Publication Information For NICHOLAS H. BARTON University of Edinburgh DEREK E.G. BRIGGS Yale University JONATHAN A. EISEN University of California, Davis DAVID B. GOLDSTEIN Duke University Medical Center NIPAM H. PATEL University of California, Berkeley COLD S PRING H ARBOR L ABORATORY P RESS Cold Spring Harbor, New York • http://www.cshlpress.com Advance Praise The scope of Barton et al’s new Evolution manuscript is magnificent. This is by far the best textbook on the subject yet and is much like another wonderful textbook The Molecular Biology of the Cell. Well-written and the level of sophistication is pretty equivalent across chapters despite having multiple authors. Figures are, in general, excellent. In its coverage of Evolutionary Processes (Section 3), the analytical and conceptual tools of the field are presented in early chapters (genetic drift, population structure, quantitative genetics) and integrated to under- stand more complex problems in later chapters (i.e. the interaction between selection and other forces). Andrew Martin, Professor of Biology, University of Colorado It is the most comprehensive book out there, with an admirable and clear presentation of the facts. In section 2, which deals with the history of life and in many texts makes for tedious reading, there was remarkable clarity and conciseness, and a focus on the best case studies. I personally learnt a great deal from reading these chapters, and the book as a whole would be useful for workers in the field as a source of reference and to give them breadth. Trevor Price, Professor of Biology, University of Chicago It's really a fascinating new textbook . a brand-new approach . especially the novel examples, which are completely appealing and refreshing. It is certainly unique . an excuse to replace the emphasis on molecular and cell biology parts-list-type courses with an integrated evolutionary approach to teaching upper-level biology. David Fitch, Professor of Biology, New York University . very modern and up-to-date, it does an excellent job integrating molecular biology and evolution, bringing in areas such as evolutionary genomics, biochemistry, and developmental biology that tend to be under-represented in older textbooks. Artym Kopp, Professor of Biology, University of California, Davis . written by people who are involved in the cutting edge of many evolutionary fields. The examples are numerous, well-chosen and up-to-date. This gives each professor the option of picking and choosing among a number of excellent case studies, regardless of the emphasis of that particular professor's course. This is by far the most complete textbook currently on the market, with thorough and expert coverage of the very latest molecular findings. Christopher Wills, Professor of Biological Sciences, University of California, San Diego Publication Information Table of Contents Book Description Book Specifications About the Publisher Contact and Ordering Information Table of Contents Detailed Table of Contents About the Authors Preface Aim and Scope of the Book Sample Chapter: Evidence for Evolution (Chapter 3) Book Description Evolution elegantly synthesizes traditional evolutionary theories with contemporary concepts from genomics, developmental biology, human genetics, and other areas of molecular biology. As an innovative, interdisciplinary, and thoroughly integrated book on evolutionary biology with world- renowned authors, Evolution thoroughly illuminates this major paradigm of modern science. Evolutionary principles are introduced with examples from across the spectrum of life—from “jumping genes” and RNA molecules, to populations of yeast and E. coli reared in the laboratory, to dung flies, lizards, and deer in their natural habitats. A section is also devoted to human evolu- tion and diversity, merging recent insights from molecular techniques with paleontological evi- dence. Evolution is recommended as a primary textbook for undergraduate courses in evolution and well as for biologists seeking a clear, current and comprehensive account of evolutionary theory and mechanisms. Book Specifications ISBN: 978-087969684-9, Printed in four colors, 1200 illustrations, 850 pages, 8.5" x 11" trim size, $100.00 list About the Publisher Cold Spring Harbor Laboratory Press is an internationally renowned publisher of books, journals, and electronic media located on Long Island, New York. Since 1933, it has furthered the advance and spread of scientific knowledge in all areas of genetics and molecular biology, including cancer biology, plant science, bioinformatics, and neurobiology. It is a division of Cold Spring Harbor Laboratory, an innovator in life science research and the education of scientists, students, and the public. Contact and Ordering Information