Evolutionary Genomics and Systems Biology -- Contents -- Preface -- Contributors -- Part I Evolution of Life -- 1. Evolutionary Genomics Leads the Way -- 1.1 Introduction -- 1.2 Evolution and the Power of Genomes -- 1.3 The Problem of Deep Phylogeny and "The Tree" -- 1.4 Fred, the Last Common Ancestor of Modern Eukaryotes -- 1.5 Eukaryote Origins: Continuity from the RNA World? -- 1.6 Minimal Genomes and Reductive Evolution -- 1.7 Evolutionary Genomics for the Future -- References -- 2. Current Approaches to Phylogenomic Reconstruction -- 2.1 Phylogenomics and Supermatrices -- 2.2 Phylogenetic Signal Versus Nonphylogenetic Signal -- 2.3 Probabilistic Models and Nonphylogenetic Signal -- 2.3.1 Homogeneous Models -- 2.3.2 Handling of Rate Signal -- 2.3.3 Handling of Compositional Signal -- 2.3.4 Other Model Violations -- 2.3.5 Future Developments -- 2.4 Reduction of Nonphylogenetic Signal Under Fixed Models -- 2.4.1 Variations in Taxon Sampling -- 2.4.2 Recoding and Removal of Offending Data -- 2.5 CAT Model -- 2.6 Case Study: Cambrian Explosion -- 2.7 Conclusion -- References -- 3. The Universal Tree of Life and the Last Universal Cellular Ancestor: Revolution and Counterrevolutions -- 3.1 Introduction -- 3.2 The Woesian Revolution -- 3.3 A Rampant "Prokaryotic" Counterrevolution -- 3.4 How to Polarize Characters Without a Robust Root? -- 3.5 The Hidden Root: When the Weather Became Cloudy -- 3.6 LUCA and Its Companions -- 3.7 The Problem of Horizontal Gene Transfer and Ancient Phylogenies: Trees Versus Gene Webs -- 3.8 The Nature of the RNA World -- 3.9 The DNA Replication Paradox and the Nature of LUCA -- 3.10 When Viruses Find Their Way into the Universal Tree of Life -- 3.11 Future Directions -- References -- 4. Eukaryote Evolution: The Importance of the Stem Group -- 4.1 Introduction.

4.1.1 What is Significant About the Origin of the Eukaryote Cell? -- 4.2 Interpreting Trees -- 4.3 Moving Beyond the Deep Roots of Eukaryotes -- 4.3.1 Origin of the Mitochondrion -- 4.3.2 Stepwise Development of Mitochondria -- 4.3.3 Intron Proliferation and Eukaryote Origins -- 4.4 Concluding Remarks -- References -- 5. The Role of Information in Evolutionary Genomics of Bacteria -- 5.1 Introduction -- 5.2 Revisiting Information -- 5.3 Ubiquitous Functions for Life -- 5.4 The Cenome and the Paleome -- 5.5 Functions Corresponding to Nonessential Persistent Genes -- 5.6 A Ubiquitous Information-Gaining Process: Making a Young Organism from an Aged One -- 5.7 Provisional Conclusion -- Acknowledgments -- References -- 6. Evolutionary Genomics of Yeasts -- 6.1 Introduction -- 6.2 A Brief History of Hemiascomycetous Yeast Genomics -- 6.3 The Scientific Attractiveness of S. cerevisiae -- 6.3.1 Functional Genomics -- 6.3.2 Genome Duplication -- 6.3.3 A Bunch of Fermentative Engines -- 6.3.4 Speciation and Species Definition -- 6.4 Evolutionary Genomics of Hemiascomycetes -- 6.4.1 Distinct and Specific Genome Organization of Three Major Evolutionary Subdivisions of Hemiascomycetes -- 6.4.2 Comparison of Proteins: Pan- and Core-Proteomes -- 6.4.3 Genome Redundancy and Paralogues -- 6.4.4 Conservation of Synteny -- 6.4.5 Genes for Noncoding RNAs, Introns, and Genetic Code Variation -- 6.4.6 Sex, Transposons, Plasmids, Inteins, and Horizontal Gene Transfer -- 6.4.7 Mitochondrial Genomes and NUMTs -- 6.5 Surprises -- 6.6 What Next? -- Acknowledgments -- Epilogue -- References -- Part II Evolution of Molecular Repertoires -- 7. Genotypes and Phenotypes in the Evolution of Molecules -- 7.1 The Landscape Paradigm -- 7.2 Molecular Phenotypes -- 7.2.1 Protein Structures -- 7.2.2 Nucleic Acid Structures -- 7.3 The RNA Model -- 7.3.1 RNA Replication and Mutation.

