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Molecular Evolution PDF

438 Pages·1996·13.93 MB·English
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Biomathematics Volume 24 Managing Editor S.A. Levin Editorial Board C. DeLisi M. Feldman J. Keller R. M. May J. D. Murray A. Perelson L. A. Segel Springer-Verlag Berlin Heidelberg GmbH Vadim A. Ratner Andrey A. Zharkikh Nikolay Kolchanov Sergey N. Rodin Viktor V. Solovyov Andrey S. Antonov Molecular Evolution With 157 Figures Springer Vadim A. Ratner Sergey N. Rodin Academy of Sciences, Siberian Branch Beckman Research Institute Institute of Cytology and Genetics of the City of Hope Dept. of Reproductive Genetics 10 Lavrentyev Ave 1450 East Duarte Road 630090 Novosibirsk, Russia Duarte, CA 91010-0269, USA Andrey A. Zharkikh Viktor V. Solovyov University of Texas Baylor College of Medicine Health Sciences Centre of Houston Dept. of Cell Biology Graduate School of Biomedical 1 Baylor Plaza Sciences, Genetic Centres Houston, TX 77030, USA Houston, TX 77225, USA Andrey S. Antonov Nikolay Kolchanov Moscow State University A.N. Belozersky Institute of Academy of Sciences, Siberian Branch Bioorganic Chemistry Institute of Cytology and Genetics 119899 Moscow, Russia 10 Lavrentyev Ave 630090 Novosibirsk, Russia Title of the Russian edition: Problemy Teorii molekulamoi evolutsii Publisher: Nauka, Moscow, 1985 Cover figure: Phylogenetic tree of haemagglutinins H3 (see page 310) Translated from the Russian by A.Antonov, I. Kochubey and S. Wilson Library of Congress Cataloging-In-Publication Data Prob 1e my teor II mo I eku I Tarno 1 evo 1 rutS Ii. Eng II sh Molecular evolution I Vadlm A. Ratner [et al.l. p. cm. -- (Biomathematics; v. 24) Includes bibliographical references. ISBN 978-3-642-08174-3 ISBN 978-3-662-12530-4 (eBook) DOI 10.1007/978-3-662-12530-4 1. Molecular blology--Phllosophy. 2. Molecular evolutlon- -Philosophy. I. Ratner, Vadlm Aleksandrovlch. II. Title. III. Series. OH506.P7513 1996 574.87'328--dc20 ISBN 978-3-642-08174-3 This work is subject to copyright. All rights are reserved, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other way, and storage in data banks. Duplication of this publication or parts thereof is permitted only under the provisions of the German Copyright Law of September 9, 1965, in its current version, and permission for use must always be obtained from Springer-Verlag Berlin Heidelberg GmbH. Violations are liable for prosecution under the German Copyright Law. © Springer-Verlag Berlin Heidelberg 1996 Originally published by Springer-Verlag Berlin Heidelberg New York in 1996 Softcover reprint of the hardcover 1s t edition 1996 Typesetting: TEX output by Stephen S. Wilson, using a Springer TEX macro-package. SPIN: 10054093 41/3143 - 5 43 2 1 0 - Printed on acid-free paper Preface to the English Edition Since the first, Russian edition of this book was published by Nauka, in Novosibirsk, as early as 1985, the present English version called for some revision of the original text. Thus, Prof. A.S. Antonov has joined the authors in contributing a chapter on genosystematics. The other chapters have been updated where necessary. For convenience, we have placed all the essential changes in the Addendum which complements the main text. As far as the latter is concerned, we have made only minor changes by correcting some of the definitions, figures, tables and cross references, in such a way that the numbering is preserved. In the past five years, phylogenetic analysis of sequences has attracted a large number of scientists, with some new and original results being obtained. The authors have not been idle either. Combined effort has produced new methods, computer programs, fresh ideas, and reviews of novel data. We have presented and defended our views at several international and regional conferences. The Addendum of this book is largely a reflection of these events. We should like to thank our colleagues for their interest in our publications, in the new version of the present book, and in the ideology of the theory of molecular evolution. In particular, we are greatly indebted to S.G. Inge- Vechtomov, M.V. Volkenstein, V.A. Berdnikov, L.Z. Kaidanov, R.S. Karpinskaya, G.G. Gause, R. Lewontin, S. Karlin, M. Feldman, L. Ginsburg, F. Scudo, A. Fontdevila, S. Ohno, W. Fitch, M. Goodman, M. Nei, W.