Population Genetics, Molecular Biometry, and Evolution
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IN EVOLUTION JACK LESTER KING UNIVERSITY of CALIFORNIA, SANTA BARBARA This Paper Is Dedicated to Retiring University of California Professors Curt Stern and Everett R
THE ROLE OF MUTATION IN EVOLUTION JACK LESTER KING UNIVERSITY OF CALIFORNIA, SANTA BARBARA This paper is dedicated to retiring University of California Professors Curt Stern and Everett R. Dempster. 1. Introduction Eleven decades of thought and work by Darwinian and neo-Darwinian scientists have produced a sophisticated and detailed structure of evolutionary ,theory and observations. In recent years, new techniques in molecular biology have led to new observations that appear to challenge some of the basic theorems of classical evolutionary theory, precipitating the current crisis in evolutionary thought. Building on morphological and paleontological observations, genetic experimentation, logical arguments, and upon mathematical models requiring simplifying assumptions, neo-Darwinian theorists have been able to make some remarkable predictions, some of which, unfortunately, have proven to be inaccurate. Well-known examples are the prediction that most genes in natural populations must be monomorphic [34], and the calculation that a species could evolve at a maximum rate of the order of one allele substitution per 300 genera- tions [13]. It is now known that a large proportion of gene loci are polymorphic in most species [28], and that evolutionary genetic substitutions occur in the human line, for instance, at a rate of about 50 nucleotide changes per generation [20], [24], [25], [26]. The puzzling observation [21], [40], [46], that homologous proteins in different species evolve at nearly constant rates is very difficult to account for with classical evolutionary theory, and at the very least gives a solid indication that there are qualitative differences between the ways molecules evolve and the ways morphological structures evolve. -
Experiments on the Role of Deleterious Mutations As Stepping Stones In
Experiments on the role of deleterious mutations as PNAS PLUS stepping stones in adaptive evolution Arthur W. Covert IIIa,b,c,d, Richard E. Lenskia,c,e,1, Claus O. Wilkec,d, and Charles Ofriaa,b,c,1 aProgram in Ecology, Evolutionary Biology and Behavior, Departments of bComputer Science and Engineering and eMicrobiology and Molecular Genetics, and cBEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI 48824; and dCenter for Computational Biology, Institute for Cellular and Molecular Biology, and Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712 Contributed by Richard E. Lenski, July 16, 2013 (sent for review April 22, 2013) Many evolutionary studies assume that deleterious mutations spread unless they are tightly linked (5, 6). In an asexual pop- necessarily impede adaptive evolution. However, a later mutation ulation, however, the fortuitous combination, once formed, will that is conditionally beneficial may interact with a deleterious be stably inherited, thereby providing a simple way to traverse a predecessor before it is eliminated, thereby providing access to fitness valley (5–10). adaptations that might otherwise be inaccessible. It is unknown Previous research on a variety of systems, both biological and whether such sign-epistatic recoveries are inconsequential events computational, has documented many examples of epistatic inter- or an important factor in evolution, owing to the difficulty of actions between mutations (3, 6, 11, 14–24), including a few cases monitoring the effects and fates of all mutations during experi- of mutational pairs that are individually deleterious but jointly ments with biological organisms. -
Motoo Kimura (1924-1994)
