Population Genetics and Molecular Evolution (Papers Marking the Sixtieth Birthday of Motoo Kimura). Edited by Ohta Tomoko and Ao

Total Page:16

File Type:pdf, Size:1020Kb

Population Genetics and Molecular Evolution (Papers Marking the Sixtieth Birthday of Motoo Kimura). Edited by Ohta Tomoko and Ao Genet. Res., Camb. (1988), 51, pp. 75-82 Printed in Great Britain 75 Book reviews Population Genetics and Molecular Evolution {Papers coverage of current problems in population genetics Marking the Sixtieth Birthday of Motoo Kimurd). and molecular evolution, but not surprisingly, there is Edited by TOMOKO OHTA and KENICHI AOKI, 1985. little on selection. A few papers involve very formal Tokyo: Japan Scientific Societies Press and Berlin: mathematics, but the rest should be accessible to the Springer-Verlag. numerate population geneticist. With the exception of Most population geneticists would agree that, sub- a few of the Japanese, the authors are well known. sequent to the foundations laid by Fisher, Haldane Only a few papers can be mentioned, so as to give and Wright, Motoo Kimura has contributed more to the flavour. For example, Ohta reviews her elegant the theoretical development of their subject than any analyses of variation in multi-gene families, Nei his other. There would be no controversy about the group's work on human molecular evolution, Mukai importance of Kimura's mathematical analyses of his analyses of neutral populations of Drosophila and finite populations or of his neutral theory of molecular Ikemura discusses codon usage. Kimura himself evolution, but there is still heated debate about the analyses the fixation time of slightly deleterious generality of the neutral theory. Thus he has con- mutants at one and two loci. Among the non-natives, tributed a major body of knowledge and been a major Watterson discusses estimation of divergence times stimulus to the collection and interpretation of new between species and Charlesworth the evolution of knowledge. This volume reports a conference held in transposable elements. There are two interesting Japan to honour Motoo Kimura's sixtieth birthday papers using bacteria as a model: Selander discusses on 13 November 1984. Both the titles and the enzyme polymorphisms and Hartl selection in chemo- authorship of the papers illustrates Kimura's inflence: stats. The whole volume has been put together well by many are contributed by notable Japanese population the editors Tomako Ohta and Kenichi Aoki, and geneticists, working at home or abroad, and it is should serve either as an introduction to newcomers Kimura who has made population genetics a fashion- or as a review and development of a large component able science in Japan. of population genetics. Several of the papers are essentially biographical. In Finally, I shall quote from the science writer Nigel particular there is a memoir by Kimura explaining Calder, who contributes a chapter: 'During the how he became interested in population genetics and preliminary work [in 1972 on a TV programme on eventually went to study with James Crow at Madison. evolution], the BBC producer and I were...with John Kimura's formal training was in plant cytogenetics; Maynard Smith and Richard Lewontin...I remember his mathematics was largely self taught, stimulated by Maynard Smith saying to Lewontin; "I wonder if we a desire to read Wright's papers, notably that of 1931. should tell them about Kimura". The two evolu- (Another account of this appears in Provine's recent tionists looked at each other doubtfully, as if biography of Sewall Wright.) Crow contributes two wondering whether to burden the BBC with such a chapters, one some anecdotes on Kimura, the other a controvesial person.' They did, to the subsequent discussion of the scientific standing and influence of consternation of Ayala and Dobzhansky! the neutral theory. Apparently after Kimura reported This is a nice book. It will tell you something about his Ph.D. work at the Cold Spring Harbor Symposium Kimura as a person. It will tell you much about the in 1955, Wright stood up to pay him the compliment influence he has had through the work of others. ' that only those who had tried to solve such problems, WILLIAM G. HILL as he had, could appreciate the magnitude of Kimura's Institute of Animal Genetics, work'. University of Edinburgh The 25 or so scientific papers included report a whole range of studies, some being essentially reviews, others reports of new work. They give a broad Downloaded from https://www.cambridge.org/core. IP address: 170.106.202.226, on 29 Sep 2021 at 12:15:13, subject to the Cambridge Core terms of use, available at https://www.cambridge.org/core/terms. https://doi.org/10.1017/S0016672300023983.
