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Evolutionary genomics and systems biology / edited by Gustavo Caetano-Anolles. — Hoboken, N.J. : Wiley-Blackwell, c2010. – (58.21/E93e) |
Contents
Contents
Preface
Contributors
Part I Evolution of life
1. Evolutionary Genomics Leads the Way 3
1.1 Introduction 3
1.2 Evolution and the Power of Genomes 4
1.3 The Problem of Deep Phylogeny and "The Tree" 5
1.4 Fred， the Last Common Ancestor of Modem Eukaryotes 7
1.5 Eukaryote Origins: Continuity from the RNA World? 10
1.6 Minimal Genomes and Reductive Evolution 12
1.7 Evolutionary Genomics for the Future 13
References 14
2. Current Approaches to Phylogenomic Reconstruction
2.1 Phylogenomics and Supermatrices 17
2.2 Phylogenetic Signal Versus Nonphylogenetic Signal 19
2.3 Probabilistic Models and Nonphylogenetic Signal 22
2.4 Reduction of Nonphylogenetic Signal Under Fixed Models 28
2.5 CAT Model 31
2.6 Case Study: Cambrian Explosion 33
2.7 Conclusion 35
References 36
3. The Universal Tree of Life and the Last Universal Cellular Ancestor: Revolution and Counterrevolutions 43
3.1 Introduction 43
3.2 The Woesian Revolution 45
3.3 A Rampant "Prokaryotic" Counterrevolution 47
3.4 How to Polarize Characters Without a Robust Root? 50
3.5 The Hidden Root: When the Weather Became Cloudy 51
3.6 LUCA and Its Companions 54
3.7 The Problem of Horizontal Gene Transfer and Ancient Phylogenies: Trees Versus Gene Webs 54
3.8 The Nature of the RNA World 55
3.9 The DNA Replication Paradox and the Nature of LUCA 56
3.10 When Viruses Find Their Way into the Universal Tree of Life 58
3.11 Future Directions 59
References 60
4. Eukaryote Evolution: The Importance of the Stem Group 63
4.1 Introduction 63
4.2 Interpreting Trees 68
4.3 Moving Beyond the Deep Roots of Eukaryotes 70
4.4 Concluding Remarks 76
References 77
5. The Role of Information in Evolutionary Genomics of Bacteria
5.1 Introduction 81
5.2 Revisiting Information 83
5.3 Ubiquitous Functions for Life 84
5.4 The Cenome and the Paleome 87
5.5 Functions Corresponding to Nonessential Persistent Genes 89
5.6 A Ubiquitous Information-Gaining Process: Making a Young Organism from an Aged One 89
5.7 Provisional Conclusion 91
Acknowledgments 92
References 92
6. Evolutionary Genomics of Yeasts 95
6.1 Introduction 95
6.2 A Brief History of Hemiascomycetous Yeast Genomics 96
6.3 The Scientific Attractiveness of S. cerevisiae 98
6.4 Evolutionary Genomics of Hemiascomycetes 104
6.5 Surprises 111
6.6 What Next? 113
Acknowledgments 115
Epilogue 115
References 115
Part II Evolution of Molecular Repertoires
7. Genotypes and Phenotypes in the Evolution of Molecules 123
7.1 The Landscape Paradigm 123
7.2 Molecular Phenotypes 125
7.3 The RNA Model 132
7.4 Conclusions and Outlook 148
Acknowledgments 149
References 149
8. Genome Evolution Studied Through Protein Structure
8.1 Introduction 153
8.2 Structural Granularity and Its Implications 156
8.3 Protein Domains in the Study of Genome Rearrangements 158
8.4 Protein Domain Gain and Loss 160
8.5 And in the Beginning ... 161
8.6 But Let Us Not Forget the Influence of the Environment 161
8.7 Conclusions 162
References 163
9. Chromosomal Rearrangements in Evolution
9.1 Introduction 165
9.2 Genome Representation 166
9.3 Constructing Genome Permutations from Sequence Data 167
9.4 Genomic Distances 168
9.5 Reconstruction of Ancestors and Evolutionary Scenarios 174
9.6 Recent Applications on Large Genomes 177
9.7 Challenges and Promising New Approaches 178
Acknowledgment 179
References 179
10. Molecular Structure and Evolution of Genomes
10.1 Introduction 183
10.2 Overview of Considerations in Studying Protein Evolution 184
10.3 Function and Evolutionary Genomics 186
10.4 Integrating Inferences to Detect and Interpret Adaptation: An Example with Snake Metabolic Proteins 194
10.5 Conclusion 200
References 200
11. The Evolution of Protein Material Costs