7.3.2 RNA Secondary Structures -- 7.3.3 Neutrality and Its Consequences -- 7.3.4 Stochastic Effects in RNA Evolution -- 7.3.5 Beyond the One Sequence-One Structure Paradigm -- 7.4 Conclusions and Outlook -- Acknowledgments -- References -- 8. Genome Evolution Studied Through Protein Structure -- 8.1 Introduction -- 8.2 Structural Granularity and Its Implications -- 8.3 Protein Domains in the Study of Genome Rearrangements -- 8.4 Protein Domain Gain and Loss -- 8.5 And in the Beginning . . . -- 8.6 But Let Us Not Forget the Influence of the Environment -- 8.7 Conclusions -- References -- 9. Chromosomal Rearrangements in Evolution -- 9.1 Introduction -- 9.2 Genome Representation -- 9.3 Constructing Genome Permutations from Sequence Data -- 9.4 Genomic Distances -- 9.4.1 Model-Free Distances -- 9.4.2 Rearrangement-Based Distances -- 9.5 Reconstruction of Ancestors and Evolutionary Scenarios -- 9.5.1 Model-Free Reconstruction Algorithms -- 9.5.2 Rearrangement-Based Reconstruction Algorithms -- 9.6 Recent Applications on Large Genomes -- 9.7 Challenges and Promising New Approaches -- Acknowledgment -- References -- 10. Molecular Structure and Evolution of Genomes -- 10.1 Introduction -- 10.2 Overview of Considerations in Studying Protein Evolution -- 10.3 Function and Evolutionary Genomics -- 10.3.1 Deciphering Complexities of Protein Evolution -- 10.3.2 The Future of Modeling Protein Evolution: Merging Realism with Tractability -- 10.3.3 The Effect of Increasing Taxon Sampling and Sequence Biodiversity -- 10.3.4 Removing the Mutational Noise and Context-Dependent Biases from Protein Evolution -- 10.3.5 Where is Protein Evolution Going? -- 10.3.6 Detecting Adaptation and Functional Innovation -- 10.4 Integrating Inferences to Detect and Interpret Adaptation: An Example with Snake Metabolic Proteins.

