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Evolutionary Genomics and Systems Biology

ISBN: 978-1-118-21071-0
465 pages
September 2011, Wiley-Blackwell
Evolutionary Genomics and Systems Biology (1118210719) cover image
A comprehensive, authoritative look at an emergent area in post-genomic science, Evolutionary genomics is an up-and-coming, complex field that attempts to explain the biocomplexity of the living world. Evolutionary Genomics and Systems Biology is the first full-length book to blend established and emerging concepts in bioinformatics, evolution, genomics, and structural biology, with the integrative views of network and systems biology.

Three key aspects of evolutionary genomics and systems biology are covered in clear detail: the study of genomic history, i.e., understanding organismal evolution at the genomic level; the study of macromolecular complements, which encompasses the evolution of the protein and RNA machinery that propels life; and the evolutionary and dynamic study of wiring diagrams—macromolecular components in interaction—in the context of genomic complements. The book also features:

  • A solid, comprehensive treatment of phylogenomics, the evolution of genomes, and the evolution of biological networks, within the framework of systems biology
  • A special section on RNA biology—translation, evolution of structure, and micro RNA and regulation of gene expression
  • Chapters on the mapping of genotypes to phenotypes, the role of information in biology, protein architecture and biological function, chromosomal rearrangements, and biological networks and disease
  • Contributions by leading authorities on each topic

Evolutionary Genomics and Systems Biology is an ideal book for students and professionals in genomics, bioinformatics, evolution, structural biology, complexity, origins of life, systematic biology, and organismal diversity, as well as those individuals interested in aspects of biological sciences as they interface with chemistry, physics, and computer science and engineering.

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Preface xiii

Contributors xvii

Part I Evolution of Life.

1. Evolutionary Genomics Leads the Way 3
David Penny and Lesley J. Collins

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 Modern Eukaryotes 7

1.5 Eukaryote Origins: Continuity from the RNAWorld? 10

1.6 Minimal Genomes and Reductive Evolution 12

1.7 Evolutionary Genomics for the Future 13

2. Current Approaches to Phylogenomic Reconstruction 17
Denis Baurain and Herve Philippe

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

3. The Universal Tree of Life and the Last Universal Cellular Ancestor: Revolution and Counterrevolutions 43
Patrick Forterre

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 RNAWorld 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

4. Eukaryote Evolution: The Importance of the Stem Group 63
Anthony M. Poole

4.1 Introduction 63

4.2 Interpreting Trees 68

4.3 Moving Beyond the Deep Roots of Eukaryotes 70

4.4 Concluding Remarks 76

5. The Role of Information in Evolutionary Genomics of Bacteria 81
Antoine Danchin and Agnieszka Sekowska

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

6. Evolutionary Genomics of Yeasts 95
Bernard Dujon

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

Part II Evolution of Molecular Repertoires.

7. Genotypes and Phenotypes in the Evolution of Molecules 123
Peter Schuster

7.1 The Landscape Paradigm 123

7.2 Molecular Phenotypes 125

7.3 The RNA Model 132

7.4 Conclusions and Outlook 148

8. Genome Evolution Studied Through Protein Structure 153
Philip E. Bourne, Kristine Briedis, Christopher Dupont, Ruben Valas, and Song Yang

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

9. Chromosomal Rearrangements in Evolution 165
Hao Zhao and Guillaume Bourque

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

10. Molecular Structure and Evolution of Genomes 183
Todd A. Castoe, A. P. Jason de Koning, and David D. Pollock

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

11. The Evolution of Protein Material Costs 203
Jason G. Bragg and Andreas Wagner

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 206

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

12. Protein Domains as Evolutionary Units 213
Andrew D. Moore and Erich Bornberg-Bauer

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

13. Domain Family Analyses to Understand Protein Function Evolution 231
Adam James Reid, Sarah Addou, Robert Rentzsch, Juan Ranea, and Christine Orengo

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 234

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 HowSafely Can Function Be Inherited Between Homologues? 245

13.7 HowAre Domain Families Distributed in Protein Complexes? 247

14. Noncoding RNA 251
Alexander Donath, Sven Findeib, Jana Hertel, Manja Marz, Wolfgang Otto, Christine Schulz, Peter F. Stadler, and Stefan Wirth

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

15. Evolutionary Genomics of microRNAs and Their Relatives 295
Andrea Tanzer, Markus Riester, Jana Hertel, Clara Isabel Bermudez-Santana, Jan Gorodkin, Ivo L. Hofacker, and Peter F. Stadler

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

16. Phylogenetic Utility of RNA Structure: Evolution’s Arrow and Emergence of Early Biochemistry and Diversified Life 329
Feng-Jie Sun, Ajith Harish, and Gustavo Caetano-Anolles

16.1 Introduction 329

16.2 Structural Characters and Derived Phylogenetic Trees 333

16.3 Applications 344

16.4 Conclusions 353

Part III Evolution of Biological Networks.

17. A Hitchhiker’s Guide to Evolving Networks 363
Charles G. Kurland and Otto G. Berg

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

18. Evolution of Metabolic Networks 397
Eivind Almaas

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

19. Single-Gene and Whole-Genome Duplications and the Evolution of Protein–Protein Interaction Networks 413
Grigoris Amoutzias and Yves Van de Peer

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

20. Modularity and Dissipation in Evolution of Macromolecular Structures, Functions, and Networks 431
Gustavo Caetano-Anolles, Liudmila Yafremava, and Jay E. Mittenthal

20.1 Introduction 431

20.2 Biological Structure as an Emergent Property of Dissipative Systems 432

20.3 Information and Its Dissipation 435

20.4 Time, Thermodynamic Irreversibility, and Growth of Order in the Universe 437

20.5 Information Dissipation and Modularity Pervade Structure in Biology 440

20.6 Modularity and Dissipation in Protein Evolution 443

20.7 Conclusions 447

Acknowledgments 448

References 448

Index 451

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Gustavo Caetano-Anollés, PhD, is Professor in the Department of Crop Sciences at the University of Illinois in Urbana-Champaign, Illinois. He has more than 150 well-cited original research publications in areas related to DNA technology and genomics, and holds half a dozen US patents in various areas of DNA science and biotechnology. His successful book, DNA Markers: Protocols, Applications, and Overviews, was published by Wiley in 1997.
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