Motoo Kimura (1924-1994) OR decades the field of mathematical population prize-winners. When our textbook (CROW and KIMURA F genetics and evolutionary theory was dominated 1970) was published, he used his royalties to build a by the three pioneers,J. B. S. HALDANE,R. A. FISHER, tiny greenhouse attached to his home. Every Sunday and SEM'A1.L. WRIGHT.M'ith WRIGI-IT'Sdeath (CROW was orchid day. He used his artistic talent to paint pic- 1988), and for some time before, the leadingsuccessor tures of his favorite flowers, usually on chinaware. to this great heritage was MOTOO KIMURA.Although From age 17 to 19 KIMURA was in high school, where best known for his daring neutral theory of molecular a friendly and scientifically literate teacher encouraged evolution, a concept of great interest andequally great his study of chromosome morphology, and hebecame controversy, he is admired by populationgeneticists a plant cytogeneticist. At that time, cytogenetics was even more forhis deep contributions to the mathemati- very popular in Japan,and he joined thearmy of chro- cal theory. mosome watchers. During this period he was also fasci- MOTOO KIMURA was born November 13,1924 in Oka- nated by a physics course. HIDEKIYUKAWA, later to win zaki, Japan. He diedNovember 13, 1994, on theseventi- the Nobel Prize for predicting the meson, became his eth anniversary of his birth. For some timehe had been scientific hero, and KIMURA began to take an interest a victim of amyotrophic lateral sclerosis and was pro- in mathematics as the language of science. gressively weakening. Nevertheless, his death was acci- Japan was then in themidst of World War 11, and the dental. -
Detecting Selection on Noncoding Nucleotide Variation: Methods and Applications
University of Pennsylvania ScholarlyCommons Publicly Accessible Penn Dissertations 2015 Detecting Selection on Noncoding Nucleotide Variation: Methods and Applications Yang Ding University of Pennsylvania, [email protected] Follow this and additional works at: https://repository.upenn.edu/edissertations Part of the Bioinformatics Commons, Biology Commons, and the Evolution Commons Recommended Citation Ding, Yang, "Detecting Selection on Noncoding Nucleotide Variation: Methods and Applications" (2015). Publicly Accessible Penn Dissertations. 1687. https://repository.upenn.edu/edissertations/1687 This paper is posted at ScholarlyCommons. https://repository.upenn.edu/edissertations/1687 For more information, please contact [email protected]. Detecting Selection on Noncoding Nucleotide Variation: Methods and Applications Abstract There has been a long tradition in molecular evolution to study selective pressures operating at the amino-acid level. But protein-coding variation is not the only level on which molecular adaptations occur, and it is not clear what roles non-coding variation has played in evolutionary history, since they have not yet been systematically explored. In this dissertation I systematically explore several aspects of selective pressures of noncoding nucleotide variation: The first project (Chapter 2) describes research on the determinants of eukaryotic translation dynamics, which include selection on non-coding aspects of DNA variation. Deep sequencing of ribosome-protected mRNA fragments and polysome gradients in various eukaryotic organisms have revealed an intriguing pattern: shorter mRNAs tend to have a greater overall density of ribosomes than longer mRNAs. There is debate about the cause of this trend. To resolve this open question, I systematically analysed 5’ mRNA structure and codon usage patterns in short versus long genes across 100 sequenced eukaryotic genomes. -
The Neutral Theory of Molecular Evolution
Copyright 2000 by the Genetics Society of America Perspectives Anecdotal, Historical and Critical Commentaries on Genetics Edited by James F. Crow and William F. Dove Thomas H. Jukes (1906±1999) James F. Crow Genetics Department, University of Wisconsin, Madison, Wisconsin 53706 OM Jukes accepted our invitation to write a Perspec- duced an immediate outcry from traditional students Ttives on the early history of molecular evolution, of evolution, undoubtedly abetted by the title. In the and in August 1999 he sent a rough beginning con- ensuing polemics, Kimura played the major role. King taining some now-forgotten early history. He planned an died prematurely in 1983 and Jukes wrote mainly about extensive revision and continuation, but on November 1 other things, although he did participate in one joint his death intervened. We have decided to publish his