Download Fundamentals of Molecular Evolution

FUNDAMENTALS OF
MOLECULAR EVOLUTION
Second Edition
Dan Graur
Wen-Hsiung Li
TEL AVIV UNIVERSITY
UNIVERSITY OF CHICAGO
SINAUER ASSOCIATES, INC., Publishers
Sunderland, Massachusetts
© Sinauer Associates, Inc. This material cannot be copied, reproduced, manufactured
or disseminated in any form without express written permission from the publisher.
Contents
Preface xiii
Introduction 1
CHAPTER 1 Genes, Genetic Codes, and Mutation 5
TRANSLATION AND GENETIC CODES 22
MUTATION 25
Substitution mutations 26
Recombination 29
Deletions and insertions 32
Inversions 35
Mutation rates 35
Spatial distribution of mutations 37
Patterns of mutation 38
Are mutations random? 38
NUCLEOTIDE SEQUENCES 5
GENOMES AND DNA REPLICATION 8
GENES AND GENE STRUCTURE 9
Protein-coding genes 9
RNA-specifying genes 12
Posttranscriptional modifications
of RNA 13
Untranscribed genes 13
Pseudogenes 14
AMINO ACIDS 15
PROTEINS 20
FURTHER READINGS 38
CHAPTER 2 Dynamics of Genes in Populations 39
RANDOM GENETIC DRIFT 47
EFFECTIVE POPULATION SIZE 52
GENE SUBSTITUTION 53
Fixation probability 54
Fixation time 55
Rate of gene substitution 57
CHANGES IN ALLELE FREQUENCIES 40
NATURAL SELECTION 41
Codominance 43
Dominance 44
Overdominance and underdominance 45
vi
© Sinauer Associates, Inc. This material cannot be copied, reproduced, manufactured
or disseminated in any form without express written permission from the publisher.
Contents
GENETIC POLYMORPHISM 57
Gene diversity 57
Nucleotide diversity 58
THE DRIVING FORCES IN EVOLUTION 59
vii
The neo-Darwinian theory and the
neutral mutation hypothesis 61
Testing the neutral mutation
hypothesis 63
FURTHER READINGS 65
CHAPTER 3 Evolutionary Change in Nucleotide Sequences 67
NUCLEOTIDE SUBSTITUTION IN A DNA
SEQUENCE 67
Jukes and Cantor’s one-parameter
model 68
Kimura’s two-parameter model 71
NUMBER OF NUCLEOTIDE SUBSTITUTIONS
BETWEEN TWO DNA SEQUENCES 74
Number of substitutions between two
noncoding sequences 75
Substitution schemes with more than
two parameters 77
Violation of assumptions 79
Number of substitutions between two
protein-coding genes 79
CHAPTER 4
Indirect estimations of the number of
nucleotide substitutions 85
AMINO ACID REPLACEMENTS
BETWEEN TWO PROTEINS 86
ALIGNMENT OF NUCLEOTIDE AND
AMINO ACID SEQUENCES 86
Manual alignment by visual
inspection 87
The dot matrix method 87
Distance and similarity methods 90
Alignment algorithms 94
Multiple alignments 97
FURTHER READINGS 98
Rates and Patterns of Nucleotide Substitution 99
RATES OF NUCLEOTIDE
SUBSTITUTION 100
Coding regions 101
Noncoding regions 105
Similarity profiles 107
CAUSES OF VARIATION IN
SUBSTITUTION RATES 108
Functional constraints 108
Synonymous versus nonsynonymous
rates 110
Variation among different gene
regions 111
Variation among genes 113
Acceleration of nucleotide substitution
rates following partial loss of
function 115
Estimating the intensity of purifying
selection 116
Mutational input: Male-driven
evolution 117
POSITIVE SELECTION 119
Detecting positive selection 119
Parallelism and convergence 121
Prevalence of positive selection 123
PATTERNS OF SUBSTITUTION AND
REPLACEMENT 123
Pattern of spontaneous mutation 124
Pattern of substitution in human
mitochondrial DNA 127
Patterns of amino acid replacement 128
What protein properties are conserved
in evolution? 130
© Sinauer Associates, Inc. This material cannot be copied, reproduced, manufactured
or disseminated in any form without express written permission from the publisher.