Recommended publications
  • 701.Full.Pdf
    THE AVERAGE NUMBER OF GENERATIONS UNTIL EXTINCTION OF AN INDIVIDUAL MUTANT GENE IN A FINITE POPULATION MOT00 KIMURA' AND TOMOKO OHTA Department of Biology, Princeton University and National Institute of Genetics, Mishima, Japan Received June 13, 1969 AS pointed out by FISHER(1930), a majority of mutant genes which appear in natural populations are lost by chance within a small number of genera- tions. For example, if the mutant gene is selectively neutral, the probability is about 0.79 that it is lost from the population during the first 7 generations. With one percent selective advantage, this probability becomes about 0.78, namely, it changes very little. In general, the probability of loss in early generations due to random sampling of gametes is very high. The question which naturally follows is how long does it take, on the average, for a single mutant gene to become lost from the population, if we exclude the cases in which it is eventually fixed (established) in the population. In the present paper, we will derive some approximation formulas which are useful to answer this question, based on the theory of KIMURAand OHTA(1969). Also, we will report the results of Monte Carlo experiments performed to check the validity of the approximation formulas. APPROXIMATION FORMULAS BASED ON DIFFUSION MODELS Let us consider a diploid population, and denote by N and Ne, respectively, its actual and effective sizes. The following treatment is based on the diffusion models of population genetics (cf. KIMURA1964). As shown by KIMURAand OHTA (1969), if p is the initial frequency of the mutant gene, the average number of generations until loss of the mutant gene (excluding the cases of its eventual fixation) is - In this formula, 1 On leave from the National Institute of Genetics, Mishima, Japan.
    [Show full text]
  • National Institute of Genetics Japan
    NATIONAL INSTITUTE OF GENETICS JAPAN ANNUAL REPORT No. 20 1969 Publi8l&ed bll THE NATIONAL INS'ITI'UTE OF GENETICS Mitlima. Simoka-ken. Japtm 1970 Annual Report of the National Institute of Genetics No. 20, 1969 Published by The National Institute of Genetics, Japan 1970 CONTENTS General statement 1 Staff..................................... .. 2 Council............................................................ 5 Association for propagation of the knowledge of genetics... 5 Projects of research for 1969 ................ 6 Researches carried out in 1969 .......................... 9 1. Cytogenetics Segregation of three types of the largest No.1 (A-I) chromosome in Rattus rattus bred in a population room. YOSIDA, T. H. and TSUCHIYA, K. 9 Polymorphism of No.9 (A-9) and No. 13 (A-13) autosomes in Rattus rattus collected in Japan. YOSIDA, T. H. and TSUCHIYA, K. and MASUJI, H.......................................... 10 Frequency of chromosome polymorphism in Rattus rattus col- lected in East and Southeast Asia. YOSIDA, T. H. and TSUCHIYA, K. 11 Fl and F2 hybrids between Asian and Oceanian black rats with different karyotypes. YOSIDA, T. H., KATO, H. and SAKAKI- BARA, K.................................................... 13 Karyotypes of black rats, Rattus rattus, obtained from Honolulu, Hawaii. YOSIDA, T. H. and TSUCHIYA, K. 14 Local differences in the frequencies of chromosome polymorphism in the house rat, Rattus rattus, in Japan. YOSIDA, T. H., TSUCHIYA, K. and SONODA, J. 15 Karyotypes of Rattus bowersii collected in Malaysia. YOSIDA, T. H. and TSUCHIYA, K. 16 Protective effects of protamine sulfate on disintegration of isolated metaphase chromosomes. KATO, H., SEKIYA, K. and YOSIDA, T. H. 17 A preliminary study on the uptake of isolated nuclei by mam­ malian cells in vitro.