11.1 Introduction 203
11.2 Protein Material Costs 204
11.3 An Example: Proteomic Sulfur Sparing 205
11.4 Episodic Nutrient Scarcity Can Shape Protein Material Costs 205
11.5 Highly Expressed Gene Products Often Exhibit Reduced Material Costs
11.6 Material Costs and the Evolution of Genomes 207
11.7 Material Costs and Other Costs of Making Proteins 208
11.8 Conclusions 209
Acknowledgments 209
References 209
12. Protein Domains as Evolutionary Units
12.1 Modular Protein Evolution 213
12.2 Domain-Based Homology Identification 215
12.3 Domains in Genomics and Proteomics 222
12.4 The Coverage Problem 225
12.5 Conclusion 227
References 228
13. Domain Family Analyses to Understand Protein Function Evolution
13.1 Introduction 231
13.2 Universal Domain Structure Families Identified in the Last Universal Common Ancestor 232
13.3 Some Domain Families Recur More Frequently and Are Structurally Very Diverse
13.4 Correlation of Structural Diversity in Superfamilies with Functional Diversity 234
13.5 To What Extent Does Function Vary Between Homologous? 238
13.6 How Safely Can Function Be Inherited Between Homologues? 245
13.7 How Are Domain Families Distributed in Protein Complexes? 247
References 248
14. Noncoding RNA
14.1 Introduction 251
14.2 Ancient RNAs 254
14.3 Domain-Specific RNAs 259
14.4 Conserved ncRNAs with Limited Distribution 267
14.5 ncRNAs from Repeats and Pseudogenes 276
14.6 mRNA-like ncRNAs 277
14.7 RNAs with Dual Functions 281
14.8 Concluding Remarks 282
Acknowledgments 283
References 283
15. Evolutionary Genomics of microRNAs and Their Relatives
15.1 Introduction 295
15.2 The Small RNA Zoo 296
15.3 Small RNA Biogenesis 298
15.4 Computational microRNA Prediction 302
15.5 microRNA Targets 304
15.6 Evolution of microRNAs 307
15.7 Origin(s) of microRNA Families 313
15.8 Genomic Organization 316
15.9 Summary and Outlook 320
References 321
16. Phylogenetic Utility of RNA Structure: Evolution's Arrow and Emergence of Early Biochemistry and Diversified
16.1 Introduction 329
16.2 Structural Characters and Derived Phylogenetic Trees 333
16.3 Applications 344
16.4 Conclusions 353
Acknowledgments 354
References 354
17. A Hitchhiker's Guide to Evolving Networks
17.1 Introduction 363
17.2 Phylogenetic Continuities， Biological Coherence 367
17.3 Nested Structural Networks 371
17.4 Optimal Networks 374
17.5 The Emperor's BLAST Search Revisited 381
17.6 Will the Real Missing Link Please Stand Up? 388
17.7 All's Well 389
Acknowledgments 391
References 391
18. Evolution of Metabolic Networks 397
18.1 Introduction 397
18.2 Metabolic Network Properties 398
18.3 Network Models For Metabolic Evolution 403
18.4 Dynamic Models Of Genome-Level Metabolic Function 407
References 410
19. Single-Gene and Whole-Genome Duplications and the Evolution of Protein-Protein Interaction Networks
19.1 Introduction 413
19.2 Evolution of PINs 414
19.3 Single-Gene Duplications 416
19.4 Whole-Genome Duplications 416
19.5 Diploidization Phase 416
19.6 Dosage Balance Hypothesis 417
19.7 Types of Interactions 417
19.8 WGDs， Transient Interactions， and Organismal Complexity 418
19.9 Studies on PPIs of Ohnologues 419
19.10 Concerns About the Methods of Analysis and the Quality of the Data 420
19.11 The Importance of Medium-Scale Studies: the Case of Dimerization 422
19.12 Evolution of Dimerization Networks 424
19.13 Conclusions 426
Acknowledgment 426
References 427
20. Modularity and Dissipation in Evolution of Macromolecular Structures， Functions， and Networks
20.1 Introduction 431
20.2 Biological Structure as an Emergent Property of Dissipative Systems
20.3 Information and Its Dissipation 435
20.4 Time， Thermodynamic Irreversibility， and Growth of Order in the Universe
20.5 Information Dissipation and Modularity Pervade Structure in Biology
20.6 Modularity and Dissipation in Protein Evolution 443
20.7 Conclusions 447
Acknowledgments 448
References 448
Index
