ALBERT

Note: Contents Part I Introduction Population Genomics: Advancing Understanding of Nature / Gordon Luikart, Marty Kardos, Brian K. Hand, Om P. Rajora, Sally N. Aitken, and Paul A. Hohenlohe Part II Methods Genotyping and Sequencing Technologies in Population Genetics and Genomics / J. A. Holliday, E. M. Hallerman, and D. C. Haak Computational Tools for Population Genomics / Jarkko Salojärvi Population and Evolutionary Genetic Inferences in the Whole-Genome Era: Software Challenges / Alexandros Stamatakis Part III Concepts and Approaches Population Epigenomics: Advancing Understanding of Phenotypic Plasticity, Acclimation, Adaptation and Diseases / Ehren R. V. Moler, Abdulkadir Abakir, Maria Eleftheriou, Jeremy S. Johnson, Konstantin V. Krutovsky, Lara C. Lewis, Alexey Ruzov, Amy V. Whipple, and Om P. Rajora Landscape Genomics: Understanding Relationships Between Environmental Heterogeneity and Genomic Characteristics of Populations / Niko Balkenhol, Rachael Y. Dudaniec, Konstantin V. Krutovsky, Jeremy S. Johnson, David M. Cairns, Gernot Segelbacher, Kimberly A. Selkoe, Sophie von der Heyden, Ian J. Wang, Oliver Selmoni, and Stéphane Joost Paleogenomics: Genome-Scale Analysis of Ancient DNA and Population and Evolutionary Genomic Inferences / Tianying Lan and Charlotte Lindqvist Genome-Wide Association Studies and Heritability Estimation in the Functional Genomics Era / Dunia Pino Del Carpio, Roberto Lozano, Marnin D. Wolfe, and Jean-Luc Jannink Genomic Selection / Elisabeth Jonas, Freddy Fikse, Lars Rönnegård, and Elena Flavia Mouresan Part IV Population, Evolutionary and Ecological Genetics Applications and Inferences Population Genomics Provides Key Insights in Ecology and Evolution / Paul A. Hohenlohe, Brian K. Hand, Kimberly R. Andrews, and Gordon Luikart Inferring Demographic History Using Genomic Data / Jordi Salmona, Rasmus Heller, Martin Lascoux, and Aaron Shafer Advancing Biogeography Through Population Genomics / Jeremy S. Johnson, Konstantin V. Krutovsky, Om P. Rajora, Keith D. Gaddis, and David M. Cairns Adaptation Without Boundaries: Population Genomics in Marine Systems / Marjorie F. Oleksiak Population Genomics of Speciation and Admixture / Nicola J. Nadeau and Takeshi Kawakami Population Genomics of Colonization and Invasion / Shana R. Welles and Katrina M. Dlugosch Population Genomics of Crop Domestication: Current State and Perspectives / Philippe Cubry and Yves Vigouroux Population Genomics of Animal Domestication and Breed Development / Samantha Wilkinson and Pamela Wiener Population Genomics of Domestication and Breed Development in Canines in the Context of Cognitive, Social, Behavioral, and Disease Traits / Kristopher J. L. Irizarry and Elton J. R. Vasconcelos Index

Note: Contents I Plants as Unique Organisms; History and Tools of Plant Anatomy 1 The Nature of Plants 1.1 Plants Have Multiple Pigments with Multiple Functions 1.2 Plants Use Water, and the Properties of Water, in Unique Ways 1.3 Plants Use Anabolic Metabolism to Manufacture Every Molecule Needed for Growth and Produce Virtually No Waste 1.4 Cell Walls Are Nonliving Matrices Outside the Plant Cell Membrane that House and/or Perform a Variety of Functions 1.5 The Plant Life Cycle Alternates Between a Haploid Gametophyte Stage and a Diploid Sporophyte Stage 1.6 Meristematic Activity Continues Throughout the Life of a Plant 1.7 Fruits Disperse Seeds Through Space: Dormancy Disperses Seeds Through Time 1.8 Earth’s History Is Divided into Four Major Time Periods 1.8.1 The Precambrian: 4550 to 542 mya 1.8.2 The Paleozoic Era: 542 to 251 mya 1.8.3 The Mesozoic Era: 251–66 mya 1.8.4 The Cenozoic Era: 66 mya to Present 1.9 Life on Earth Has Experienced Five Mass Extinctions: A Sixth Is in Progress 1.10 Many Plants and Animals Have Coevolved 1.11 The Plant Body Consists of Four Organs 1.11.1 Roots 1.11.2 Stems 1.11.3 Leaves 1.11.4 Flowers and Fruit 1.12 Plant Organs Are Initially Made of Three Tissues 1.13 “Plant” Can Be Broadly Defined 1.14 Bryophytes Lack Vasculature and Produce Spores 1.15 Ferns and Fern Allies Are Seedless Tracheophytes 1.16 Gymnosperms Are Seed-Producing Tracheophytes that Lack Flowers and Fruit 1.17 Monocots and Eudicots Are the Two Largest Groups of Angiosperms 1.18 Understanding Plant Structure Requires a Sense of Scale 1.19 “Primary” and “Secondary” Are Important Concepts in Plant Anatomy 1.19.1 Primary Versus Secondary Growth and Meristems 1.19.2 Primary Versus Secondary Xylem and Phloem 1.19.3 Primary Versus Secondary Cell Walls 1.20 Chapter Review References and Additional Readings 2 Microscopy and Imaging 2.1 Robert Hooke, 1635–1703, Described a Cell as the Basic Unit of Life by Studying the Bark of the Cork Oak Tree, Quercus suber 2.2 Antoni Van Leeuwenhoek, 1632–1723, Was