    [Show full text]
  • Manipulating Underdetermination in Scientific Controversy: the Case of the Molecular Clock
    Dartmouth College Dartmouth Digital Commons Open Dartmouth: Published works by Dartmouth faculty Faculty Work 9-1-2007 Manipulating Underdetermination in Scientific Controversy: The Case of the Molecular Clock Michael Dietrich Dartmouth College Robert A. Skipper University of Cincinnati Follow this and additional works at: https://digitalcommons.dartmouth.edu/facoa Part of the Biology Commons Dartmouth Digital Commons Citation Dietrich, Michael and Skipper, Robert A., "Manipulating Underdetermination in Scientific Controversy: The Case of the Molecular Clock" (2007). Open Dartmouth: Published works by Dartmouth faculty. 16. https://digitalcommons.dartmouth.edu/facoa/16 This Article is brought to you for free and open access by the Faculty Work at Dartmouth Digital Commons. It has been accepted for inclusion in Open Dartmouth: Published works by Dartmouth faculty by an authorized administrator of Dartmouth Digital Commons. For more information, please contact [email protected]. Manipulating Underdetermination in Scientiªc Controversy: The Case of the Molecular Clock Michael R. Dietrich Dartmouth College Robert A. Skipper, Jr. University of Cincinnati Where there are cases of underdetermination in scientiªc controversies, such as the case of the molecular clock, scientists may direct the course and terms of dispute by playing off the multidimensional framework of theory evaluation. This is because assessment strategies themselves are underdetermined. Within the framework of assessment, there are a variety of trade-offs between differ- ent strategies as well as shifting emphases as speciªc strategies are given more or less weight in assessment situations. When a strategy is underdetermined, scientists can change the dynamics of a controversy by making assessments using different combinations of evaluation strategies and/or weighting what- ever strategies are in play in different ways.
    [Show full text]
  • The Average Number of Generations Until Fixation of a Mutant Gene in a Finite Population'
    THE AVERAGE NUMBER OF GENERATIONS UNTIL FIXATION OF A MUTANT GENE IN A FINITE POPULATION' MOT00 KIMURA AND TOMOKO OHTA, National Institute of Genetics, Mishima, Japan Received July 26, 1968 A mutant gene which appeared in a finite population will eventually either be lost from the population or fixed (established) in it. The mean time until either of these alternative events takes place was studied by WATTERSON(1962) and EWENS(1963). They made use of a method previously announced by DARL- ING and SIEGERT(1953), and, independently by FELLER(1954). Actually, DARL- ING and SIEGERTrefer to its application to genetics. From the standpoint of population genetics, however, it is much more desirable to determine separately the mean time until fixation and that until loss. Since the gene substitution in a population plays a key role in the evolution of the species, it may be of particular interest to know the mean time for a rare mutant gene to become fixed in a finite population, excluding the cases in which such a gene is lost from the population. In the present paper, a solution to this problem will be presented together with Monte Carlo experiments to test some of the theoretical results. Throughout this paper, the senior author (M. K.) is responsible for the mathematical treatments, while the junior author (T. 0.) is responsible for the numerical treatments based on computers. BASIC THEORY Let us consider a diploid population consisting of N individuals and having the variance effective number Ne, which may be different from the actual number (for the definition of Ne, see KIMURAand CROW1963).
    [Show full text]
  • National Institute of Genetics Japan
    NATIONAL INSTITUTE OF GENETICS JAPAN ANNUAL REPORT No. 19 1968 Published bll THE NATIONAL INSTITUTE OF GENETICS Misima. Sizuoka·ken, Japan 1969 Annual Report of the National Institute of Genetics No. 19, 1968 Published by The National Institute of Genetics, Japan 1969 CONTENTS General statement. ................................................. 1 Research member.................................................. 2 Council............................................................ 5 Projects of research for 1968....................................... 6 Researches carried out in 1968 ..................................... 9 I. Cytogenetics Scientific expedition for the study of rodents to South East Asia and Oceania. I. Members, aims and schedule of the scienti- fic expedition. YOSIDA, T. H. 9 Scientific expedition for the study of rodents to South East Asia and Oceania. II. Species and chromosome numbers of rodents collected from South East Asia and Oceania. YOSIDA, T. H., TSUCHlYA, K. and IMAI, H. T......................... 10 Scientific expedition for the study of rodents to South East Asia and Oceania. III. Chromosomal polymorphism and new karyotypes of black rat, Rattus rattus, collected in South East Asia and Oceania. YOSIDA, T. H. and TSUCHIYA, K......... 11 Scientific expedition for the study of rodents to South East Asia and Oceania. IV. Comparative idiogram analysis in several species belonging to genus Rattus collected from South East Asia and Oceania. YOSIDA, T. H. and TSUCHlYA, K......... 12 Scientific expedition for the study of rodents to South East Asia and Oceania. V. Breeding of wild rodents collected from South East Asia and Oceania. TSUCHIYA, K., YOSIDA, T. H... 13 Rat metaphase chromosomes incorporated into mouse metaphase cells. YOSIDA, T. H. and SEKIGUCHl, T...................... 15 Autoradiographic analysis of the rate of protein synthesis in diploid and tetraploid MSPC-l myeloma cells.
