Fundamentals of Molecular Evolution

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ISBN: 9780878932665 | 0878932666
Cover: Paperback
Copyright: 1/15/2000

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Tel Aviv Univ., Israel. Introductory textbook for beginners in molecular evolution. Describes the dynamics of evolutionary change at the molecular level, the driving forces behind this process, and the effects of the various molecular mechanisms on the long-term evolution of genomes, genes, and their products. Previous edition: c1991. Softcover.

Preface

xiii

Introduction

(4)

Genes, Genetic Codes, and Mutation

(34)

Nucleotide Sequences

(3)

Genomes and DNA Replication

(1)

Genes and Gene Structure

(6)

Protein-coding genes

(3)

RNA-specifying genes

(1)

Posttranscriptional modifications of RNA

(1)

Untranscribed genes

(1)

Pseudogenes

(1)

Amino Acids

(5)

Proteins

(2)

Translation and Genetic Codes

(3)

Mutation

(13)

Substitution mutations

(3)

Recombination

(3)

Deletions and insertions

(3)

Inversions

(1)

Mutation rates

(2)

Spatial distribution of mutations

(1)

Patterns of mutation

(1)

Are mutations random?

(1)

Further Readings

(1)

Dynamics of Genes in Populations

(28)

Changes in Allele Frequencies

(1)

Natural Selection

(6)

Codominance

(1)

Dominance

(1)

Overdominance and under-dominance

(2)

Random Genetic Drift

(5)

Effective Population Size

(1)

Gene Substitution

(4)

Fixation probability

(1)

Fixation time

(2)

Rate of gene substitution

(1)

Genetic Polymorphism

(2)

Gene diversity

(1)

Nucleotide diversity

(1)

The Driving Forces in Evolution

(6)

The neo-Darwinian theory and the neutral mutation hypothesis

(2)

Testing the neutral mutation hypothesis

(2)

Further Readings

(2)

Evolutionary Change in Nucleotide Sequences

(32)

Nucleotide Substitution in a DNA Sequence

(7)

Jukes and Cantor's one-parameter model

(3)

Kimura's two-parameter model

(3)

Number of Nucleotide Substitutions Between Two DNA Sequences

(12)

Number of substitutions between two noncoding sequences

(2)

Substitution schemes with more than two parameters

(2)

Violation of assumptions

(1)

Number of substitutions between two protein-coding genes

(6)

Indirect estimations of the number of nucleotide substitutions

(1)

Amino Acid Replacements between Two Proteins

(1)

Alignment of Nucleotide and Amino Acid Sequences

(12)

Manual alignment by visual inspection

(1)

The dot matrix method

(3)

Distance and similarity methods

(4)

Alignment algorithms

(3)

Multiple alignments

(1)

Further Readings

(1)

Rates and Patterns of Nucleotide Substitution

(66)

Rates of Nucleotide Substitution

100

(8)

Coding regions

101

(4)

Noncoding regions

105

(2)

Similarity profiles

107

(1)

Causes of Variation in Substitution Rates

108

(11)

Functional constraints

108

(2)

Synonymous versus nonsynonymous rates

110

(1)

Variation among different gene regions

111

(2)

Variation among genes

113

(2)

Acceleration of nucleotide substitution rates following partial loss of function

115

(1)

Estimating the intensity of purifying selection

116

(1)

Mutational input: Male-driven evolution

117

(2)

Positive Selection

119

(4)

Detecting positive selection

119

(2)

Parallelism and convergence

121

(2)

Prevalence of positive selection

123

(1)

Patterns of Substitution and Replacement

123

(9)

Pattern of spontaneous mutation

124

(3)

Pattern of substitution in human mitochondrial DNA

127

(1)

Patterns of amino acid replacement

128

(2)

What protein properties are conserved in evolution?

130

(2)

Nonrandom Usage of Synonymous Codons

132

(7)

Measures of codon-usage bias

132

(1)

Universal and species-specific patterns of codon usage

133

(1)

Codon usage in unicellular organisms

134

(3)

Codon usage in multicellular organisms

137

(2)

Codon usage and population size

139

(1)

Molecular Clocks

139

(3)

Relative Rate Tests

142

(4)

Margoliash, Sarich, and Wilson's test

142

(2)

Tajima's 1D method

144

(1)

Tests involving comparisons of duplicate genes

145

(1)

Local Clocks

146

(4)

Nearly equal rates in mice and rats

146

(1)

Lower rates in humans than in African apes and monkeys

147

(1)

Higher rates in rodents than in primates

148

(2)

Evaluation of the Molecular Clock Hypothesis

150

(5)

Causes of variation in substitution rates among evolutionary lineages

151

(2)

Are living fossils molecular fossils too?

