Washington D.C. 20052 USA e-mail: [email protected] © 1998, D. Lipscomb 2 Introduction to Systematics All of the many different kinds of organisms on Earth are the result of evolution. If the evolutionary history, or phylogeny, of an organism is traced back, it connects through shared ancestors to lineages of other organisms. That all of life is connected in an immense phylogenetic tree is one of the most significant discoveries of the past 150 years. The field of biology that reconstructs this tree and uncovers the pattern of events that led to the distribution and diversity of life is called systematics. Systematics, then, is no less than understanding the history of all life. In addition to the obvious intellectual importance of this field, systematics forms the basis of all other fields of comparative biology: • Systematics provides the framework, or classification, by which other biologists communicate information about organisms • Systematics and its phylogenetic trees provide the basis of evolutionary interpretation • The phylogenetic tree and corresponding classification predicts properties of newly discovered or poorly known organisms THE SYSTEMATIC PROCESS The systematic process consists of five interdependent but distinct steps: 1.
    [Show full text]
  • Characters and Parsimony Analysis Genetic Relationships
    Introduction to characters and parsimony analysis Genetic Relationships • Genetic relationships exist between individuals within populations • These include ancestor-descendent relationships and more indirect relationships based on common ancestry • Within sexually reducing populations there is a network of relationships • Genetic relations within populations can be measured with a coefficient of genetic relatedness Phylogenetic Relationships • Phylogenetic relationships exist between lineages (e.g. species, genes) • These include ancestor-descendent relationships and more indirect relationships based on common ancestry • Phylogenetic relationships between species or lineages are (expected to be) tree-like • Phylogenetic relationships are not measured with a simple coefficient Phylogenetic Relationships • Traditionally phylogeny reconstruction was dominated by the search for ancestors, and ancestor-descendant relationships • In modern phylogenetics there is an emphasis on indirect relationships • Given that all lineages are related, closeness of phylogenetic relationships is a relative concept. Phylogenetic relationships • Two lineages are more closely related to each other than to some other lineage if they share a more recent common ancestor - this is the cladistic concept of relationships • Phylogenetic hypotheses are hypotheses of common ancestry Frog Toad Oak Hypothetical (Frog,Toad)Oak ancestral lineage Phylogenetic Trees LEAVES terminal branches ABCDEFGHIJ node 2 node 1 polytomy interior branches A CLADOGRAM ROOT CLADOGRAMS AND PHYLOGRAMS E C D A BCDEH I J F G A B G I F H J RELATIVE TIME ABSOLUTE TIME or DIVERGENCE Trees - Rooted and Unrooted ABCDEFGHIJ A BCDEH I J F G ROOT ROOT D E ROOT A F B H J G C I Characters and Character States • Organisms comprise sets of features • When organisms/taxa differ with respect to a feature (e.g.
    [Show full text]