Evolution of the Genome (eBook)

Front Cover 1
The Evolution of the Genome 4
Copyright Page 5
Contents 14
Part I: The C-value Enigma 28
Chapter 1. Genome Size Evolution in Animals 30
Why Should Anyone Care about Genome Size? 31
Genome Size in Animals: A Historical Perspective 32
The State of Knowledge of Animal Genome Size 37
Patterns of Variation 39
Intraspecific Variation in Animals 51
Mechanisms of Genome Size Change 54
Assessing the Directionality of Animal Genome Size Evolution 67
Genome Size and Cell Size 68
Genome Size and Organismal Phenotypes 79
Measuring Animal Genome Sizes 94
Concluding Remarks and Future Prospects 98
Chapter 2. Genome Size Evolution in Plants 116
A Brief History of Genome Size Study in Plants 117
The State of Knowledge Regarding Plant Genome Sizes 121
Patterns in Plant Genome Size Evolution 125
How Do Plant Genome Sizes Evolve? 130
Key Correlates of Genome Size across Plant Species 141
Ecological and Evolutionary Implications of Genome Size Variation 156
Intraspecific Variation in Genome Size 161
Methodology for Estimating Genome Size in Plants 168
Concluding Remarks and Future Prospects 176
Part II: The Evolution of Genomic Parasites 190
Chapter 3. Transposable Elements 192
A Brief History of the Study of Transposable Elements 192
Who Cares about Transposable Elements? 197
How Are TEs Classified? 197
Hallmarks of TE Sequences 207
Methods Used in the Identification and Study of TEs 209
Applications of TEs to Other Areas of Biology 213
The Prevalence of TEs in Eukaryotic Genomes 215
The Distribution of TEs Within Genomes 220
The Dynamics of TE Evolution 224
Regulation of TE Activity 228
TEs as Mutagens and Sources of Genomic Variation 232
Concluding Remarks and Future Prospects 240
Chapter 4. B Chromosomes 250
A Brief History of the Study of B Chromosomes 251
The Frequency of B Chromosome Infection 254
The Biology of B Chromosomes 260
The Origin(s) of B Chromosomes 273
Interactions with the Host Genome 279
Interactions with the Host Organism 288
The Dynamics of B Chromosome Evolution 292
Concluding Remarks and Future Prospects 300
Part III: Duplications, Duplications... 314
Chapter 5. Small-Scale Gene Duplications 316
The Long Pedigree of Gene Duplication Research 317
Mechanisms of Gene Duplication 325
The Life and Death of Gene Duplicates in the Genome 328
What Happens to Duplicated Genes? 333
Hox Gene Duplication and the Evolution of Animal Development 343
The General Evolutionary Importance of Gene Duplications 346
Concluding Remarks and Future Prospects 347
Chapter 6. Large-Scale Gene and Ancient Genome Duplications 356
Historical Perspectives on the Importance of Large-Scale Duplications 357
Mechanisms of Large-Scale Duplication 358
How Large-Scale Gene Duplications Are Studied 361
Dating Duplication Events 371
Putting Theory into Practice: Evidence for Large-Scale Gene Duplication Events 374
Large-Scale Duplications in the Evolutionary Process 383
Concluding Remarks and Future Prospects 390
Part IV: ... And More Duplications 396
Chapter 7. Polyploidy in Plants 398
History of the Study of Polyploidy in Plants 399
Types of Polyploids 400
Frequency of Polyploids 406
Polyploid Formation and Establishment 411
Multiple Origins of Polyploid Species 417
Impacts of Polyploidization at the Cellular and Organismal Levels 423
Impacts of Polyploidization at the Genome Level 431
Concluding Remarks and Future Prospects 441
Chapter 8. Polyploidy in Animals 454
The Origins and Classification of Polyploid Animals 455
Identifying Polyploids 456
Why Is Polyploidy Less Common in Animals than in Plants? 460
Polyploidy and Unisexuality 467
Polyploidy in Vertebrates 471
Jawless Fishes 471
Cartilaginous Fishes 472
Lungfishes 472
Chondrosteans 473
Teleosts 474
Amphibians 488
Reptiles 499
Mammals and Birds 502
Vertebrate Polyploids: A Summary 504
Polyploidy in Invertebrates 505
Crustaceans 505
Insects 507
Molluscs 513
Annelids 517
Flatworms 520
Miscellaneous Invertebrates 521
Polyploidy and Geographic Distribution in Invertebrates 523
The Evolutionary Fate of Polyploids 527
Concluding Remarks and Future Prospects 528
Part V: Sequence and Structure 546
Chapter 9. Comparative Genomics in Eukaryotes 548
The Early History of Comparative Eukaryotic Genomics 549
Working with Eukaryotic Genomes 560
The Genesis of Large-Scale Sequencing Projects for Eukaryotes 563
Genome Sequencing in Fungi 568
Caenorhabditis elegans and Drosophila melanogaster: The First Animal Genomes to Be Sequenced 571
The Human Genome Project 573
The Mouse and Rat Genomes: The Rise of Modern Mammalian Comparative Genomics 582
Genome Sequencing in Plants and Their Pathogens 586
Other Invertebrate Animal Genomes 589
Protist Genomes 591
Comparative Genomics and Phylogenetics in Eukaryotes 593
Concluding Remarks and Future Prospects 596
Chapter 10. Comparative Genomics in Prokaryotes 612
What Is a Prokaryote? 613
The Rise of Complete Prokaryotic Genome Sequencing 617
General Insights about Prokaryote Genomes 620
Horizontal Transfer of Genetic Material 633
Highlights from Specific Prokaryote Genome Sequencing Projects 643
The Evolution of Genome Size in Prokaryotes 658
The Minimal Genome Concept 668
Genomic Insights into Prokaryotic Abundance and Diversity 672
Applications of Prokaryote Genomics 678
Concluding Remarks and Future Prospects 683
Part VI: The Genome in Evolution 704
Chapter 11. Macroevolution and the Genome 706
Part One—Macroevolutionary Theory and Genome Evolution 707
A Brief History of Evolutionary Theory 707
Is a Theory of Macroevolution Necessary? 711
The Structure of Macroevolutionary Theory 720
A Macroevolutionary Look at the Genome 725
Part Two—“Nonstandard” Genomic Processes and 735
The Origin of Genomes and Cells 736
The Evolution of Sex 736
The Origin of Eukaryotes 737
The Origin of Multicellularity and the Emergence of Complex Metazoa 739
The Evolution of Immunity 741
The Origin of Vertebrates 742
Human Uniqueness 743
Concluding Remarks and Future Prospects 747
Index 758