-H. Li, E. Zuckerkandl, M. Waterman, R. Holmquist, 1. Crow, K. Ebeling and others. We would also like to thank Dr. S.S. Wilson, the scientific editor of the English version, and Dr. CM. Byrne and Frau U. Wieland of Springer-Verlag Mathematics Editorial for their support and cooperation in preparation of the English edition of this book. October 1995 The authors Preface to the Russian Edition The present book is the combined work of several authors. In it, they set out and evaluate a number of basic problems relevant to the contemporary theory of molecular evolution. This theory has been built up from research in a number of directions. Thus, in the 1950s and 1960s, J. Crow and M. Kimura [1], following S. Wright [2] and 1. Haldane [3], devised the fundamentals of the theory of the stochastic evolution of populations and the genetic-load theory which were subsequently used to establish some of the divisions of the theory of molecular evolution. In 1963, E. Zuckerkandl and L. Pauling [7] were the first to consider the quantitative problems of the construction of phylogenetic trees for macromolecules; while in 1966, W. Fitch and E. Margoliash [8] and R. Eck and M. Dayhoff [9], working independently, suggested the first methods for c·omputerized construction of these trees. In addition, M. Dayhoff also compiled a protein-sequence database [11] and an atlas of protein sequences [10], which remain one of the most informative sources for phylogenetic constructions. Major contributions to the development of the theory and methods of molecular phylogeny, were made by M. Kimura, W. Fitch, M. Dayhoff, M. Goodman, M. Nei, R. Holmquist, and T. Jukes, among others. In 1970, M. Eigen published a series of theoretical studies of the self- reproducing systems of macromolecules. His works grew into a study of a wide range of problems bearing on the origin of these systems and their evolution. This period also saw the beginning of our own studies of the theory of the evolution of molecular genetic regulatory systems [13-19]. A new stage was ushered in after 1977 with the development of large-scale nucleotide sequencing. Concrete factual material was accumulating so rapidly that computer methods of data accumulation and processing were called for. Despite the variety of theoretical methods, controversial problems and research trends that need further elaboration, it is now clear that a unified approach to the development of the theory of molecular evolution is required. This has been the underlying purpose and prime thrust of our work. As a key object of our study, we selected the molecular genetic regulatory systems (MGRS) of cells [18]. We have tried to effect a constructive synthesis of concepts, essential factual data, methods, theoretical models, results and interpretations with the theory of the origination and evolution of MGRS, their macromolecular components (genes, RNA, proteins, VIII Preface to the Russian Edition genomes, etc.) and various subsystems (replication and translation systems, sysers, multigene families, etc.). Proceeding from this standpoint, we considered the following problems: the origins of molecular-genetic organization; the evolution of genes and proteins; the principles of the structural organization of macromolecules and their evolution; and finally, the evolution of genomes and genosystematics. It is with these problems that the authors have been directly involved. It will be noted that the extent to which different problems have been investigated varies. In some instances, the models are mature, provable and productive while, in others, only the initial steps have been taken. In yet other instances, only the broad outlines of an approach, a 'scenario' for the main events, can be delineated. In the case of the latter, we felt it was sensible to give an adequate indication of the state of the problems, without glossing over their incompleteness or even their tentative formulation. Their hour is yet to come. Now that the book has been written, in retrospect, we must acknowledge the problems of the collective authorship process. An attentive reader will certainly spot some textual incongruities due to differences in author style and temperament. However, our joint work has led us to clarify many standpoints, formulate new tasks and determine the main directions for the future. The book has been a potent stimulus for all involved. Stringent, mutual criticism has freed the text of inaccuracies, ambiguities and generalities. We hope that the final product is lucid and readable. The