Molecular Evolution. Wen-Hsiung Li

Transcription

1 Molecular Evolution Wen-Hsiung Li

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3 INTRODUCTION Molecular Evolution: A Brief History of the Pre-DNA Era 1 CHAPTER I Gene Structure, Genetic Codes, and Mutation 7 CHAPTER 2 Dynamics of Genes in Populations 35 CHAPTER 3 Evolutionary Change in Nucleotide Sequences 59 CHAPTER 4 Estimating the Number of Nucleotide Substitution s Between Sequences 79 CHAPTER 5 Molecular Phylogenetics: Methods 9 9 CHAPTER 6 Molecular Phylogenetics: Examples 14 9 CHAPTER 7 Rates and Patterns of Nucleotide Substitution 177 CHAPTER 8 Molecular Clocks 21 5 CHAPTER 9 DNA Polymorphism in Populations 23 7 CHAPTER 10 Evolution by Gene Duplication and Domain Shuffling 26 9 CHAPTER 11 Concerted Evolution of Multigene Families 309 CHAPTER 12 Evolution by Transposition and Horizontal Transfer 33 5 CHAPTER 13 Genome Organization and Evolution 379 CHAPTER 14 Roles of Mutation and Selection in Molecular Evolution 419

4 Preface xiii Substitutional Mutation 24 Acknowledgments xv Crossing-Over and Gene Conversion 25 Deletions and Insertions 2 6 INTRODUCTION Spatial Distribution of Mutations 29 Pattern of Nucleotide Susbtitution in Non- Molecular Evolution: A Brief History coding Sequences 3 0 of the Pre-DNA Era 1 Substitution Pattern in Pseudogenes 3 1 Substitution Patterns in the Control CHAP TER Region of mtdna 33 Gene Structure, Genetic Codes, and CHAPTER 2 Mutation 7 Dynamics of Genes in Populations Nucleotide Sequences 7 35 Gene Structure 9 Protein-Coding Genes 9 Changes in Allele Frequencies 35 RNA-Specifying Genes 12 Natural Selection 3 6 Regulatory Genes 12 Codominance 3 8 Amino Acids 13 Overdominance 40 Amino Acids with Nonpolar Random Genetic Drift 4 1 (Hydrophobic) R Groups 13 Effective Population Size 46 Amino Acids with Uncharged Polar R Gene Substitution 47 Groups 15 Fixation Probability 47 Amino Acids with Negatively Charged Fixation Time 4 8 (Acidic) R Groups 15 Rate of Gene Substitution 4 9 Amino Acids with Positively Charged Extinction of an Allele Under Mutation (Basic) R Groups 15 Pressure 5 0 Protein Structure 17 Genetic Polymorphism 52 Genetic Codes 21 The Neo-Darwinian Theory and the Neu - Mutation 23 tral Mutation Hypothesis 54 Problems 56

