DOCSLIB.ORG

National Institute of Genetics Japan

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read 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. SEKIYA, K., KATO, H. and YOSIDA, T. H. 18 Nondisjunction of chromosomes in a synchronized cell population initiated by reversal of colcemid inhibition. KATO, H. and YOSIDA, T. H. .............................................. 19 Establishment of several Chinese hamster cell lines with specific chromosomal trisomies. KATO, H. ........................... 20 ii ANNUAL REPORT OF NATIONAL INSTITUTE OF GENETICS NO. 20 Peculiar marker chromosomes in Yoshida rat sarcoma. MATSUSHIMA, T. and YOSIDA, T. H".............................. 21 Synthesis rate of intracellular gamma·globulin in diploid and tetraploid MSPC·l myeloma cells. MORIWAKI, K. and IMAI, H. T. 22 Exchange between cell populations during serial transplantation of MSPC-l mouse myeloma. MORIWAKI, K. and YAMASHITA, J... 23 Cytological studies of mouse gliomas. YAMASHITA, J. 24 Aggregate·promoting substance from HeLa cells in rotation culture. KURODA, Y................................................. 25 Pachytene pairing in translocation heterozygotes having a huge knob close to the breakpoint. OHTA, Y..................... 26 II. Physiological and developmental genetics An attempt to obtain long·term culture cells from Drosophila melanogaster. KURODA, Y. 28 Clonal analysis of embryonic limb cartilage cells in creeper mu- tant of chicken. KURODA, Y. and SHIBUYA, T. 29 Effect of molting hormone on the cell cycle in insect epidermis. MINATO, K. .. .............................................. 31 Cytoplasmic male sterility and virus infection in Capsicum annuum L. OHTA, Y. 32 A variant found in the progeny from grafting in Capsicum an- nuum. OHTA, Y. 34 Induction and inhibition of nucellar embryo development in Citrus. FURUSATO, K. and OHTA, Y. 35 III. Biochemical genetics Syntheses of drosopterins. NAWA, S. ........................... 37 Genetic effects of DNA in Bombyx. NAWA, S., YAMADA, M. A. and TSUJITA, M. 37 Characterization of incorporated DNA in Ephestia eggs treated with DNA. YAMADA, M. A. and NAWA, S. 38 DNA specific in early development in Ephestia. YAMADA, M. A. .. 39 Incorporation of 14C-phenylalanine or 14C-tyrosine into the hypodermal cuticle of the silkworm. I. Lethal lemon larvae. TSUJITA, M. and SAKURAI, S. ..••.......................... 39 Incorporation of 14C·phenylalanine or 14C·tyrosine in to the hypodermal cuticle of the silkworm. II. Lethal albino larvae. TSUJITA, M. and SAKURAI, S. .............................. 40 Sepiapterin reductase in thesilkworm. TSUJITA, M. and SAKURAI, S. 40 CONTENTS iii Characterization of pteridine granule membrane in larval skin cells of the silkworm. SAKURAI, S. and TSUJITA, M. 41 Immunochemical study of pteridine granule membrane in hypodermal cells of silkworm larvae. SAKURAI, S. ......... 42 Aldolase isozyme patterns of brain and brain tumors in mammals. YAMASHITA, J. and MORIWAKI, K........................... 43 Biochemical characters of serum transferrin in several Rattus species collected from South-East Asia and Oceania. MORIWAKI, K., TSUCHIYA, K. and SAKATA, H. 44 Organ-specific expression of allelic peroxidase isozymes in hetero- zygotes of Oryza perennis. ENDO, T. 45 IV. Evolutionary genetics Intraspecific differentiation of genome in AegiloPs caudata. KIHARA, H. and OHTA, Y. 47 Comparison of the developmental pattern between cultivated and wild types of rice. MORISHIMA, H. and OKA, H. I. 49 A survey of genetic variations in the populations of wild Oryza species and their cultivated relatives. MORISHIMA, H. and OKA, H. I. 49 Y. Mathematical studies on population genetics The rate of molecular evolution considered from the standpoint of population genetics. KIMURA, M. 51 The number of heterozygous nucleotide sites maintained in a finite population due to steady flux of mutations. KIMURA, M.......................................................... 52 The average number of generations until extinction of an in­ dividual mutant gene in a finite population. KIMURA, M. and OHTA, T. ........................................ .. .... 53 Linkage disequilibrium at steady state determined by random genetic drift and recurrent mutation. OHTA, T. and KIMURA, M. .....................•................................... 54 Some relationships between local and global genetic variabilities. MARUYAMA, T.............................................. 55 Speed of gene substitution in a geographically structured popu- lation. MARUYAMA, T...................................... 56 On the fixation probability of mutant genes in a subdivided population. MARUYAMA, T. 57 The variance effective number of human population. YASUDA, N. .. 58 iv ANNUAL REPORT OF NATIONAL INSTITUTE OF GENETICS NO. 20 VI. Experimental studies on population genetics Characteristics of Japanese natural populations of D. melanogas:er. OSHIMA, C. and WATANABE, T. K. 61 Recessive autosomal sterility genes concealed in natural popula- tions. OSHIMA, C. and WATANABE, T. K. 61 A new mutant gene' tra-b' on the second chromosome. WATANABE, T. K. 64 A heterotic inversion on the second chromosome of D. melanogaster. WATANABE, T. K. and WATANABE, T....................... 64 VII. Radiation genetics and chemical mutagenesis in animals Studies on strain differences in radiosensitivity in the silkworm. VII. Strain differences in sensitivity to germ cell killing. TAZIMA, Y. and ONUMA, A. 66 Studies on strain differences in radiosensitivity in the silkworm. VIII. Strain specificity at various response levels. T AZIMA, Y. and ONIMARU, K. 67 Studids on strain differences in radiosensitivity in the silkworm. IX. Relation between mutation induction and cell killing. TAZIMA, Y. and FUKASE, Y. 68 Studies on strain differences in radiosensitivity in the silkworm. X. Spontaneous mutation frequencies observed in different radiosensitive strains to mutation induction. TAZIMA, Y. and ONIMARU, K. 69 A comparison of mutagenicity of 14 MeV fast neutrons on pri­ mordial germ cells among different X-ray sensitive silkworm strains. MURAKAMI, A. .................................... 70 Effects of ultraviolet light on the oocytes of the silkworm with special regard to strain sensitivity. MURAKAMI, A. .. 71 Comparison of stage sensitivity to X-ray during meiosis in silk- worm oocytes. MURAKAMI, A. 71 Changes in radiosensitivity during the second meiotic stage of silkworm oocytes. MURAKAMI, A........................... 72 Radiation-dependent loss of sorting-out activity of HeLa cells. KURODA, Y................................................. 73 VIII. Radiation genetics in microorganisms and plants Correlations between mutation, transformation efficiency and radio­ sensitivity in mutants of Bacillus subtilis. SADAIE, Y. and KADA, T. 75- Gamma-ray mutagenesis, repair and chemical radiosensitization CONTENTS v in bacteria. KADA, T...................................... 75 Macromolecular synthesis in bacteria radiosensitized with iodine compounds. NOGUTI, T. and KADA, T...................... 77 Rejoining inhibition of radiation-induced DNA strand-breaks in radiosensitized bacteria with iodine compounds. NOGUTI, T, and KADA, T............................................... 78 Genetic resistance to radiosensitization with iodine compounds. KADA, T................................................... 79 Possible toxic effects of halogen atoms in radiosensitization with some halogenated pyrimidines. KADA, T., SADAIE, Y. and NOGUTI, T.... .............................................. 80 Repair systems for UV damage in phage T6. AMANO, E. and SEKIGUCHI, M. 82 Wave length dependence of photoreactivation of UV irradiated maize pollen. AMANO, E. .................................. 83 Preliminary intragenic mapping of induced wx mutants in maize. AMANO, E.................................................. 85 Fractionation and dose rate effects of
Load more