Preface, Chapters 1, 2 and 3 and the Conclusion were written by V.A. Ratner; Chapter 4 by A.A. Zharkikh and V.A. Ratner; Chapter 5 by A.A. Zharkikh, V.A. Ratner and S.N. Rodin; Chapter 6 by N.A. Kolchanov, V.V. Solovyev and V.A. Ratner; Chapter 7 by V.A. Ratner and S.N. Rodin and Chapter 8 was written by A.S. Antonov. Some of the results were obtained in collaboration with A.G. Bachinsky, V.A. Kulichkov, M.A. Korostyshevsky, M.R. Stabnoy, V.B. Bokhonov, G.K. Kananyan, L.V. Dmelyanchuk, IN. Shindyalov, Yu.G. Matushkin, A.E. Kel', V.V. Kapitonov, I.B. Rogozin, A.Yu. Rzetsky, lA. Shakhmuradov, L.A. Vasiljeva, S.A. Zabanov, B.M. Mednikov, N.B. Petrov, A.V. Troitsky and others, to whom we are sincerely grateful. We are greatly indebted to the late A.N. Belozersky and D.K. Belyayev, and to R.I. Salganik for their steadfast support for our studies. We would also like to thank V.A. Berdnikov, A.D. Ruvinsky and V.N. Stegny for their useful critical comments. Table of Contents Preface to the English Edition .................................... V Preface to the Russian Edition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. VII 1. Introduction: Approaches and Problems . . . . . . . . . . . . . . . . . . . . . . . . . 1 1.1 Molecular-Genetic Regulatory Systems (MGRS) .............. 1 1.2 Biological Molecular Evolution . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 1.3 Prebiological Molecular Evolution. . . . . . . . . . . . . . . . . . . . . . . . . . 7 1.4 Basic Problems in the Theory of Molecular Evolution. . . . . . . . . . 8 2. Dynamic Properties of Self-Reproducing Molecular Systems: Theoretical Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 11 2.1 Eigen's Kinetic Models.. . . .. . . .. . . . .. . . . . . . . .. . .. . . . . .. .. 11 2.2 Replication Errors and Stability of Quasispecies . . . . . . . . . . . . . .. 20 2.3 Universal Self-Reproducing Systems, Sysers. . . . . . . . . . . . . . . . .. 25 2.4 The Evolutionary and Dynamic Properties of Sysers ........... 29 2.4.1 A Minisyser with Two Unlinked Templates. . . . .. . . .. .. 30 2.4.2 A Minisyser with Two Linked Templates [43] .......... 31 2.4.3 A Syser with One Template for I > 2 Proteins. . . . . . . . .. 35 3. The Origin and Evolution of the Genetic Coding-System . . . . . . . . . .. 39 3.1 The Translation Apparatus and the Genetic Code. . . . . . . . . . . . .. 39 3.2 Noise Immunity of the Genetic Code and Texts. . . . . . . . . . . . . .. 44 3.3 A 'Scenario' for the Process of Prebiological Evolution ........ 50 3.3.1 The Emergence of Proteinoids and Microspheres . . . . . . .. 52 3.3.2 Microspheres (Protocells) . . . . . . . . . . . . . . . . . . . . . . . . . .. 53 3.3.3 Peptide-Oligonucleotide Relationships ................ 54 3.3.4 Modular Elongation of Polymers. . . . . . . . . . . . . . . . . . . .. 56 3.3.5 The Emergence of the Translation System and Sysers . . .. 57 3.4 The Emergence and Evolution of Properties of the Genetic Code. 59 4. Methods for Studying the Evolution of Macromolecules. . . . . . . . . . .. 71 4.1 Genetic Sequences. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 71 4.2 Methods for Assessing the Similarity of Sequences. . . . . . . . . . .. 74 X Table of Contents 4.2.1 Measure of Similarity of Genetic Texts. . . . . . . . . . . . . . .. 74 4.2.2 Searching for Related Species ....................... 76 4.3 Optimum Alignment of Sequences. . . . . . . . . . . . . . . . . . . . . . . . .. 80 4.4 Methods of Phylogenetic Analysis . . . . . . . . . . • . . . . . . . . . . . . . .. 83 5. Theoretical Analysis of the Evolution of Genes and Proteins . . . . . . .. 93 5.1 Phylogenetic Analysis of Genes and Proteins. . . . . . . . . . . . . . . .. 93 5.1.1 Globin Superfamily. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 95 5.1.2 Cytochrome C Family of Eukaryotes ................. 101 5.1.3 Global Trees of Evolution and Taxonomy .............. 103 5.2 Evolutionary Rates and Protein Variability ................... 106 5.3 The Evolutionary Dynamics of Protein Variability ............. 112 5.4 Models of Microevolutionary Process Dynamics .............. 115 5.4.1 Deterministic Models of Population Dynamics .......... 116 5.4.2 Stochastic Models of Population Dynamics ............. 117 5.4.3 The Genetic Load and Haldane's Dilemma ............. 119 5.4.4 Connection Between Parameters of Micro- and Macroevolutionary Processes ........................ 