viii Contents
NONRANDOM USAGE OF
SYNONYMOUS CODONS 132
Measures of codon-usage bias 132
Universal and species-specific
patterns of codon usage 133
Codon usage in unicellular organisms
134
Codon usage in multicellular
organisms 137
Codon usage and population size 139
MOLECULAR CLOCKS 139
RELATIVE RATE TESTS 142
Margoliash, Sarich, and Wilson’s
test 142
Tajima’s 1D method 144
Tests involving comparisons of
duplicate genes 145
LOCAL CLOCKS 146
Nearly equal rates in mice and rats
146
Lower rates in humans than in
African apes and monkeys 147
Higher rates in rodents than in
primates 148
EVALUATION OF THE MOLECULAR
CLOCK HYPOTHESIS 150
Causes of variation in substitution
rates among evolutionary lineages 151
Are living fossils molecular fossils
too? 153
“Primitive” versus “advanced”:
A question of rates 153
Phyletic gradualism versus punctuated
equilibria at the molecular level 154
RATES OF SUBSTITUTION IN
ORGANELLE DNA 155
Mammalian mitochondrial genes 157
Plant nuclear, mitochondrial, and
chloroplast DNAs 157
Substitution and rearrangement rates
160
RATES OF SUBSTITUTION IN RNA
VIRUSES 160
Estimation models 161
Human immunodeficiency viruses
162
FURTHER READINGS 163
CHAPTER 5 Molecular Phylogenetics 165
IMPACTS OF MOLECULAR DATA ON
PHYLOGENETIC STUDIES 165
ADVANTAGES OF MOLECULAR DATA
IN PHYLOGENETIC STUDIES 167
TERMINOLOGY OF PHYLOGENETIC
TREES 167
Rooted and unrooted trees 169
Scaled and unscaled trees 169
The Newick format 170
Number of possible phylogenetic
trees 170
True and inferred trees 173
Gene trees and species trees 174
Taxa and clades 176
TYPES OF DATA 177
Character data 177
Assumptions about character
evolution 178
Polarity and taxonomic distribution
of character states 180
Distance data 180
METHODS OF TREE RECONSTRUCTION
181
DISTANCE MATRIX METHODS 182
Unweighted pair-group method with
arithmetic means (UPGMA) 183
Transformed distance method 185
© Sinauer Associates, Inc. This material cannot be copied, reproduced, manufactured
or disseminated in any form without express written permission from the publisher.
Contents
Sattath and Tversky’s neighborsrelations method 186
Saitou and Nei’s neighbor-joining
method 189
MAXIMUM PARSIMONY METHODS 189
Weighted and unweighted parsimony
193
Searching for the maximum parsimony
tree 194
MAXIMUM LIKELIHOOD METHODS 198
ROOTING UNROOTED TREES 200
ESTIMATING BRANCH LENGTHS 202
ESTIMATING SPECIES DIVERGENCE
TIMES 204
TOPOLOGICAL COMPARISONS 206
Penny and Hendy’s topological
distance 206
Consensus trees 206
ASSESSING TREE RELIABILITY 208
The bootstrap 209
Tests for two competing trees 211
CHAPTER 6
PROBLEMS ASSOCIATED WITH PHYLOGENETIC RECONSTRUCTION 212
Strengths and weaknesses of different
methods 214
Minimizing error in phylogenetic
analysis 216
MOLECULAR PHYLOGENETIC
EXAMPLES 217
Phylogeny of humans and apes 217
Cetartiodactyla and SINE phylogeny
225
The origin of angiosperms 228
MOLECULAR PHYLOGENETIC
ARCHEOLOGY 230
Phylogeny of the marsupial wolf 232
Is the quagga extinct? 232
The dusky seaside sparrow 234
THE UNIVERSAL PHYLOGENY 237
The first divergence events 238
The cenancestor 243
Endosymbiotic origin of mitochondria
and chloroplasts 245
FURTHER READINGS 247
Gene Duplication, Exon Shuffling,
and Concerted Evolution 249
TYPES OF GENE DUPLICATION 250
DOMAINS AND EXONS 250
DOMAIN DUPLICATION AND GENE
ELONGATION 255
The ovomucoid gene 258
Enhancement of function in the 2
allele of haptoglobin 258
Origin of an antifreeze glycoprotein
gene 260
Prevalence of domain duplication 262
FORMATION OF GENE FAMILIES AND
THE ACQUISITION OF NEW
FUNCTIONS 262
ix
RNA-specifying genes 265
Isozymes 268
Opsins 269
DATING GENE DUPLICATIONS 271
GENE LOSS 273
Unprocessed pseudogenes 274
Unitary pseudogenes 275
Nonfunctionalization time 276
THE GLOBIN SUPERFAMILY 278
PREVALENCE OF GENE DUPLICATION,
GENE LOSS, AND FUNCTIONAL
DIVERGENCE 281
© Sinauer Associates, Inc. This material cannot be copied, reproduced, manufactured
or disseminated in any form without express written permission from the publisher.