153

(1)

``Primitive'' versus ``advanced'': A question of rates

153

(1)

Phyletic gradualism versus punctuated equilibria at the molecular level

154

(1)

Rates of Substitution in Organelle DNA

155

(5)

Mammalian mitochondrial genes

157

(1)

Plant nuclear, mitochondrial, and chloroplast DNAs

157

(3)

Substitution and rearrangement rates

160

(1)

Rates of Substitution in RNA Viruses

160

(3)

Estimation models

161

(1)

Human immunodeficiency viruses

162

(1)

Further Readings

163

(2)

Molecular Phylogenetics

165

(84)

Impacts of Molecular Data on Phylogenetic Studies

165

(2)

Advantages of Molecular Data in Phylogenetic Studies

167

(1)

Terminology of Phylogenetic Trees

167

(10)

Rooted and unrooted trees

169

(1)

Scaled and unscaled trees

169

(1)

The Newick format

170

(1)

Number of possible phylogenetic trees

170

(3)

True and inferred trees

173

(1)

Gene trees and species trees

174

(2)

Taxa and clades

176

(1)

Types of Data

177

(4)

Character data

177

(1)

Assumptions about character evolution

178

(2)

Polarity and taxonomic distribution of character states

180

(1)

Distance data

180

(1)

Methods of Tree Reconstruction

181

(1)

Distance Matrix Methods

182

(7)

Unweighted pair-group method with arithmetic means (UPGMA)

183

(2)

Transformed distance method

185

(1)

Sattath and Tversky's neighbors-relations method

186

(3)

Saitou and Nei's neighbor-joining method

189

(1)

Maximum Parsimony Methods

189

(9)

Weighted and unweighted parsimony

193

(1)

Searching for the maximum parsimony tree

194

(4)

Maximum Likelihood Methods

198

(2)

Rooting Unrooted Trees

200

(2)

Estimating Branch Lengths

202

(2)

Estimating Species Divergence Times

204

(2)

Topological Comparisons

206

(2)

Penny and Hendy's topological distance

206

(1)

Consensus trees

206

(2)

Assessing Tree Reliability

208

(4)

The bootstrap

209

(2)

Tests for two competing trees

211

(1)

Problems Associated with Phylogenetic Reconstruction

212

(5)

Strengths and weaknesses of different methods

214

(2)

Minimizing error in phylogenetic analysis

216

(1)

Molecular Phylogenetic Examples

217

(13)

Phylogeny of humans and apes

217

(8)

Cetartiodactyla and SINE phylogeny

225

(3)

The origin of angiosperms

228

(2)

Molecular Phylogenetic Archeology

230

(7)

Phylogeny of the marsupial wolf

232

(1)

Is the quagga extinct?

232

(2)

The dusky seaside sparrow

234

(3)

The Universal Phylogeny

237

(10)

The first divergence events

238

(5)

The cenancestor

243

(2)

Endosymbiotic origin of mitochondria and chloroplasts

245

(2)

Further Readings

247

(2)

Gene Duplication, Exon Shuffling, and Concerted Evolution

249

(74)

Types of Gene Duplication

250

(1)

Domains and Exons

250

(5)

Domain Duplication and Gene Elongation

255

(7)

The ovomucoid gene

258

(1)

Enhancement of function in the α2 allele of haptoglobin

258

(2)

Origin of an antifreeze glycoprotein gene

260

(2)

Prevalence of domain duplication

262

(1)

Formation of Gene Families and the Acquisition of New Functions

262

(9)

RNA-specifying genes

265

(3)

Isozymes

268

(1)

Opsins

269

(2)

Dating Gene Duplications

271

(2)

Gene Loss

273

(5)

Unprocessed pseudogenes

274

(1)

Unitary pseudogenes

275

(1)

Nonfunctionalization time

276

(2)

The Globin Superfamily

278

(3)

Prevalence of Gene Duplication, Gene Loss, and Functional Divergence

281

(2)

Exon Shuffling

283

(8)

Mosaic proteins

283

(3)

Phase limitations on exon shuffling

286

(3)

Exonization and pseudoexonization

289

(1)

Different strategies of multidomain gene assembly

290

(1)

The ``Introns-Early'' versus ``Introns-Late'' Hypotheses

291

(3)

Intron sliding

292

(2)

The relative fraction of ``early'' and ``late'' introns

294

(1)

Alternative Pathways for Producing New Functions

294

(9)

Overlapping genes

294

(2)

Alternative splicing

296

(3)

Intron-encoded proteins and nested genes

299

(1)

Functional convergence

299

(2)

RNA editing

301

(1)

Gene sharing

302

(1)

Molecular Tinkering

303

(1)

Concerted Evolution

304

(4)

Mechanisms of Concerted Evolution

308

(5)

Gene conversion

308

(1)