    [Show full text]
  • The Neoselectionist Theory of Genome Evolution
    The neoselectionist theory of genome evolution Giorgio Bernardi* Molecular Evolution Laboratory, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy Edited by Tomoko Ohta, National Institute of Genetics, Mishima, Japan, and approved April 4, 2007 (received for review February 22, 2007) The vertebrate genome is a mosaic of GC-poor and GC-rich isoch- of chance in evolution. A very significant modification of the ores, megabase-sized DNA regions of fairly homogeneous base neutral theory was the nearly neutral theory of Ohta (11, 12), composition that differ in relative amount, gene density, gene who proposed that a substantial fraction of changes are caused expression, replication timing, and recombination frequency. At by random fixation of nearly neutral changes, a class that the emergence of warm-blooded vertebrates, the gene-rich, mod- ‘‘includes intermediates between neutral and advantageous, as erately GC-rich isochores of the cold-blooded ancestors underwent well as between neutral and deleterious classes’’ (13). The first a GC increase. This increase was similar in mammals and birds and four schemes of Fig. 1 display a qualitative picture of the classical was maintained during the evolution of mammalian and avian theories just mentioned. orders. Neither the GC increase nor its conservation can be ac- All classical theories proposed that natural selection acted on counted for by the random fixation of neutral or nearly neutral the ‘‘phenotype’’ [called the ‘‘classical phenotype’’ by Bernardi single-nucleotide changes (i.e., the vast majority of nucleotide and Bernardi (14), to distinguish it from the ‘‘genome pheno- substitutions) or by a biased gene conversion process occurring at type’’ presented below].
    [Show full text]
  • National Institute of Genetics Japan
    ISSN 0077-4995 NATIONAL INSTITUTE OF GENETICS JAPAN ANNUAL REPORT No. 40 1989 Published by THE NATIONAL INSTITUTE OF GENETICS Mi.ima, Sizuoka-ken, Japan 1990 Annual Report of the National Institute of Genetics No. 40, 1989 Published by The National Institute of Genetics, Japan 1990 CONTENTS General statement .........................................I Staff 3 Council and Advisory Committee. ................................ 6 Association for propagation of the knowledge of genetics 8 Projects of research for 1989 9 Research activities in 1989 14 I. Molecular Genetics Promoter selectivity of Escherichia coli RNA polymerase, I. Effect of base substitutions in promoter - 35 region on the promoter strength. KOBAYASHI, M., NAGATA, K. and ISHIHAMA, A. ... 14 The promoter selectivity of Escherichia coli RNA polymerase, II. Random screening of promoters and classification based on the promoter strength. KUBOTA, M., YAMAZAKI, Y. and ISHIHAMA, A. 15 Promoter selectivity of Escherichia coli RNA polymerase, III. Structural and functional modulations of RNA polymerase during growth phase transition. OZAKI, M., FUJITA, N., WADA, A. and ISHIHAMA, A. ..... 16 Structural modulation of ribosomes during growth phase transition of Escherichia coli. WADA, A., YAMAZAKI, Y., FUJITA, N. and ISHIHAMA, A. 17 The molecular anatomy of Escherichia coli RNA polymerase: Func­ tional mapping of the a subunit. IGARASHI, K., HAYWARD, R. S., FUJITA, N., YAMAGISHI, M. and ISHIHAMA, A. 18 Promoter selectivity of Micrococcus luteus RNA polymerase: Identification and characterization of the major sigma factor. NAKAYAMA, M., FUJITA, N., OSAWA, S. and ISHIHAMA, A..... 19 Molecular mechanisms of transcription and replication of phage Qfi: Cloning, sequencing and mapping of host factor. KAJI- TANI, M. and ISHIHAMA, A.
