Note: Front Cover -- Evolution of Primary Production in the Sea -- Copyright Page -- Contents -- List of Contributors -- Preface -- Chapter 1: An Introduction to Primary Producers in the Sea: Who They Are, What They Do, and When They Evolved -- I. What Is Primary Production? -- II. How Is Photosynthesis Distributed in the Oceans? -- III. What Is the Evolutionary History of Primary Production in the Oceans? -- IV. Concluding Comments -- References -- Chapter 2: Oceanic Photochemistry and Evolution of Elements and Cofactors in the Early Stages of the Evolution of Life -- I. Energy Requirements for Life -- II. Prebiotic Photochemistry-UV and Oceanic Photochemistry -- III. Evolution of Cofactors -- A. Metals -- B. Cofactors -- IV. Conclusions -- Acknowledgments -- References -- Chapter 3: The Evolutionary Transition from Anoxygenic to Oxygenic Photosynthesis -- I. Earliest Evidence for Photosynthesis and the Nature of the Earliest Phototrophs -- II. Structural Conservation of the Core Structure of Photosynthetic Reaction Centers During Evolution -- III. The Structural and Mechanistic Differences Between the Anoxygenic Reaction Centers of Type II and Photosystem II of Oxygenic Organisms -- IV. Evolutionary Scenarios for How the Transition from Anoxygenic to Oxygenic Photosynthesis May Have Taken Place -- V. Conclusions and Prospects for the Future -- Acknowledgments -- References -- Chapter 4: Evolution of Light-Harvesting Antennas in an Oxygen World -- I. How Cyanobacteria Changed the World -- II. Light-Harvesting Antennas and the Evolution of the Algae -- III. Phycobilisomes -- IV. The ISIA/PCB Family -- V. About Chlorophylls -- VI. The LHC Superfamily -- A. The Light-Harvesting Antennas -- B. The Stress-Response Connection -- C. Prokaryotic Ancestry of the LHC Superfamily -- VII. Overview -- Acknowledgments -- References. , Chapter 5: Eukaryote and Mitochondrial Origins: Two Sides of the Same Coin and Too Much Ado About Oxygen -- I. Cell Evolution With and Without Endosymbiosis -- II. The Standard Model of How and Why the Mitochondrion Become Established -- III. There are at Least 12 Substantial Problems with the Standard Model -- IV. The Same 12 Issues from the Standpoint of an Alternative Theory -- V. Criticism and Defense of the Hydrogen Hypothesis -- VI. Intermezzo -- VII. Conclusions -- Acknowledgments -- References -- Chapter 6: Photosynthesis and the Eukaryote Tree of Life -- I. The Eukaryotes -- II. Overview of the Tree -- A. Opisthokonts -- B. Amoebozoa -- C. Rhizaria (Formerly Cercozoa) -- D. Archaeplastida -- E. Chromalveolates -- F. Excavates -- G. Incertae Sedis -- III. The Eukaryote Root -- IV. Oxygenic Photosynthesis Across the Eukaryote Tree of Life -- A. Opisthokonts -- B. Amoebozoa -- C. Rhizaria -- D. Archaeplastida -- E. Chromalveolates -- F. Excavates and Incertae Sedis -- V. Conclusions -- References -- Chapter 7: Plastid Endosymbiosis: Sources and Timing of the Major Events -- I. General Introduction to Plastid Endosymbiosis -- II. Primary Plastid Origin and Plantae Monophyly -- A. Generating the Eukaryotic Phylogeny -- B. Molecular Clock Analyses -- C. Conclusions of Plantae Phylogenetic and Molecular Clock Analyses -- III. Secondary Plastid Endosymbiosis -- IV. Tertiary Plastid Endosymbiosis -- V. Summary -- References -- Chapter 8: The Geological Succession of Primary Producers in the Oceans -- I. Records of Primary Producers in Ancient Oceans -- A. Microfossils -- B. Molecular Biomarkers -- II. The Rise of Modern Phytoplankton -- A. Fossils and Phylogeny -- B. Biomarkers and the Rise of Modern Phytoplankton -- C. Summary of the Rise of Modern Phytoplankton -- III. Paleozoic Primary Production -- A. Microfossils. , B. Paleozoic Molecular Biomarkers -- C. Paleozoic Summary -- IV. Proterozoic Primary Production -- A. Prokaryotic Fossils -- B. Eukaryotic Fossils -- C. Proterozoic Molecular Biomarkers -- D. Summary of the Proterozoic Record -- V. Archean Oceans -- VI. Conclusions -- A. Directions for Continuing Research -- Acknowledgments -- References -- Chapter 9: Life in Triassic Oceans: Links Between Planktonic and Benthic Recovery and Radiation -- I. Benthos -- A. Benthic Wastelands of the Early Triassic -- B. Middle Triassic Recovery of Benthic Ecosystems -- C. Late Triassic Benthic Boom: Supersize Me -- II. Plankton -- A. Early Triassic Disaster Species -- B. Middle Triassic Oxygen and Evolution -- C. Late Triassic Rise of Modern Phytoplankton -- III. Benthic-Planktonic Coupling in Triassic Oceans -- A. Common Driver -- B. Plankton Control -- C. Feedback from the Benthos -- D. Assistance from the Plankton -- IV. Conclusions -- Acknowledgments -- References -- Chapter 10: The Origin and Evolution of Dinoflagellates -- I. Paleontological Data -- II. Phylogeny of Dinoflagellates -- A. Sources of Information -- B. The Phylogeny -- C. Reconciling Molecular and Morphological Phylogenies -- III. The Plastids of Dinoflagellates -- IV. Dinoflagellates in the Plankton -- References -- Chapter 11: The Origin and Evolution of the Diatoms: Their Adaptation to a Planktonic Existence -- I. The Hallmark of the Diatoms: The Silica Frustule -- A. Frustule Shape and Ornamentation and Their Bearings on Diatom Taxonomy -- B. Frustule Construction -- II. Diatom Phylogeny -- A. The Heterokont Ancestry of the Diatoms -- B. Diatom Phylogenies -- C. The Life Cycle and Its Bearings on Phylogeny -- III. The Origin of the Frustule -- A. The Origin of Silica Sequestering and Metabolism -- B. The Evolution of the Frustule in Vegetative Cells -- IV. The Fossil Record. , A. The Early Fossil Record of the Heterokontophytes -- B. The Fossil Record of the Diatoms -- V. The Success of the Diatoms in the Plankton -- A. The Paleo-Environmental Settings and the Fates of the Various Phytoplankton Lineages -- B. Why Did Chromists Win Over Prasinophytes or Red Microalgae? -- C. Why Did Heterokontophytes Win Over Haptophytes and Dinoflagellates? -- D. Why Did Diatoms Win Over Other Heterokontophytes? -- VI. Cryptic Diversity in Planktonic Diatoms and Its Bearing on Evolution -- VII. The Dawning Future of Diatom Research: Genomics -- Acknowledgments -- References -- Chapter 12: Origin and Evolution of Coccolithophores: From Coastal Hunters to Oceanic Farmers -- I. Coccolithophores and the Biosphere -- II. What Is a Coccolithophore? -- A. Coccoliths and Coccolithogenesis -- III. The Haptophytes -- IV. Tools and Biases in the Reconstruction of Coccolithophore Evolution -- V. The Evolution of Haptophytes up to the Invention of Coccoliths: From Coastal Hunters to Oceanic Farmers? -- A. The Origin of the Haptophytes and Their Trophic Status -- B. Paleozoic Haptophytes and the Ancestors of the Coccolithophores -- VI. The Origin of Calcification in Haptophytes: When, How Many Times, and Why? -- A. Genetic Novelties? -- B. Multiple Origins for Coccolithogenesis? -- C. Environmental Forcing on the Origin of Haptophyte Calcification -- D. Why Were Coccoliths Invented? -- VII. Macroevolution Over the Last 220 Million Years -- A. Forces Shaping the Evolution of Coccolithophores and Coccolithogenesis -- B. Broad Patterns of Morphological Diversity -- C. Oligotrophy and Water Chemistry -- D. Changes in Morphostructural Strategies -- VIII. The Future of Coccolithophores -- Acknowledgments -- References -- Chapter 13: The Origin and Early Evolution of Green Plants -- I. Green Plants Defined -- II. Green Plant Body Plans. , A. Green Plant Life Histories -- III. The Core Structure of the Green Plant Phylogenetic Tree -- A. The Archegoniate Line -- B. The Chlorophyte Line -- C. The Prasinophytes -- IV. Difficulties in the Green Plant Phylogenetic Tree -- A. The Identity of the Lineage Ancestral to Green Plants -- B. The Early Diversification of the "Seaweed" Orders -- V. Green Plants in the Modern Marine Environment -- VI. Conclusions -- Acknowledgments -- References -- Chapter 14: Armor: Why, When, and How -- I. Why Armor -- A. History of The Concept "Armor" Applied to Plankton -- B. Why Should Protists and the Pelagial Be Different? -- C. Form and Function in Sessile and Drifting Photoautotrophs -- D. Attacking Organisms/Attacking Tools -- E. Ingestors or Predators -- II. When -- III. How -- A. Material -- B. The Geometry -- C. Lightweight Constructions of Phytoplankton Armor -- D. Spines and Large Size -- E. Other Functional Explanations -- IV. Conclusions -- Acknowledgments -- References -- Chapter 15: Does Phytoplankton Cell Size Matter? The Evolution of Modern Marine Food Webs -- I. Size Matters: From Physiological Rates to Ecological and Evolutionary Patterns -- A. Size Scaling of Physiological Rates -- B. Size-Abundance Relationship -- C. Size-Diversity Relationship -- D. Size Matters: Food Web Structure and Function -- II. Resource Availability, Primary Production, and Size Structure of Planktonic and Benthic Food Webs -- III. Size and the Evolution of Marine Food Webs -- A. Increase in the Maximum Size of Living Organisms Through Time -- B. Organism Size Within Lineages Through Time (Cope's Rule) -- C. Climatically Driven Macroevolutionary Change in Organism Size -- D. The Evolution of the Modern Marine Food Web -- Acknowledgments -- References -- Chapter 16: Resource Competition and the Ecological Success of Phytoplankton. , I. Resource Acquisition and Measures of Competitive Ability.