Scientific, Historical, and Conceptual Significance of the First Tree of Life
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Sol Spiegelman, a Pioneer in Molecular Biology
They Wand 0SS tk Slmsldera of Giants: Sol S@egelman, a Piomer in l$lokcular Biology Number 21 May 23,1983 Science in our century has been Indeed, it is upon his widely acclaimed marked by tremendous upheavals in un- discoveries that much of the framework derstanding, brought about by momen- of the discipline now rests. Sol was still tous discoveries and extraordinary pe~ deeply involved in a number of projects ple. One such upheaval has occurred in when, tragically, he died following a biology. It began in the 1930s, when a brief illness on January 21, 1983.2 This new field, molecular biology, was born essay is dedicated to his memory, and to of the synthesis of five distinct disci- the surviving members of his family: hw plines: physical chemistry, crystallogra- wife, Helen; his daughter, Marjorie; and phy, genetics, microbiology, and bio- hk sons, Willard and George. chemistry.1 I deeply regret that Sol did not have Molecular biologists try to explain the opportunity to read this long biological phenomena at the molecular overdue discussion of his work. I had level. By the mid-twentieth century, planned to do this as part of our series of they had settled several problems that essays on various awards in science—in plagued previous generations of biolo- particular, the Feltnnelfi prize, men- gists. For instance, proteins and nucleic tioned later. Sol was one of the true acids had been known since the nine- giants of modem science. So it is with a teenth century to be very large mole- mixed sense of pain and gratitude that I cules, each consisting of long chains of use thk opportunity to pay tribute to a subunits—amino acids in the case of man whose genius was unique. -
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). -
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. -
National Academy of Sciences Annual Meeting
National Academy of Sciences Annual Meeting The 107th Annual Meeting of the National Academy of Sciences was held on April 27-29, 1970, in Washington, D.C. Academy Awards were presented at a ceremony held in the Great Hall on Monday evening. The presentation was followed by an informal reception for members and their guests in honor of the award recipients. At the Academy Dinner on Tuesday night, Barnaby C. Keeney, Chairman of the National Endowment for the Humanities, was the guest speaker. Scientific sessions were comprised of symposia, sessions of in- vited papers, and contributed papers. Abstracts of contributed papers and groups of invited papers appear in this issue. PRESENTATION OF ACADEMY AWARDS George P. Merrill Award KLAUS KEIL, University of New Mexico National Academy of Sciences Award in Microbiology EARL REECE STADTMAN, National Heart and Lung Institute U.S. Steel Foundation Award in Molecular Biology ARMIN DALE KAISER, Stanford University Jessie Stevenson Kovalenko Medal THOMAS FRANCIS, JR. (Posthumous presentation), University of Michigan Mary Clark Thompson Medal RAYMOND CECIL MOORE, University of Kansas J. Lawrence Smith Medal EDWARD PORTER HENDERSON, Smithsonian Institution Downloaded by guest on September 27, 2021 222 N. A. S. ANNUAL MEETING 1970 PROC. N. A. S. Monday Morning: SYMPOSIUM ON THE CRISIS IN FEDERAL FUNDING OF SCIENCE CURRENT PROBLEMS Moderator: HARVEY BROOKS Harvard University Cambridge, Massachusetts WILLIAM G. ANLYAN, Duke University Medical Center, Durham, North Carolina HERBERT E. CARTER, University of Illinois, Urbana, Illinois CARL M. YORK, Office of Science and Technology, Washington, D. C. VICTOR F. WEISSKOPF, Massachusetts Institute of Technology, Cambridge, Massachusetts YARON EzRAHI, Harvard University, Cambridge, Massachusetts FUTURE COURSES Moderator: EMANUEL R. -
History of the Department of Microbiology 1868 – 2009
June 2015 HISTORY OF THE DEPARTMENT OF MICROBIOLOGY 1868 – 2009 University of Illinois at Urbana-Champaign 1 A HISTORY OF THE DEPARTMENT OF MICROBIOLOGY 1868 – 2009 This 141 year history of the Department of Microbiology includes an article (Chapter 1), written and published in 1959 by the Department, which covers the period 1868 to 1959. I joined the Department in 1953, and my recounting of the Department’s history includes personal observations as well as anecdotes told to me by H. O. Halvorson and others. Later I realized what a unique experience it had been to join a first-class department, and I resolved to play a role in maintaining its research stature. Ralph Wolfe 2 Department of Microbiology History of the Headship: 1950 – 1959 Halvor Halvorson 1960 – 1963 Kim Atwood 1963 – 1972 Leon Campbell 1972 – 1982 Ralph DeMoss 1982 – 1987 Samuel Kaplan 1987 – 1990 Jordan Konisky 1990 – 1991 Ralph Wolfe (Acting Head) 1991 – 1997 Charles Miller 1997 – 2002 John Cronan 2003 – 2004 Jeffrey Gardner (Acting Head) 2005 – Present John Cronan 3 Organization of the History of the Department In Chapters 2 to 6 the data are divided into Academic Decades, each containing the following sections: Section I, an overview of the decade; Section II, some events for each year of the decade; Section III, a summary of the research interests, honors received, publications, and invited off-campus lectures or seminars for each faculty member. These data have been obtained from the annual reports of the faculty submitted to the departmental secretary. 4 CHAPTER 1 1868 – 1959 During this time period the name of the Department was Department of Bacteriology (Anecdotes by Ralph Wolfe) A SHORT HISTORY OF THE DEPARTMENT OF BACTERIOLOGY H. -