paper (Jukes and Kimura 1984). One of his interests early draft, realizing that it was but a start toward the was the evolution of the genetic code (Jukes 1983). I article that he had planned. particularly liked his showing how, in an orderly sequen- Tom, along with Jack L. King and Motoo Kimura, tial way, mutation pressure in the codon and anti-codon formulated the neutral theory of molecular evolution. could produce the unexpected codes in bacteria and Earlier, the idea had been foreshadowed by Sueoka mitochondria (Jukes 1985). He also developed a widely (1962) and Freese (1962). They had each suggested used correction for multiple undetected changes in evo- mutation pressure of near-neutral changes to account lutionary base substitutions (Jukes and Cantor 1969). -
Population Genetics of Neutral Mutations in Exponentially
The Annals of Applied Probability 2013, Vol. 23, No. 1, 230–250 DOI: 10.1214/11-AAP824 c Institute of Mathematical Statistics, 2013 POPULATION GENETICS OF NEUTRAL MUTATIONS IN EXPONENTIALLY GROWING CANCER CELL POPULATIONS By Rick Durrett1 Duke University In order to analyze data from cancer genome sequencing projects, we need to be able to distinguish causative, or “driver,” mutations from “passenger” mutations that have no selective effect. Toward this end, we prove results concerning the frequency of neutural mutations in exponentially growing multitype branching processes that have been widely used in cancer modeling. Our results yield a simple new population genetics result for the site frequency spectrum of a sample from an exponentially growing population. 1. Introduction. It is widely accepted that cancers result from an accu- mulation of mutations that increase the fitness of tumor cells compared to the cells that surround them. A number of studies [Sj¨oblom et al. (2006), Wood et al. (2007), Parsons et al. (2008), The Cancer Genome Atlas (2008) and Jones et al. (2008, 2010)] have sequenced the genomes of tumors in or- der to find the causative or “driver” mutations. However, due to the large number of genes being sequenced, one also finds a large number of “passen- ger” mutations that are genetically neutral and hence have no role in the disease. To explain the issues involved in distinguishing the two types of mutations, it is useful to take a look at a data set. Wood et al. (2007) did a “discovery” screen in which 18,191 genes were sequenced in 11 colorectal cancers, and then a “validation” screen in which the top candidates were sequenced in 96 additional tumors. -
Effectively Neutral Mutations
Proc. Natl. Acad. Sci. USA Vol. 76, No. 7, pp. 3440-3444, July 1979 Genetics Model of effectively neutral mutations in which selective constraint is incorporated (molecular evolution/protein polymorphism/population genetics/neutral mutation theory) MOTOO KIMURA National Institute of Genetics, Mishima 411, Japan Contributed by Motoo Kimura, April 25, 1979 ABSTRACT Based on the idea that selective neutrality is however, Ohta's model has a drawback in that it cannot ac- the limit when the selective disadvantage becomes indefinitely commodate enough mutations that behave effectively as neutral small, a model of neutral (and nearly neutral) mutations is pro- when the population size gets large. This difficulty can be posed that assumes that the selection coefficient (s') against the overcome by assuming that the selection coefficients follow a mutant at various sites within a cistron (gene) follows a r dis- r distribution. tribution; Ass') = aPe-as's.-l/P(,B), in which a = fi/i and s' is the mean selection coefficient against the mutants (?'> 0; 1 _ ft > 0). The mutation rate for alleles whose selection coef- MODEL OF EFFECTIVELY NEUTRAL ficients s' lie in the range between 0 and 1/(2Ne), in which Ne MUTATIONS is the effective population size, is termed the effectively neutral mutation rate (denoted by ye). Using the model of "infinite Let us assume that the frequency distribution of the selective sites" in population genetics, formulas are derived giving the disadvantage (denoted by s') of mutants among different sites average heterozygosity (he) and evolutionary rate per generation follows the r distribution (kg) in terms of mutant substitutions. -