5 CHAPTER 3 Methods of Tree Reconstruction 105 Unweighted Pair-Group Method with Evolutionary ychange in Nucleotide Arithmetic Mean (UPGMA) 106 Sequences 59 Transformed Distance Method 10 8 Neighbors Relation Methods 109 Nucleotide Substitution in a DNA Neighbor-Joining Method 11 1 Sequence 59 Minimum-Evolution Method 11 2 Jukes and Cantor's One Parameter Maximum Parsimony Methods 11 2 Model 59 Maximum Likelihood Methods 11 6 Kimura's Two-Parameter Model 62 Methods of Invariants 11 9 Other Models of Nucleotide Computer Programs 122 Substitution 66 Estimation of Branch Lengths 12 2 Divergence Between DNA Sequences 69 Phenetics Versus Cladistics 12 6 Sequence Similarity 69 Comparison of Methods 12 7 Sequence Dissimilarity 73 Assumptions and Computational Tim e Nonuniform Rates Among Nucleotide 127 Sites 74 Consistency 127 Problems 77 Simulation Studies 13 2 Statistical Tests : Analytical Methods 136 CHAPTER 4 Parsimony Tests 13 6 Distance Tests 13 9 Statistical Tests : The Bootstrap 141 Estimating the Number of Nucleotide Substitutions Between The Procedure 14 1 Sequences 79 Effective Number of Competing Tree s 142 Noncoding sequences 80 Estimation Bias 14 4 Jukes and Cantor's Method 80 The Complete-and-Partial Bootstrap Kimura's Two-Parameter Method 80 Technique 145 Tajima and Nei 's Method 81 Problems 146 Other Methods 8 1 An Example 8 2 Comparison of Methods 84 CHAPTER 6 Nonuniform Rates Among Nucleotide Molecular Phylogenetics : Examples Sites 86 Protein-Coding Sequences Sequence Alignment 91 Man's Closest Relatives 149 The Dot-Matrix Method 92 Whale Stories 155 Similarity and Distance Methods 92 Are the Yews Conifers or Not? 160 Multiple Sequences 95 The Origin of Angiosperms 164 Problems 96 The Origin of Eukaryotes 16 7 Ancient DNA 174 CHAPTER 5 Molecular Phylogenetics : Methods CHAPTE R 7 99 Rates and Pa tterns of Nucleotide Phylogenetic Trees 100 Substitution 177 Rooted and Unrooted Trees 101 Estimation of Substitution Rates 17 7 True and Inferred Trees 102 Mammalian Nuclear Genes 17 8 Gene Trees and Species Trees 103 Coding Regions 179 Monophyletic Groups and Clades 104 Noncoding Regions 182

6 Causes of Variation in Substitution Rates Testing the Neutral Mutation Hypothesis Variation Among Different Gene The Hudson-Kreitman-Aguade Test 25 0 Regions 185 The McDonald-Kreitman Test 254 Variation Among Genes 188 Joint Effects of Linkage and Selection 25 6 Drosophila Nuclear Genes 190 MHC Polymorphism 25 9 Rates of Substitution in Organelle DNA 192 Protein and DNA Polymorphisms in Amer- Viral Genes 194 ican Oysters: Contrasting Pictures o f Nonrandom Usage of Synonymous Geographic Differentiation 265 Codons 196 Codon Usage in Unicellular Organisms CHAPTER Codon Usage in Multicellular Organ- Evolution by Gene Duplication an d isms 200 Domain Shuffling 269 Adaptive Evolution of Lysozyme in Cow, Langur, and Hoatzin 202 Types of DNA Duplication 270 Adaptation of Hemoglobin to High Alti- Domain Duplication and Gene Elongation tudes Structure and Function of Hemoglobin The a2 Type I Collagen Gene Apolipoprotein Genes 274 Llama Hemoglobin 208 Prevalence of Domain Duplication 278 Bird Hemoglobins 210 T-IA Formation of Gene Families and Acquisition of New Functions 278 RNA-Specifying Genes 28 1 Isozymes 282 Molecular Clocks 215 Color-Sensitive Pigment Proteins 28 2 The Relative-Rate Test 216 A Local Clock in Mice, Rats, and Hamsters 218 Lower Rates in Humans Than in Monkeys 219 Higher Rates in Rodents than in Primates 220 Male-Driven Sequence Evolution 225 Causes of Rate Variation Among Lineages 228 Overdispersed Clocks 231 Ratios of Synonymous and Nonsynony- mous Rates in Different Lineages 234 Nonfunctionalization of Redundant Dupli - cates 284 Dating Gene Duplications 28 8 The Globin Superfamily of Genes 28 9 Homeobox Genes 29 2 Domain and Exon Shuffling 297 Mosaic Proteins 29 8 Phase Limitations on Exon Shuffling 29 9 Alternative Pathways for Producing New Functions 30 1 Alternative Splicing 30 2 Overlapping ppmg Genes 304 Gene Sharing 30 5 RNA Editing 30 8 CHAPTER 9 CHAPTER 1 1 DNA Polymorphism in Populations Concerted Evolution of Multigen e 237 Families 309 Measures of DNA Polymorphism 237 Gene Genealogy and the Coalescent Theory 243 Estimation of Population Parameters 245 Detection of Natural Selection 248 Gene Conversion and Unequal Crossing- Over 310 Gene Conversion 31 0 Unequal Crossing-Over 31 4