121 5.4.5 Macroevolutionary Rates and the Role of Multicellular Organization ..................................... 123 5.5 Synonymous Macroevolutionary Drift ....................... 125 5.5.1 Genetic Drift of Neutral Alleles ...................... 127 5.5.2 Qualitative Principles of a Unified Theory ............. 130 5.5.3 Evolution of Isoacceptor tRNAs ...................... 136 5.6 Problems of Molecular Phyletic Coevolution ................. 139 6. The Structural Organization and Evolution of Macromolecules ..... 147 6.1 The Structural Organization of Globular Proteins .............. 147 6.2 Regularities of the Evolutionary Transformation of the Globular Protein Structure ........................................ 151 6.2.1 Primitive Functional Centres and Factors Accounting for Their Evolution . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 151 6.2.2 Modular Rearrangements of Genes as the Main Mechanism for Polypeptide-Chain Elongation .......... 152 6.2.3 Specialization of the Globular Protein Three-Dimensional Structure During Evolution. . . . . . . . . . . . . . . . . . . . . . . . .. 157 6.3 Mechanisms for Mutational Lesion of Three-Dimensional Globular Protein Structure ................................ 160 6.3.1 The Influence of Mutation on the Secondary Structure of Globular Proteins. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 161 6.3.2 The Effect of Mutations on the Tertiary Structure of Globular Proteins. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 164 6.3.3 The Effect of Deletions and Insertions on the Packing of Helices in Globins ................................. 169 Table of Contents XI 6.4 Mechanisms for Evolutionary Transformation of Genes and Products Encoded by Them, Associated with the Structural Characteristics of their Organization ........................ 173 6.4.1 Identification of Non-Random Direct Repeats in Poly- nucleotide Sequences (Contextual Analysis) ............ 174 6.4.2 Non-Random Direct Repeats in Genes Coding for Globular Proteins .................................. 175 6.4.3 Direct Repeats and Modular (Combinatorial) Evolution of Protein Molecules ........., ......................' .. 178 6.5 The Structural Organization and Evolution of RNA ............ 183 6.5.1 The Secondary Structure and Mutational Spectra of tRNA 183 6.5.2 The Structure of Genomic and mRNAs ................ 186 6.6 Detection of Non-Random Inverted Repeats and Complementary Palindromes ...................., ........................ 187 6.6.1 The Method of Contextual Analysis: Inverted Repeats and Palindromes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 187 6.6.2 Analysis of the mRNA Secondary Structure ............ 188 6.6.3 Constraints Imposed by the mRNA Secondary Structure on the Evolution of Genes ........................... 189 6.6.4 Inverted Repeats and Modular Gene Rearrangements ..... 192 6.7 The Principles of Structural Organization and the Origin and Evolution of Macromolecules. . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 196 7. The Principles of the Origin and Evolution of Genomes ............ 201 7.1 Genome Dimensions and the Density of Information Coding .... 201 7.2 Factors of the Evolution of Genomes and Plasmids . . . . . . . . . . . . 204 7.3 Evolutionary Properties of Polyreplicon Systems .............. 207 7.4 Evolutionary Possibilities for the Emergence of Multi-Operon Systems in Prokaryotes .................................... 217 7.5 The Evolution of Multigene Families. . . . . . . . . . . . . . . . . . . . . . . . 220 7.5.1 Parallel (Concerted) Evolution in Multigene Families .... 223 7.5.2 The Microevolution of MF Size ...................... 227 7.5.3 The Macroevolution of MF Size and the Evolution of the Size of Eukaryotic Genomes ........................ 229 7.6 A Possible Pathway of Genome and MGRS Evolution ......... 234 7.6.1 The Origin of Genomes and MGRS of Prokaryotic Cells . 234 7.6.2 The Origin of Genomes and MGRS of Eukaryotic Cells .. 237 7.6.3 The Origin of Genomes and MGRS of Multicellular Eukaryotes ........................................ 238 8. Genosystematics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 241 8.1 Genosystematics and Phenosystematics ...................... 241 8.2 Genosystematics: Its Methods and Main Results ............... 244 8.2.1 Statistical Methods ................................. 244 8.2.2 Direct Methods .................................... 258

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