x Contents
EXON SHUFFLING 283
Mosaic proteins 283
Phase limitations on exon shuffling
286
Exonization and pseudoexonization
289
Different strategies of multidomain
gene assembly 290
THE “INTRONS-EARLY” VERSUS
“INTRONS-LATE” HYPOTHESES 291
Intron sliding 292
The relative fraction of “early” and
“late” introns 294
ALTERNATIVE PATHWAYS FOR
PRODUCING NEW FUNCTIONS 294
Overlapping genes 294
Alternative splicing 296
Intron-encoded proteins and nested
genes 299
Functional convergence 299
RNA editing 301
Gene sharing 302
MOLECULAR TINKERING 303
CONCERTED EVOLUTION 304
MECHANISMS OF CONCERTED
EVOLUTION 308
Gene conversion 308
Unequal crossing over 309
Relative roles of gene conversion and
unequal crossing over 312
DETECTION AND EXAMPLES OF
CONCERTED EVOLUTION 313
The A and G -globin genes in the
great apes 314
The concerted evolution of genes and
pseudogenes 315
FACTORS AFFECTING THE RATE OF
CONCERTED EVOLUTION 317
Number of repeats 318
Arrangement of repeats 318
Structure of the repeat unit 318
Functional requirement 319
Populational processes 320
EVOLUTIONARY IMPLICATIONS OF
CONCERTED EVOLUTION 320
Spread of advantageous mutations
320
Retardation of paralogous gene
divergence 321
Generation of genic variation 321
METHODOLOGICAL PITFALLS DUE TO
CONCERTED EVOLUTION 322
FURTHER READINGS 322
CHAPTER 7 Evolution by Transposition 323
TRANSPOSITION AND RETROPOSITION
323
TRANSPOSABLE ELEMENTS 325
Insertion sequences 326
Transposons 327
Taxonomic, developmental, and target
specificity of transposition 328
Autonomy of transposition 329
RETROELEMENTS 329
Retroviruses 330
Retroposons and retrotransposons 330
Retrons 333
Pararetroviruses 333
Evolutionary origin of retroelements 334
RETROSEQUENCES 336
Retrogenes 336
Semiprocessed retrogenes 338
Retropseudogenes 338
Sequence evolution of retropseudogenes 341
© Sinauer Associates, Inc. This material cannot be copied, reproduced, manufactured
or disseminated in any form without express written permission from the publisher.
Contents
LINES AND SINES 343
SINEs derived from 7SL RNA 344
SINEs derived from tRNAs 346
Where there’s a SINE, there’s a LINE
347
DNA-mediated transposable elements
and transposable fossils 349
Rate of SINE evolution 349
GENETIC AND EVOLUTIONARY EFFECTS
OF TRANSPOSITION
349
Hybrid dysgenesis 354
CHAPTER 8
xi
Transposition and speciation 357
Evolutionary dynamics of transposable element copy number 358
HORIZONTAL GENE TRANSFER 359
Horizontal transfer of virogenes from
baboons to cats 361
Horizontal transfer of P elements
between Drosophila species 363
Promiscuous DNA 365
FURTHER READINGS 366
Genome Evolution 367
C VALUES 368
THE EVOLUTION OF GENOME SIZE IN
PROKARYOTES 368
THE MINIMAL GENOME 371
The analytical approach 371
The experimental approach 373
GENOME MINIATURIZATION 374
Genome size reduction following
endosymbiosis 374
Genome size reduction in parasites 375
GENOME SIZE IN EUKARYOTES AND
THE C VALUE PARADOX 375
MECHANISMS FOR GLOBAL INCREASES
IN GENOME SIZE 380
Polyploidization 380
Polysomy 382
The yeast genome 382
Polyploidy of the vertebrate genome
384
MAINTENANCE OF NONGENIC DNA
384
The hypotheses 386
The evidence 387
Why do similar species have different
genome sizes? 388
THE REPETITIVE STRUCTURE OF THE
EUKARYOTIC GENOME 389
Localized repeated sequences 390
Dispersed repeated sequences 392
Repetitive sequences as a cause of
variation in genome size 394
MECHANISMS FOR REGIONAL
INCREASES IN GENOME SIZE 395
GENE DISTRIBUTION 397
How many genes are there, where are
they, and do we need them? 397
Gene number evolution 400
CHROMOSOMAL EVOLUTION 402
Chromosomes, plasmids, and
episomes 402
Evolution of chromosome number in
prokaryotes 402
Chromosome number variation in
eukaryotes 403
MECHANISMS FOR CHANGES IN GENE
ORDER AND GENE DISTRIBUTION
AMONG CHROMOSOMES 404
Counting gene order rearrangement
events 406
© Sinauer Associates, Inc. This material cannot be copied, reproduced, manufactured
or disseminated in any form without express written permission from the publisher.
xii Contents
Gene order rearrangements in
bacteria 408
Gene order rearrangements in
eukaryotes 410
Gene order as a phylogenetic
character 411
GC CONTENT IN BACTERIA 412
CHIROCHORES 415
COMPOSITIONAL ORGANIZATION OF
THE VERTEBRATE GENOME 417
The distribution of genes and other
genetic elements among isochores 420
Origin of isochores 422
EMERGENCE OF NONUNIVERSAL
GENETIC CODES 425
FURTHER READINGS 427
APPENDIX I Spatial and Temporal Frameworks
of the Evolutionary Process 429
APPENDIX II Basics of Probability 437
LITERATURE CITED 441
INDEX 467
TAXONOMIC INDEX 479
© Sinauer Associates, Inc. This material cannot be copied, reproduced, manufactured
or disseminated in any form without express written permission from the publisher.