Stephen Jay Gould Papers M1437
http://oac.cdlib.org/findaid/ark:/13030/kt229036tr No online items Guide to the Stephen Jay Gould Papers M1437 Jenny Johnson Department of Special Collections and University Archives August 2011 ; revised 2019 Green Library 557 Escondido Mall Stanford 94305-6064 [email protected] URL: http://library.stanford.edu/spc Guide to the Stephen Jay Gould M1437 1 Papers M1437 Language of Material: English Contributing Institution: Department of Special Collections and University Archives Title: Stephen Jay Gould papers creator: Gould, Stephen Jay source: Shearer, Rhonda Roland Identifier/Call Number: M1437 Physical Description: 575 Linear Feet(958 boxes) Physical Description: 1180 computer file(s)(52 megabytes) Date (inclusive): 1868-2004 Date (bulk): bulk Abstract: This collection documents the life of noted American paleontologist, evolutionary biologist, and historian of science, Stephen Jay Gould. The papers include correspondence, juvenilia, manuscripts, subject files, teaching files, photographs, audiovisual materials, and personal and biographical materials created and compiled by Gould. Both textual and born-digital materials are represented in the collection. Preferred Citation [identification of item], Stephen Jay Gould Papers, M1437. Dept. of Special Collections, Stanford University Libraries, Stanford, Calif. Publication Rights While Special Collections is the owner of the physical and digital items, permission to examine collection materials is not an authorization to publish. These materials are made available for use -
Evolutionary Pluralism and the Ideal of a Unified Biology
História, Ciências, Saúde-Manguinhos ISSN: 0104-5970 ISSN: 1678-4758 Casa de Oswaldo Cruz, Fundação Oswaldo Cruz Araújo, Leonardo Augusto Luvison; Reis, Claudio Ricardo Martins dos Pluralismo evolutivo e o ideal de unificação da biologia História, Ciências, Saúde-Manguinhos, vol. 28, no. 2, 2021, pp. 393-411 Casa de Oswaldo Cruz, Fundação Oswaldo Cruz DOI: https://doi.org/10.1590/S0104-59702021000200004 Available in: https://www.redalyc.org/articulo.oa?id=386167870004 How to cite Complete issue Scientific Information System Redalyc More information about this article Network of Scientific Journals from Latin America and the Caribbean, Spain and Journal's webpage in redalyc.org Portugal Project academic non-profit, developed under the open access initiative Evolutionary pluralism and the ideal of a unified biology Evolutionary pluralism and the ideal of a unified biology ARAÚJO, Leonardo Augusto Luvison; REIS, Claudio Ricardo Martins dos. Evolutionary pluralism and the ideal of a unified biology.História, Ciências, Saúde – Manguinhos, Rio de Janeiro, v.28, n.2, abr.-jun. 2021. Available at: http://dx.doi. org/10.1590/S0104-59702021000200004. Abstract Biological evolution is often regarded as a central and unifying axis of biology. This article discusses historical aspects of this ideal of unification, as well as signs of its disintegration from the 1960s to 1980s. We argue that despite new proposals for the synthesis of biological knowledge, contemporary evolutionary biology is characterized by pluralism. The main points in favor of evolutionary pluralism are discussed and some consequences of this perspective are presented, particularly in terms of the ideal of a unified biology. Finally, we defend an evolutionary pluralism that critiques the ideal of unification as a scientific objective, but still favors local Leonardo Augusto Luvison Araújoi integrations. -
Genetic Load”: How the Architects of the Modern Synthesis Became Trapped in a Scientific Ideology Alexandra Soulier