7 Examples of Concerted Evolution 315 Evolution of Alu Sequences 354 X-Linked Color Vision Genes in Higher Effects of Transposition on the Hos t Primates 315 Genome 35 7 Ribosomal RNA Genes in Humans and Hybrid Dysgenesis 360 Apes 318 Maintenance of Transposable Elements in The "360" and "500" Nongenic Repeat Populations 363 Families in Drosophila 319 Horizontal Gene Transfer: Mechanisms 36 6 Concerted Evolution by Gene Conversion Horizontal Gene Transfer : Detection 323 Methods 367 Concerted Evolution by Unequal Crossing- Horizontal Gene Transfer: Examples 372 Over 327 Evolution of Penicillin Resistance in Relative Roles of Gene Conversion and Neisseria Species 37 2 Unequal Crossing-Over 327 Horizontal. Transfer of P Transposable Other Mechanisms of Concerted Evolution Elements Factors Affecting the Rate of Concerted CHAPTER 13 Evolution 33 0 Arrangement of Repeats 330 Genome Organization an d Functional Requirement 330 Evolution 379 Structure of Repeat Unit 33 1 Natural Selection and Biased Gene Genome Size Variation and the C-Valu e Conversion 332 Paradox 379 Evolutionary Implications 332 Genome Sizes of Bacteria 380 Spread of Advantageous Mutations 332 Genome Sizes of Eukaryotes 38 1 Retardation of Divergence of Duplicate The Repetitive Structure of the Eukaryotic Genes 333 Genome 384 Evolutionary History of Duplicate Localized Repetitive Sequences 38 5 Genes 333 Dispersed Repetitive Sequences 387 Generation of Genic Variation 334 The Genomic Location of Transcribed Genes 38 8 Tandem Repetitive Sequences 388 CHAPTER 12 Classification of Tandem Repetitive Evolution by Transposition and DNA 38 9 Horizontal Transfer 335 Mutational Mechanisms 39 1 Population Genetics of VNTRs 39 3 Transposition and Retroposition 336 Mechanisms for Increasing Genome Size Transposable Elements Insertion Sequences 338 Genome Duplication 395 Transposons 338 Complete and Partial Chromosomal Retroelements 340 Duplication 39 6 Evolutionary Relationships among Transposition 397 Retroelements 342 Replication Slippage and Unequal Retrogenes 345 Crossing-Over 39 7 Retropseudogenes 348 DNA Amplification 39 8 Pseudogenes Derived from POL II Maintenance of Nongenic DNA 39 9 Transcripts 348 GC Content in Bacteria 40 1 Pseudogenes Derived from POL III Compositional Organization of the Verte- Transcripts 349 brate Genome 402 Evolutionary Fate of Retropseudogenes Origins of Isochores

8 Origins of Introns 410 ANSWERS TO PROBLEMS 433 Relationships between Exons and Unit s of Protein Structure 413 Phylogenetic Distribution of Introns 414 LITERATURE CITED 437 Mechanisms of Intron Insertion 417 INDEX 475 CHAPTER 14 Roles of Mutation and Selection in Molecular Evolution 41 9 Is Sequence Evolution Mutation or Selection Driven? 41 9 Mutation Pressure Versus Amino Acid Composition 421 Switches in Species-Specific Codon Preferences 424 Emergence of Nonuniversal Genetic Codes 425 Emergence of New Functions 427 Conclusions 428