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]
  • 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]
  • The Other Side of the Nearly Neutral Theory, Evidence of Slightly Advantageous Back-Mutations
    The other side of the nearly neutral theory, evidence of slightly advantageous back-mutations Jane Charlesworth and Adam Eyre-Walker* Centre for the Study of Evolution, School of Life Sciences, University of Sussex, Brighton BN1 9QG, United Kingdom Edited by Tomoko Ohta, National Institute of Genetics, Mishima, Japan, and approved September 5, 2007 (received for review June 13, 2007) We argue that if there is a category of slightly deleterious muta- deleterious with a disadvantage of Ϫs. Let us imagine that this tions, then there should be a category of slightly advantageous T mutation spreads through the population and becomes fixed. back-mutations. We show that when there are both slightly del- If a new C mutation then occurs at this site, it will be slightly eterious and advantageous back-mutations, there is likely to be an advantageous with an advantage of ϩs, unless the relative increase in the rate of evolution after a population size expansion. fitnesses of the C and T alleles have changed. Such a change in This increase in the rate of evolution is short-lived. However, we fitness could occur because of a change in the environment or the show how its signature can be captured by comparing the rate of fixation of mutations at other sites which have epistatic inter- evolution in species that have undergone population size expan- actions with the alleles at a site of interest. However, it seems sion versus contraction. We test our model by comparing the likely that fitnesses will remain approximately constant, at least pattern of evolution in pairs of island and mainland species in over moderate time scales.
    [Show full text]