    [Show full text]
  • The Crafoord Prize in Biosciences 2015
    THE CRAFOORD PRIZE IN BIOSCIENCES 2015 POPULAR SCIENCE BACKGROUND The Crafoord Prize in Biosciences 2015 The Crafoord Prize in Biosciences 2015 is awarded to the geneticists Richard Lewontin, USA, and Tomoko Ohta, Japan, for their contributions to knowledge of genetic variation. Thanks to Lewontin and Ohta, we know that the genetic variation within populations of plants and animals is many times greater than science once thought – and we understand why. The late twentieth century and early twenty-first century have seen a revolution in genetic research. New techniques for DNA sequencing have resulted in the rapid growth of knowledge in many areas of biology, including ecology, evolution and systematics. The influence of genetics can also be seen in popular culture, where TV series’ crime scene investigators search for traces of DNA on a hunt for the killer. These traces are able to reveal who were at the scene of the crime because each person’s genotype is as unique as his or her fingerprints. This doesn’t only apply to humans, but to all animals and plants that reproduce sexually; there is considerable genetic variation between individuals of the same species and in the same population. This variation is so significant that we can be certain that two individuals do not have identical DNA even if they are closely related. The only exception to this is identical (monozygotic) siblings. Knowledge of the great genetic variation found within populations and each individual’s unique genotype is now a well-integrated element of our understanding of the world, as well as fundamental to science.
    [Show full text]
  • Random Genetic Drift & Gene Fixation
    Random Genetic Drift & Gene Fixation Arie Zackay July 31, 2007 Abstract Random Genetic Drift is one of the evolutionary forces that effects the distribution of alleles and changes their frequencies in populations. The main idea behind this theory is that genetic changes can happen randomly. This can be explained through the Bottleneck effect. There are two main factors that have an influence on genetic drift, the first one is the Effective Population Size Ne , which creates different genetic drift outcomes within different population sizes. The second factor that influences the rate of genetic drift is the selective advantage of a drifted allele. With these fac- tors it is possible to calculate the time and probability of an allele fixation in any chosen population. 1 Introduction In order to understand the phenomenon known to us as Random Genetic Drift, we must first of all define the meaning of Population Genetics. Population Ge- netics is the study of the changes in distribution of alleles in a certain population, considering the influence of the following evolutionary forces: natural selection, genetic drift, mutation, gene flows and selective mating. The main goals of this field of study is to determine how the frequency of a mutant gene will change over time under the influence of evolutionary forces, to examine how genetic variability is maintained, and to establish the probability that a new mutant completely replaces existing variants of genes, a phenomenon called Fixation. There are a few instigators that can cause changes in the evolution of a popu- lation. Such instigators might include: • It can be caused by a mutation with a genetic advance.
    [Show full text]
  • Dobzhansky's Evolution of Tropical Populations, and the Science and Politics Of
    CARVALHO, Tito. “A most bountiful source of inspiration:” Dobzhansky’s evolution of tropical populations, and the science and politics of genetic variation. História, Ciências, Saúde – Manguinhos, Rio de Janeiro, v.26, n.1, “A most bountiful jan.-mar. 2019, p.281-297. Abstract source of inspiration:” Theodosius Dobzhansky has been studied for how he integrated Dobzhansky’s evolution of field naturalism and laboratory experimentation in ways that helped tropical populations, and produce the Modern Synthesis, as well as how he leveraged biological expertise to support liberal and cosmopolitan the science and politics of values amidst Second World War and the Cold War. Moreover, Dobzhansky genetic variation has been central in analyses of the institutionalization of genetics in Brazil, where he spent several years. This article “A mais abundante fonte situates Dobzhansky’s Brazilian research within the science of variation and the de inspiração”: Dobzhansky politics of diversity. I conclude by raising questions about how the ways in which e sua evolução sobre as science figured in politics depended on ideas about the role of scientists in society whichwere advanced in populações dos trópicos, parallel, suggesting research on the “co- a ciência e a política da production” of natural and social orders. Keywords: evolutionary genetics; variabilidade genética transnational science; eugenics; race; tropics; Theodosius Dobzhansky (1900- 1975). Resumo Theodosius Dobzhansky tem sido estudado pelo modo como ele integrou o naturalismo de campo e a experimentação científica, que deram origem à síntese moderna, assim como a alavanca que ele deu ao conhecimento biológico para apoiar valores liberais e cosmopolitas em meio à Segunda Guerra Mundial e à Guerra Fria.