Unequal crossing over

309

(3)

Relative roles of gene conversion and unequal crossing over

312

(1)

Detection and Examples of Concerted Evolution

313

(4)

The Aγ and Gγ-globin genes in the great apes

314

(1)

The concerted evolution of genes and pseudogenes

315

(2)

Factors affecting the rate of concerted evolution

317

(3)

Number of repeats

318

(1)

Arrangement of repeats

318

(1)

Structure of the repeat unit

318

(1)

Functional requirement

319

(1)

Populational processes

320

(1)

Evolutionary Implications of Concerted Evolution

320

(2)

Spread of advantageous mutations

320

(1)

Retardation of paralogous gene divergence

321

(1)

Generation of genic variation

321

(1)

Methodological Pitfalls due to Concerted Evolution

322

(1)

Further Readings

322

(1)

Evoution by Transposition

323

(44)

Transposition and Retroposition

323

(2)

Transposable Elements

325

(4)

Insertion Sequences

326

(1)

Transposons

327

(1)

Taxonomic, developmental, and target specificity of transposition

328

(1)

Autonomy of transposition

329

(1)

Retroelements

329

(7)

Retroviruses

330

(1)

Retroposons and retrotransposons

330

(3)

Retrons

333

(1)

Pararetroviruses

333

(1)

Evolutionary origin of retroelements

334

(2)

Retrosequences

336

(7)

Retrogenes

336

(2)

Semiprocessed retrogenes

338

(1)

Retropseudogenes

338

(3)

Sequence evolution of retropseudo-genes

341

(2)

LINEs and SINEs

343

(6)

SINEs derived from 7SL RNA

344

(2)

SINEs derived from tRNAs

346

(1)

Where there's a Sine, there's a Line

347

(2)

DNA-mediated transposable elements and transposable fossils

349

(1)

Rate of Sine evolution

349

(1)

Genetic and Evolutionary Effects of Transposition

349

(10)

Hybrid dysgenesis

354

(3)

Transposition and speciation

357

(1)

Evolutionary dynamics of transposable element copy number

358

(1)

Horizontal Gene Transfer

359

(7)

Horizontal transfer of virogenes from baboons to cats

361

(2)

Horizontal transfer of P elements between Drosophila species

363

(2)

Promiscuous DNA

365

(1)

Further Readings

366

(1)

Genome Evolution

367

(62)

C Values

368

(1)

The Evolution of Genome Size in Prokaryotes

368

(3)

The Minimal Genome

371

(3)

The analytical approach

371

(2)

The experimental approach

373

(1)

Genome Miniaturization

374

(1)

Genome size reduction following endosymbiosis

374

(1)

Genome size reduction in parasites

375

(1)

Genome Size in Eukaryotes and the C Value Paradox

375

(5)

Mechanisms for Global Increases in Genome Size

380

(4)

Polyploidization

380

(2)

Polysomy

382

(1)

The yeast genome

382

(2)

Polyploidy of the vertebrate genome

384

(1)

Maintenance of Nongenic DNA

384

(5)

The hypotheses

386

(1)

The evidence

387

(1)

Why do similar species have different genome sizes?

388

(1)

The Repetitive Structure of the Eukaryotic Genome

389

(6)

Localized repeated sequences

390

(2)

Dispersed repeated sequences

392

(2)

Repetitive sequences as a cause of variation in genome size

394

(1)

Mechanisms for Regional Increases in Genome Size

395

(2)

Gene Distribution

397

(5)

How many genes are there, where are they, and do we need them?

397

(3)

Gene number evolution

400

(2)

Chromosomal Evolution

402

(2)

Chromosomes, plasmids, and episomes

402

(1)

Evolution of chromosome number in prokaryotes

402

(1)

Chromosome number variation in eukaryotes

403

(1)

Mechanisms for Changes in Gene Order and Gene Distribution among Chromosomes

404

(8)

Counting gene order rearrangement events

406

(2)

Gene order rearrangements in bacteria

408

(2)

Gene order rearrangements in eukaryotes

410

(1)

Gene order as a phylogenetic character

411

(1)

GC Content in Bacteria

412

(3)

Chirochores

415

(2)

Compositional Organization of the Vertebrate Genome

417

(8)

The distribution of genes and other genetic elements among isochores

420

(2)

Origin of isochores

422

(3)

Emergence of Nonuniversal Genetic Codes

425

(2)

Further Readings

427

(2)

Appendix I Spatial and Temporal Frameworks of the Evolutionary Process

429

(8)

Appendix II Basics of Probability

437

(4)

Literature Cited

441

(26)

Index

467

(12)

Taxonomic Index

479

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Fundamentals of Molecular Evolution

Summary

Author Biography

Table of Contents

Supplemental Materials