Molecular Evolution

438 Pages·1996·13.93 MB·English

by  Nikolay Kolchanov, Vadim A. Ratner, Andrey A. Zharkikh, Sergey N. Rodin, Viktor V. Solovyov, Andrey S. Antonov (auth.)

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