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Evolution: The Molecular Landscape

Cold Spring Harbor’s 74th Symposium
The Molecular Landscape
Edited by Bruce Stillman,
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Cold Spring Harbor Laboratory



Table of Contents


Figure Index
Aim and Scope of the Book
 Evolutionary Biology Describes the History of Life and Explains Why Organisms Are the Way They Are
 Evolutionary Biology Is a Valuable Tool
 Molecular Biology and Evolutionary Biology Are Overlapping Fields of Study
 1 The History of Evolutionary Biology: Evolution and Genetics
  A Brief Summary of Modern Genetics and Evolution
  Evolution before Darwin
  Charles Darwin
  The Eclipse of Natural Selection
  The Evolutionary Synthesis
 2 The Origin of Molecular Biology
  The Beginnings of Molecular Biology
  Evolutionary and Molecular Biology: A New Synthesis?
 3 Evidence for Evolution
  Evidence for Evolution
  Objections to Evolution
  Science and Society
 4 The Origin of Life
  When Did Life Begin on Earth?
  How Did Life Begin on Earth?
 5 The Last Universal Common Ancestor and the Tree of Life
  Tracing Early Evolutionary History
  Universal Homologies, LUCA, and the Tree of Life
 6 Diversification of Bacteria and Archaea. I: Phylogeny and Biology
  Introduction to the Bacteria and Archaea
  Phylogenetic Diversification of Bacteria and Archaea
  Biological Diversification of Bacteria and Archaea
 7 Diversification of Bacteria and Archaea. II: Genetics and Genomics
  The Nature of Archaeal and Bacterial Genomes
  Lateral Transfer of DNA
 8 The Origin and Diversification of Eukaryotes
  Introduction to the Eukaryotes
  Endosymbioses Have Played a Key Role in the Evolution of Eukaryotes
  Structure and Evolution of the Nuclear Genome
  Eukaryotic Diversification
 9 Multicellularity and Development
  How Multicellularity Happens
  Division of Labor through Differentiation
  Diversity of Body Plans
  Genetics of Building a Body Plan
 10 Diversification of Plants and Animals
  Fossilization and Geological Time
  The Flow of the Evolution of Life-forms
  The Next 500 Million Years—Life Since the Cambrian Period
  Patterns of Evolution
 11 Evolution of Developmental Programs
  Anterior–Posterior Patterning: Hox Gene Regulation of Development and Evolutionary Change
  Hox Genes Are Shown to Be Involved in Evolutionary Change
  Skeletal Evolution in Sticklebacks
  Evolution of Maize from Teosinte
  Universality of Developmental Systems
 12 Generation of Variation by Mutation and Recombination
  Mutations and Mechanisms for Their Generation
  Protection, Prevention, and Correction Mechanisms Limit the Number of Mutations Caused by DNA Damage and Replication Errors
  Rates and Patterns of Mutations
  Generation of Variation by Mixing: Sex and Lateral Gene Transfer
 13 Variation in DNA and Proteins
  Genetic Variation
  Types of Genetic Variation
 14 Variation in Genetically Complex Traits
  Introduction to Quantitative Traits
  Analyzing Quantitative Variation
  The Genetic Basis of Quantitative Variation
  Generation of Quantitative Variation
 15 Random Genetic Drift
  Evolution Is a Largely Random Process
  Random Drift of Allele Frequencies
  The Neutral Theory
  Recombination and Random Drift
 16 Population Structure
  Gene Flow
  Gene Flow Interactions with Other Evolutionary Forces
  Genealogies in Structured Populations
 17 Selection on Variation
  The Nature of Selection
  Selection on Quantitative Traits
  Selection on Multiple Genes
 18 The Interaction between Selection and Other Forces
  Selection and Random Drift
  Selection and Gene Flow
  Balancing Selection
  Mutation and Selection
 19 Measuring Selection
  Direct Measurement of Selection
  Indirect Measurement
  Selection on Linked Loci
  Selection on Noncoding DNA
  The Extent of Selection
 20 Phenotypic Evolution
  Evolutionary Optimization
  Evolutionary Games
  Sexual Selection
 21 Conflict and Cooperation
  Social Evolution
  Conflict between Genes
  Interactions between Relatives
  Evolution of Cooperation
 22 Species and Speciation
  Defining Species
  The Genetics of Speciation
  Mechanisms of Speciation
  The Geography of Speciation
 23 Evolution of Genetic Systems
  Studying the Evolution of Genetic Systems
  Evolution of Mutation Rates
  Evolution of Sex and Recombination
  Consequences of Sex
  Evolution of Evolvability
 24 Evolution of Novelty
  The Basic Features of Novelty
  Changes in the Activity of Gene Products
  Changes in Gene Regulation and Interactions within a Network: Targeting, Differentiation, and Development
  Robustness, Modularity, and Compartmentalization
  Acquiring New Functions from Other Species: Gene Transfer and Symbiosis
  Natural Selection over Long Periods of Time Leads to the Origin of Novelty
 25 Human Evolutionary History
  Placing Humans on the Tree of Life
  The Evolution of Hominins
  Genetics and Human Evolution
  Genomics and Humanness
 26 Current Issues in Human Evolution
  The Genetic Basis of Disease
  Understanding Human Nature
 27 Phylogenetic Reconstruction   PDF   HTML
  Generating a Molecular Sequence Matrix for Phylogenetic Analysis
  Methods to Infer Phylogenetic Trees
  Evaluation of Methods and Trees
  Problems and Questions in Phylogenetic Reconstruction
  Using Gene Trees
 28 Models of Evolution   PDF   HTML
  Deterministic Processes
  Random Processes
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