EVOLUTION The Molecular Landscape

Symposium Participants v Foreword xix

Introduction

Darwin the Scientist J. Browne 1 On the Future of Biology E.O. Wilson 9

RNA and Proteins

Evolution of Biological Catalysis: Ribozyme to RNP Enzyme T.R. Cech 11 Evolution in an RNA World G.F. Joyce 17 The Ribosome: Some Hard Facts about Its Structure and Hot Air about Its Evolution V. Ramakrishnan 25 Step-by-Step Evolution of Vertebrate Blood Coagulation R.F. Doolittle 35 How Proteins Adapt: Lessons from Directed Evolution F.H. Arnold 41

Cellular Evolution

Reconstructing the Emergence of Cellular Life through the Synthesis of Model Protocells S.S. Mansy and J.W. Szostak 47 Dynamic Chromosome Organization and Protein Localization Coordinate the Regulatory Circuitry that Drives the Bacterial Cell Cycle E.D. Goley, E. Toro, H.H. McAdams, and L. Shapiro 55 An Integrated View of Precambrian Eumetazoan Evolution E.H. Davidson and D.H. Erwin 65 The Dawn of Developmental Signaling in the Metazoa G.S. Richards and B.M. Degnan 81

Mutation

Evolving Views of DNA Replication (In)Fidelity T.A. Kunkel 91 Protein Folding Sculpting Evolutionary Change S. Lindquist 103 Predicting Virus Evolution: The Relationship between Genetic Robustness and Evolvability of Thermotolerance C.B. Ogbunugafor, R.C. McBride, and P.E. Turner 109 Genome-wide Mutational Diversity in an Evolving Population of Escherichia coli J.E. Barrick and R.E. Lenski 119 Selection, Gene Interaction, and Flexible Gene Networks R.J. Greenspan 131

Selection and Adaptation

The Oligogenic View of Adaptation G. Bell 139 Genetic Dissection of Complex Traits in Yeast: Insights from Studies of Gene Expression and Other Phenotypes in the BYxRM Cross I.M. Ehrenreich, J.P. Gerke, and L. Kruglyak 145 Measuring Natural Selection on Genotypes and Phenotypes in the Wild C.R. Linnen and H.E. Hoekstra 155 Exploring the Molecular Landscape of Host–Parasite Coevolution D.E. Allen and T.J. Little 169 Genetic Recombination and Molecular Evolution B. Charlesworth, A.J. Betancourt, V.B. Kaiser, and I. Gordo 177 Why Sex and Recombination? N.H. Barton 187

Diversity

Eradicating Typological Thinking in Prokaryotic Systematics and Evolution W.F. Doolittle 197 The Phylogenetic Forest and the Quest for the Elusive Tree of Life E.V. Koonin, Y.I. Wolf, and P. Puigbò 205 On the Origins of Species: Does Evolution Repeat Itself in Polyploid Populations of Independent Origin? D.E. Soltis, R.J.A. Buggs, W.B. Barbazuk, P.S. Schnable,, and P.S. Soltis 215

Evolution of Systems

Molecular Evolution of piRNA and Transposon Control Pathways in Drosophila C.D. Malone and G.J. Hannon 225 Drosophila Brain Development: Closing the Gap between a Macroarchitectural and Microarchitectural Approach A. Cardona, S. Saalfeld, P. Tomancak, and V. Hartenstein 235 A General Basis for Cognition in the Evolution of Synapse Signaling Complexes S.G.N. Grant 249

Evolution of Development

Evolution in Reverse Gear: The Molecular Basis of Loss and Reversal Q.C.B. Cronk 259 Darwin's "Abominable Mystery": The Role of RNA Interference in the Evolution of Flowering Plants A. Cibrián-Jaramillo and R.A. Martienssen 267 Evolution of Insect Dorsoventral Patterning Mechanisms M.W. Perry, J.D. Cande, A.N. Boettiger, and M. Levine 275 Lophotrochozoa Get into the Game: The Nodal Pathway and Left/Right Asymmetry in Bilateria C. Grande and N.H. Patel 281 On the Origins of Novelty and Diversity in Development and Evolution: A Case Study on Beetle Horns A.P. Moczek 289 Genetic Regulation of Mammalian Diversity R.R. Behringer, J.J. Rasweiler IV, C.-H. Chen, and C.J. Cretekos 297

Domestication

Genomics, Domestication, and Evolution of Forest Trees R. Sederoff, A. Myburg, and M. Kirst 303 Studying Phenotypic Evolution in Domestic Animals: A Walk in the Footsteps of Charles Darwin L. Andersson 319 Fine Mapping a Locus Controlling Leg Morphology in the Domestic Dog P. Quignon, J.J. Schoenebeck, K. Chase, H.G. Parker, D.S. Mosher, G.S. Johnson, K.G. Lark, and E.A. Ostrander 327

Human Evolution

Human Origins and Evolution: Cold Spring Harbor, Déjà Vu T.D. White 335 Reconstructing the Evolution of Vertebrate Sex Chromosomes D.W. Bellott and D.C. Page 345 The Evolution of Human Segmental Duplications and the Core Duplicon Hypothesis T. Marques-Bonet and E.E. Eichler 355 snaR Genes: Recent Descendants of Alu Involved in the Evolution of Chorionic Gonadotropins A.M. Parrott and M.B. Mathews 363

DUF1220 Domains, Cognitive Disease, and Human Brain Evolution

L. Dumas and J.M. Sikela 375 Mitochondria, Bioenergetics, and the Epigenome in Eukaryotic and Human Evolution D.C. Wallace 383 Genetic Structure in African Populations: Implications for Human Demographic History C.A. Lambert and S.A. Tishkoff 395

Social Interaction and Human Society

A Defense of Sociobiology K.R. Foster 403 Evo-Devo and the Evolution of Social Behavior: Brain Gene Expression Analyses in Social Insects A.L. Toth and G.E. Robinson 419 Cooking and the Human Commitment to a High-quality Diet R.N. Carmody and R.W. Wrangham 427 The Cultural Evolution of Words and Other Thinking Tools D.C. Dennett 435 When Ideas Have Sex: The Role of Exchange in Cultural Evolution M.W. Ridley 443 An Evolutionary Approach to Financial History N. Ferguson 449 The Religious Essence of Intelligent Design B. Forrest 455 Deconstructing Design: A Strategy for Defending Science K.R. Miller 463 Summary B. Charlesworth 469 Author Index 475 Subject Index 477