Requests for examination copies for textbook adoptions should be directed to Jane Carter at Cold Spring Harbor Laboratory Press. Email: [email protected] Tel: (516) 422-4071. For other inquiries or to order an individual copy of the book, please contact Liz Powers at Cold Spring Harbor Laboratory Press. Email: [email protected] Tel: (516) 422-4101. Requests for review copies for book reviews or any other publicity should be directed to Ingrid Benirschke at Cold Spring Harbor Laboratory Press. Email: [email protected] Tel: (619) 275-6021. The Evolution Web site is an invaluable supplement to the textbook, including two web-only chapters, a resource for the teacher that contains downloadable figures and tables (for PowerPoint or overhead display), author notes, and chapter problems, and other material. Visit the Web site and request a detailed Table of Contents, Sample Chapters, and Exam Copies. Evolution will be available for Fall 2007 classes. www.evolution-textbook.org Contents About the Authors x Preface xi Aim and Scope of the Book 1 PART I AN OVERVIEW OF EVOLUTIONARY BIOLOGY 7 1 The History of Evolutionary Biology: Evolution and Genetics 9 2 The Origin of Molecular Biology 37 3 Evidence for Evolution 65 PART II THE ORIGIN AND DIVERSIFICATION OF LIFE 85 4 The Origin of Life 87 5 The Last Universal Common Ancestor and the Tree of Life 109 6 Diversification of Bacteria and Archaea. I: Phylogeny and Biology 137 7 Diversification of Bacteria and Archaea. II: Genetics and Genomics 169 8 The Origin and Diversification of Eukaryotes 195 9 Multicellularity and Development 225 10 Diversification of Plants and Animals 253 11 Evolution of Developmental Programs 287 PART III EVOLUTIONARY PROCESSES 323 12 Generation of Variation by Mutation and Recombination 325 13 Variation in DNA and Proteins 355 14 Variation in Genetically Complex Traits 381 15 Random Genetic Drift 413 16 Population Structure 439 v vi CONTENTS 17 Selection on Variation 457 18 The Interaction between Selection and Other Forces 489 19 Measuring Selection 521 20 Phenotypic Evolution 555 21 Conflict and Cooperation 585 22 Species and Speciation 619 23 Evolution of Genetic Systems 657 24 Evolution of Novelty 695 PART IV HUMAN EVOLUTION 725 25 Human Evolutionary History 727 26 Current Issues in Human Evolution 755 Glossary 783 Figure Credits 802 Index 811 ONLINE CHAPTERS 27 Phylogenetic Reconstruction 28 Models of Evolution Detailed Contents About the Authors x Preface xi Aim and Scope of the Book 1 Evolutionary Biology Describes the History of Life and Explains Why Organisms Are the Way They Are 1 Evolutionary Biology Is a Valuable Tool 3 Molecular Biology and Evolutionary Biology Are Overlapping Fields of Study 5 PART I AN OVERVIEW OF EVOLUTIONARY BIOLOGY 7 1 The History of Evolutionary Biology: Evolution and Genetics 9 A Brief Summary of Modern Genetics and Evolution 9 Evolution before Darwin 10 Charles Darwin 16 The Eclipse of Natural Selection 18 The Evolutionary Synthesis 30 2 The Origin of Molecular Biology 37 The Beginnings of Molecular Biology 38 Evolutionary and Molecular Biology: A New Synthesis? 58 3 Evidence for Evolution 65 Evidence for Evolution 66 Objections to Evolution 75 Science and Society 81 PART II THE ORIGIN AND DIVERSIFICATION OF LIFE 85 4 The Origin of Life 87 When Did Life Begin on Earth? 87 How Did Life Begin on Earth? 91 vii viii DETAILED CONTENTS 5 The Last Universal Common Ancestor and PART III the Tree of Life 109 Tracing Early Evolutionary History 109 EVOLUTIONARY PROCESSES 323 Universal Homologies, LUCA, and the Tree of Life 115 12 Generation of Variation by Mutation and Recombination 325 6 Diversification of Bacteria and Archaea. Mutations and Mechanisms for Their I: Phylogeny and Biology 137 Generation 325 Introduction to the Bacteria and Archaea 137 Protection, Prevention, and Correction Phylogenetic Diversification of Bacteria and Mechanisms Limit the Number of Mutations Archaea 142 Caused by DNA Damage and Replication Biological Diversification of Bacteria and Errors 334 Archaea 151 Rates and Patterns of Mutations 343 Generation of Variation by Mixing: Sex and 7 Diversification of Bacteria and Archaea. II: Lateral Gene Transfer 349 Genetics and Genomics 169 The Nature of Archaeal and Bacterial 13 Variation in DNA and Proteins 355 Genomes 169 Genetic Variation 355 Lateral Transfer of DNA 182 Types of Genetic Variation 367 8 The Origin and Diversification of 14 Variation in Genetically Complex Eukaryotes 195 Traits 381 Introduction to the Eukaryotes 195 Introduction to Quantitative Traits 381 Endosymbioses Have Played a Key Role in the Analyzing Quantitative Variation 385 Evolution of Eukaryotes 202 The Genetic Basis of Quantitative Structure and Evolution of the Nuclear Variation 399 Genome 214 Generation of Quantitative