Bringing RNA Into View: RNA and Its Roles in Biology. INSTITUTION Biological Sciences Curriculum Study, Colorado Springs
DOCUMENT RESUME ED 468 800 SE 064 476 AUTHOR Atkins, John F.; Ellington, Andrew; Friedman, B. Ellen; Gesteland, Raymond F.; Noller, Harry F.; Pasquale, Stephen M.; Storey, Richard D.; Uhlenbeck, Olke C.; Weiner, Alan M. TITLE Bringing RNA into View: RNA and Its Roles in Biology. INSTITUTION Biological Sciences Curriculum Study, Colorado Springs. SPONS AGENCY National Science Foundation, Arlington, VA. PUB DATE 2000-00-00 NOTE 194p. CONTRACT NSF-9652921 AVAILABLE FROM BSCS, Pikes Peak Research Park, 5415 Mark Dabling Blvd., Colorado Springs, CO 80918-3842. Tel: 719-531-5550; Web site: http://www.bscs.org. PUB TYPE Guides Classroom Learner (051) Guides Classroom Teacher (052) EDRS PRICE EDRS Price MF01/PC08 Plus Postage. DESCRIPTORS *Science Activities; Biology; *Genetics; Higher Education; *Instructional Materials; *RNA; Science Instruction ABSTRACT This guide presents a module for college students on ribonucleic acid (RNA) and its role in biology. The module aims to integrate the latest research and its findings into college-level biology and provide an opportunity for students to understand biological processes. Four activities are presented: (1) "RNA Structure:- Tapes to Shapes"; (2) "RNA Catalysis"; (3) "RNA and Evolution"; and (4)"RNA Evolution in Health and Disease." (Contains 28 references.) (YDS) Reproductions supplied by EDRS are the best that can be made from the original document. 00 00 7I- r21 4-1 T COPYAVAILABL U S DEPARTMENT OF EDUCATION Office of Educational Research and Improvement PERMISSION TO REPRODUCE AND EDUCATIONAL RESOURCES INFORMATION DISSEMINATE THIS MATERIAL HAS CENTER (ERIC) BEEN GRANTED BY This document has been reproduced as received from the person or organization hating it. -
David Ledbetter Nanney Papers Finding
Special Collections and University Archives UMass Amherst Libraries David Ledbetter Nanney Papers Digital 1946-2008 13 boxes (6.5 linear ft.) Call no.: MS 592 About SCUA SCUA home Credo digital Scope Overview Series 1. Correspondence Series 2. Teaching and Writing Inventory Series 1. Correspondence Series 2. Teaching and Writing Admin info Download xml version print version (pdf) Read collection overview The experimental ciliatologist David L. Nanney spent much of his career studying the protozoan Tetrahymena. Under Tracy M. Sonneborn at Indiana University, he completed a dissertation in 1951 on the mating habits of Paramecium, but soon after joining the faculty at the University of Michigan, he turned his attention to Tetrahymena. During his subsequent career in Ann Arbor (1951-1959) and at the University of Illinois (1959-1991), Nanney made a series of fundamental contributions to the cytology, genetics, developmental biology, and evolution of ciliates, influencing the work of other biologists such as Joe Frankel, Janina Kaczanowska, Linda Hufnagel, and Nicola Ricci. Since his retirement in 1991, Nanney has remained in Urbana. The Nanney Papers include a dense run of professional correspondence with ciliatologists, geneticists, students and colleagues regarding his pioneering research on ciliates and other professional matters. Of particular note is an extensive correspondence with Sonneborn, accompanied by several biographical essays written after Sonneborn's death, and a large body of correspondence of the controversial reorganization of the biological sciences departments at the University of Illinois in the 1970s. The collection also includes a selection of Nanney's writings and a handful of photographs. See similar SCUA collections: Protistology Science and technology Background on David L. -
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. -
Haeckel's 1866 Tree of Life and the Origin of Eukaryotes