    [Show full text]
  • Evolutionary Population Genetics of Promoters: Predicting Binding Sites and Functional Phylogenies
    Evolutionary population genetics of promoters: Predicting binding sites and functional phylogenies Ville Mustonen and Michael La¨ ssig* Institut fu¨r Theoretische Physik, Universita¨t zu Ko¨ln, Zu¨lpicherstrasse 77, 50937 Cologne, Germany Edited by Tomoko Ohta, National Institute of Genetics, Mishima, Japan, and approved August 8, 2005 (received for review June 30, 2005) We study the evolution of transcription factor-binding sites in neutral background DNA. As an important step in this direction, prokaryotes, using an empirically grounded model with point the notion of a fitness landscape for binding-site sequences has been mutations and genetic drift. Selection acts on the site sequence via introduced, where the fitness of a site depends on the binding its binding affinity to the corresponding transcription factor. Cal- energy of the corresponding factor (8). The evolutionary impor- ibrating the model with populations of functional binding sites, we tance of the binding energy has also been highlighted in ref. 9, where verify this form of selection and show that typical sites are under it was shown that nucleotide substitution rates within functional substantial selection pressure for functionality: for cAMP response sites in Escherichia coli depend on the energy difference induced by protein sites in Escherichia coli, the product of fitness difference the substitution as predicted from the position weight matrix. The and effective population size takes values 2N⌬F of order 10. We biophysics of factor-DNA binding imposes stringent constraints on apply this model to cross-species comparisons of binding sites in the form of the fitness landscape (10) and has important conse- bacteria and obtain a prediction method for binding sites that uses quences for bioinformatic binding site searches (11).
    [Show full text]
  • Population Genetics, a Concise Guide
    Population Genetics vdxiaovd Population Genetics A Concise Guide John H.vvvspie THEJOHNS HOPKINS UNIVERSITYPRESS Baltimore and London ._./,.,.I.,.,_,_,,.,,... ...l,.,ll.”_.~....,.,.,., ,.*..I .....I..., ..... ,..I.......,.. ,’. , , ’ 0 1998 The JohnsHopkine University Press All rights reserved. Published 1998 Printed in the United Statesof America on acid-free paper 9876543 The JohnsHopkins University Press 2715 North Charles Street Baltimore, Maryland 21218-4363 www.press.jhu.edu Library of Congress Cataloging-in-Publication Data will be'found at the endof this book. A catalog record for this book is available from the British Library. ISBN 0-8018-5764-6 ISBN 0-8018-5755-4(pbk.) To Robin Gordon Contents List of Figures ix Preface xi 1 The Hardy-Weinberg Law 1 1.1 DNA variationin Drosophila .................... 2 1.2 Loci and alleles ............................ 5 1.3 Genotypeand allele frequencies ................... 9 1.4 Randomly matingpopulations .................... 11 1.5 Answers to problems ......................... 17 2 Genetic Drift 19 2.1 A computersimulation ........................ 20 2.2 The decay of heterozygosity ..................... 22 2.3 Mutationand drift .......................... 27 2.4 Theneutral theory .......................... 32 2.5 Effective population size ....................... 35 2.6 The coalescent ............................ 38 2.7 Binomial sampling .......................... 42 2.8 Answers to problems ......................... 47 Natural Selection 3 Natural 49 3.1 The fundamental model ......................
    [Show full text]