10.4.1 Snake Metabolic Proteins-Integration of Inferences for Adaptation -- 10.4.2 Detection of Accelerated Nonsynonymous Change -- 10.4.3 Changes at Conserved Sites and Coevolutionary Signal -- 10.4.4 Integrating Evolutionary Inferences with Structure and Function Information -- 10.4.5 Further Evidence of Adaptation from Molecular Convergence -- 10.4.6 Integrating Inferences with Possible Causal Factors -- 10.5 Conclusion -- References -- 11. The Evolution of Protein Material Costs -- 11.1 Introduction -- 11.2 Protein Material Costs -- 11.3 An Example: Proteomic Sulfur Sparing -- 11.4 Episodic Nutrient Scarcity Can Shape Protein Material Costs -- 11.5 Highly Expressed Gene Products Often Exhibit Reduced Material Costs -- 11.6 Material Costs and the Evolution of Genomes -- 11.7 Material Costs and Other Costs of Making Proteins -- 11.8 Conclusions -- Acknowledgments -- References -- 12. Protein Domains as Evolutionary Units -- 12.1 Modular Protein Evolution -- 12.2 Domain-Based Homology Identification -- 12.2.1 Domain Architecture Similarity -- 12.2.2 Domain Resources and Domain-Based Search -- 12.2.3 Deciphering Circular Permutations with Domains -- 12.3 Domains in Genomics and Proteomics -- 12.3.1 Building Domain Trees -- 12.4 The Coverage Problem -- 12.5 Conclusion -- References -- 13. Domain Family Analyses to Understand Protein Function Evolution -- 13.1 Introduction -- 13.2 Universal Domain Structure Families Identified in the Last Universal Common Ancestor -- 13.3 Some Domain Families Recur More Frequently and Are Structurally Very Diverse -- 13.4 Correlation of Structural Diversity in Superfamilies with Functional Diversity -- 13.5 To What Extent Does Function Vary Between Homologous? -- 13.5.1 Phylogenetic Analysis of Protein Families -- 13.5.2 Structural Domain Characterization of Clusters of Orthologous Genes Using CATH.

13.5.3 Evolution of (COGs) Function Within CATH Superfamilies -- 13.5.4 Resolving Ambiguous Evolutionary Scenarios Between Parent and Child COGs in a CATH Superfamily -- 13.5.5 Relationship Between Domain Architecture Rearrangement and Functional Divergence Within CATH Superfamilies -- 13.6 How Safely Can Function Be Inherited Between Homologues? -- 13.7 How Are Domain Families Distributed in Protein Complexes? -- References -- 14. Noncoding RNA -- 14.1 Introduction -- 14.2 Ancient RNAs -- 14.2.1 RNase P and RNase MRP RNA -- 14.2.2 Signal Recognition Particle RNA -- 14.2.3 snoRNAs -- 14.3 Domain-Specific RNAs -- 14.3.1 Telomerase RNA -- 14.3.2 Spliceosomal snRNAs -- 14.3.3 U7 snRNA -- 14.3.4 tmRNA -- 14.3.5 6S RNA -- 14.4 Conserved ncRNAs with Limited Distribution -- 14.4.1 Y RNAs -- 14.4.2 Vault RNAs -- 14.4.3 7SK RNA -- 14.4.4 SmY RNA -- 14.4.5 Bacterial RNAs -- 14.4.6 A Zoo of Diverse Examples -- 14.5 ncRNAs from Repeats and Pseudogenes -- 14.6 mRNA-like ncRNAs -- 14.6.1 Dosage Compensation -- 14.6.2 Imprinting -- 14.6.3 Stress Response -- 14.6.4 Transcriptional Regulators -- 14.7 RNAs with Dual Functions -- 14.7.1 RNAIII -- 14.7.2 SgrS -- 14.7.3 SRA/SRAP -- 14.7.4 Enod40 -- 14.8 Concluding Remarks -- Acknowledgments -- References -- 15. Evolutionary Genomics of microRNAs and Their Relatives -- 15.1 Introduction -- 15.2 The Small RNA Zoo -- 15.2.1 Endogenous siRNAs -- 15.2.2 piRNA -- 15.2.3 rasiRNA -- 15.2.4 "Exotic" Small RNA Species -- 15.3 Small RNA Biogenesis -- 15.3.1 Components of the Small RNA Processing Machinery -- 15.3.2 MicroRNA Biogenesis -- 15.3.3 Biogenesis of Other Small RNAs -- 15.3.4 Three Main Mechanisms, Same Global Effect on Gene Expression -- 15.4 Computational microRNA Prediction -- 15.5 microRNA Targets -- 15.5.1 How Many Targets? -- 15.5.2 Target Prediction -- 15.5.3 Targets and Polymorphisms -- 15.6 Evolution of microRNAs.

15.6.1 Animal microRNAs.