PUBLISHED: 26 JULY 2016 | ARTICLE NUMBER: 16114 | DOI: 10.1038/NMICROBIOL.2016.114 correspondence Haeckel’s 1866 tree of life and the origin of eukaryotes To the Editor — In their Letter describing were summarized under the domain an expanded version of the tree of life, Eukarya, which includes all eukaryotic Hug et al.1 refer to a key publication of micro- and macroorganisms (from amoebae Carl Woese and co-workers2, wherein a to humans). 16S rRNA-phylogenetic scheme of the In chapter 26 entitled ‘Phylogenetic domains Bacteria, Archaea and Eukarya is theses’, Haeckel3 re-interpreted and shown. However, the first three-kingdom supplemented Darwin’s evolutionary tree of life that included microorganisms deductions of 1859. With reference to the was depicted by Ernst Haeckel (pictured simplest protists (bacteria), which form the at around 26 years old) in his General root of his ‘oak tree’ (see Fig. 6 in ref. 5), Morphology of Organisms, a seminal book Haeckel3 concluded that “all organisms that was published one hundred and are the descendants of such autogenous fifty years ago3. Moneren”. Hence, according to this In his Origin of Species, Charles Darwin Haeckelian interpretation of the phylogeny refers to the Linnean two-kingdom of life, the Monera (that is, Bacteria and system, with ‘Animalia’ and ‘Vegetabilia’ Archaea)2 are the progenitors of all more as the only two branches of the living complex living beings on Earth. world. Haeckel3, who was also known This 150-year-old idea is consistent with as the German Darwin4, introduced a recent discoveries and genomic analyses that three-kingdom scheme in which, as a support an archaeal origin of eukaryotes1,8. -
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, -
Introduction to Phylogenetic Comparative Methods in R Pável Matos October 17, 2019
Introduction to phylogenetic comparative methods in R Pável Matos October 17, 2019 This is a tutorial that captures the essence of comparative methods using phylogenies. We will use both simulated and real-world data, along with basic statistics implemented in R packages. The lecture is divided in three sections: 1) Handling and visualizing phylogenies and species traits data in the R environment; 2) Understanding the principles of Brownian motion and its use in evolutionary correlations among species traits; 3) Working with phylogenetically independent contrasts (PIC) and phylogenetic generalized least squares regression (PGLS) using R. Package installations This tutorial was created using R v.3.6.1. You can download the latest R version from the CRAN site. We require two of the most popular phylogenetic R packages: ape and phytools: • ape is an essential R package for handling phylogenetic trees and running analyses of comparative data, including ancestral state reconstruction, diversification rate analyses, and DNA distance computation. • phytools is also handy for manipulating phylogenetic trees and includes other comparative methods and functions not available in ape. We begin this tutorial by installing them: if(!require(ape))install.packages("ape") if(!require(phytools))install.packages("phytools") # the nlme package will allow us to fit Gaussian linear mixed-effects model if(!require(phytools))install.packages("nlme") # the dplyr package will help us to handle data tables if(!require(phytools))install.packages("dplyr") And loading the phylogenetic R packages into our R working space: library(ape) library(phytools) library(nlme) Other important phylogenetic packages include phylobase (manipulating trees and comparative data), geiger (methods for fitting evolutionary models to phylogneies), and caper (phylogenetic comparative analyses). -
Archaea, Eukarya
Chapter 3 To study the diversity of life, biologists use a classification system to name organisms and group them in a logical manner. Common names can be confusing . An organism may have the same name in different languages. It can be misleading! Also common names often refer to more than one organism. What we call corn is wheat in Britain Scientist use scientific names to exchange info and be certain that they are referring to the same organism When taxonomists classify organisms, they organize them into groups that have biological significance. In the discipline of taxonomy, scientists classify organisms and assign each organism a universally accepted name. In a good system of classification, organisms placed into a particular group are more similar to each other than they are to organisms in other groups. Copyright Pearson Prentice Hall Common names of organisms vary from country to country (or even within countries), so scientists assign one specific scientific name for each species. Because 18th century scientists around the world understood Latin and Greek, they used those languages for scientific names. This practice is still followed in naming new species. Copyright Pearson Prentice Hall Early Efforts at Naming Organisms The first attempts at standard scientific names described the physical characteristics of a species in great detail. The name of a wild violet might be: “small purple flower with four petals and heart shaped leaves that grows by the brook in the spring.” These names were not standardized because different scientists described different characteristics. Copyright Pearson Prentice Hall Binomial Nomenclature What is binomial nomenclature? Carolus Linneaus developed a naming system called binomial nomenclature.