“Genetic Load”: How the Architects of the Modern Synthesis Became Trapped in a Scientific Ideology Alexandra Soulier To cite this version: Alexandra Soulier. “Genetic Load”: How the Architects of the Modern Synthesis Became Trapped in a Scientific Ideology. Transversal: International Journal for the Historiography of Science, Graduate Program in History of Federal University of Minas Gerais, 2018, 4 (4), pp.118-139. 10.24117/2526- 2270.2018.i4.11. hal-01818407 HAL Id: hal-01818407 https://hal.archives-ouvertes.fr/hal-01818407 Submitted on 19 Jun 2018 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Transversal: International Journal for the Historiography of Science, 4 (2018) 118-139 ISSN 2526-2270 www.historiographyofscience.org © The Author 2018 – This is an open access article “Genetic Load”: How the Architects of the Modern Synthesis Became Trapped in a Scientific Ideology Alexandra Soulier1 Abstract The term “genetic load” first emerged in a paper written in 1950 by the geneticist H. Muller. It is a mathematical model based on biological, social, political and ethical arguments describ- ing the dramatic accumulation of disadvantageous mutations in human populations that will occur in modern societies if eugenic measures are not taken. -
History of Genetics Book Collection Catalogue
History of Genetics Book Collection Catalogue Below is a list of the History of Genetics Book Collection held at the John Innes Centre, Norwich, UK. For all enquires please contact Mike Ambrose [email protected] +44(0)1603 450630 Collection List Symposium der Deutschen Gesellschaft fur Hygiene und Mikrobiologie Stuttgart Gustav Fischer 1978 A69516944 BOOK-HG HG œ.00 15/10/1996 5th international congress on tropical agriculture 28-31 July 1930 Brussels Imprimerie Industrielle et Finangiere 1930 A6645004483 œ.00 30/3/1994 7th International Chromosome Conference Oxford Oxford 1980 A32887511 BOOK-HG HG œ.00 20/2/1991 7th International Chromosome Conference Oxford Oxford 1980 A44688257 BOOK-HG HG œ.00 26/6/1992 17th international agricultural congress 1937 1937 A6646004482 œ.00 30/3/1994 19th century science a selection of original texts 155111165910402 œ14.95 13/2/2001 150 years of the State Nikitsky Botanical Garden bollection of scientific papers. vol.37 Moscow "Kolos" 1964 A41781244 BOOK-HG HG œ.00 15/10/1996 Haldane John Burdon Sanderson 1892-1964 A banned broadcast and other essays London Chatto and Windus 1946 A10697655 BOOK-HG HG œ.00 15/10/1996 Matsuura Hajime A bibliographical monograph on plant genetics (genic analysis) 1900-1929 Sapporo Hokkaido Imperial University 1933 A47059786 BOOK-HG HG œ.00 15/10/1996 Hoppe Alfred John A bibliography of the writings of Samuel Butler (author of "erewhon") and of writings about him with some letters from Samuel Butler to the Rev. F. G. Fleay, now first published London The Bookman's Journal -
A Century of Geneticists Mutation to Medicine a Century of Geneticists Mutation to Medicine
A Century of Geneticists Mutation to Medicine http://taylorandfrancis.com A Century of Geneticists Mutation to Medicine Krishna Dronamraju CRC Press Taylor & Francis Group 6000 Broken Sound Parkway NW, Suite 300 Boca Raton, FL 33487-2742 © 2019 by Taylor & Francis Group, LLC CRC Press is an imprint of Taylor & Francis Group, an Informa business No claim to original U.S. Government works Printed on acid-free paper International Standard Book Number-13: 978-1-4987-4866-7 (Paperback) International Standard Book Number-13: 978-1-138-35313-8 (Hardback) This book contains information obtained from authentic and highly regarded sources. Reasonable efforts have been made to publish reliable data and information, but the author and publisher cannot assume responsibility for the validity of all materials or the consequences of their use. The authors and publishers have attempted to trace the copyright holders of all material reproduced in this publication and apologize to copyright holders if permission to publish in this form has not been obtained. If any copyright material has not been acknowledged please write and let us know so we may rectify in any future reprint. Except as permitted under U.S. Copyright Law, no part of this book may be reprinted, reproduced, trans- mitted, or utilized in any form by any electronic, mechanical, or other means, now known or hereafter invented, including photocopying, microfilming, and recording, or in any information storage or retrieval system, without written permission from the publishers. For permission to photocopy or use material electronically from this work, please access www.copyright .com (http://www.copyright.com/) or contact the Copyright Clearance Center, Inc.