the First Scientist to Observe Microorganisms 2.3 Nehemiah Grew, 1641–1712, Was the Father of Plant Anatomy 2.4 Robert Brown, 1773–1858, Discovered the Nucleus of the Cell by Studying Orchid Petals 2.5 Katherine Esau, 1898–1997, Advanced the Field of Plant Anatomy with Her Influential Textbooks 2.6 Light Microscopy: The Most Useful Tool of the Plant Anatomist 2.7 The Compound Light Microscope Uses Multiple Lenses to Form and Capture Images 2.8 The Resolving Power of a Lens Places Limits on Resolution and Magnification 2.9 The Confocal Microscope Allows for Sharper Detail, Computer Control, and 3-D Imaging with a Modified Compound Microscope 2.10 Electron Microscopy Allows a View into the World of Cellular Ultrastructure 2.11 The Transmission Electron Microscope Reveals Internal Cellular Detail 2.12 The Scanning Electron Microscope Resolves Surface Detail 2.13 Different Microscopies Produce Different Images of the Same Specimen 2.14 Chapter Review References and Additional Readings II Cellular Plant Anatomy 3 Plant Cell Structure and Ultrastructure 3.1 Plant Cells Are Complex Structures 3.2 Plant Cells Synthesize an External Wall and Contain a Variety of Internal Compartments 3.3 Cells and Cell Organelles Are Typically Bound by Lipid Bilayer Membranes 3.4 Vacuoles Play a Role in Water and Ion Balance 3.5 Plastids Are a Diverse Family of Anabolic Organelles 3.5.1 Proplastid 3.5.2 Etioplast 3.5.3 Elaioplast 3.5.4 Amyloplast 3.5.5 Chromoplast 3.5.6 Gerontoplast 3.5.7 Chloroplast 3.5.8 Chloroplast Functions 3.5.9 The Dimorphic Chloroplasts of C 4 Photosynthesis 3.5.10 Guard Cell Chloroplasts 3.5.11 Sun Versus Shade Chloroplasts 3.6 All Plastids Are Developmentally Related 3.7 Mitochondria Synthesize ATP and Small Carbon Skeletons 3.8 Microbodies Are the Site of Specific Biochemical Pathways 3.9 The Endoplasmic Reticulum Synthesizes Proteins and Some Lipids 3.10 The Golgi Apparatus Processes and Packages Polysaccharides and Proteins for Secretion 3.11 The Nucleus Houses the Cell’s Genetic Material and Participates in Ribosome Synthesis 3.12 The Cytoskeleton Organizes the Cell and Helps Traffic Organelles 3.13 Chapter Review References and Additional Readings 4 Mitosis and Meristems 4.1 The Plant Cell Cycle Includes Interphase, Mitosis, and Cytokinesis 4.2 A Pre-prophase Microtubule Band Precedes Mitosis and Defines the Plane of Cell Division 4.3 Mitosis May Be Divided into Distinct, but Continuous, Stages 4.4 Cytokinesis Begins with Initiation of the Cell Plate and Grows by the Deposition of Callose 4.5 Microtubules Play a Critical Role in Mitosis and Cytokinesis 4.6 Apical Meristems Are the Sites of Primary Growth 4.7 The Shoot Apical Meristem Is the Site of Lateral Organ Initiation 4.8 Axillary Buds Arise De Novo in the Developing Leaf Axis 4.9 Tunica-Corpus Organization Describes Shoot Apical Meristem Growth in Many Eudicots 4.10 Gymnosperms Do Not Possess a Tunica-Corpus 4.11 The Root Apical Meristem Provides the Primary Growth of Roots 4.12 Lateral Roots Originate from Inside the Pericycle, Not from the Root Apical Meristem 4.13 Intercalary Meristems Contribute to Stem and Leaf Growth in Monocots 4.14 Many Lower Vascular Plants Have a Single Initial Cell in the Shoot and Root Apical Meristems 4.15 Lateral Meristems Are the Site of Secondary Growth in Eudicots 4.16 Chapter Review References and Additional Readings 5 Cell Walls 5.1 Transparent Plant Cell Walls Contain Cellulose and Are Synthesized to the Exterior of the Protoplast 5.2 Primary Cell Walls Are a Structural Matrix of Cellulose and Several Other Components 5.3 Plasmodesmata Connect Adjacent Cells Via Holes in the Primary Cell Wall 5.4 Secondary Cell Walls Are Rigid, Thick, and Lignified 5.5 Pits Are Holes in the Secondary Cell Wall 5.6 Transfer Cells Have Elaborated Primary Cell Walls for High Rates of Transport 5.7 Chapter Review References and Additional Readings 6 Parenchyma, Collenchyma, and Sclerenchyma 6.1 Parenchyma Cells Are the Most Common Plant Cell Type 6.2 Parenchyma Cells May Exhibit Totipotency 6.3 Collenchyma Cells Are Used for Support and Are the Least Common Cell Type 6.4 Birefringence Is a Common Phenomenon in Collenchyma Walls 6.5 Sclerenchyma Cells Provide Support, Protection, and Long-Distance Water Transport 6.6 Fibers Impart Support and Protection 6.7 Sclereids Are Reduced Sclerenchyma Cells That Occur Singly or in Clumps 6.8 Xylem Vessel Elements Are Water-Conducting Sclerenchyma 6.9 Chapter Review References and Additional Readings III Vascular Tissues 7 Xylem 7.1 Xylem Is a Complex Tissue Containing Multiple Cell Types, Each with a Specific Structure and Function 7.2 The Primary Functions of Xylem Are Water Conduction, Mineral Transport, and Support 7.3 Tracheids Are Imperforate Tracheary Elements and the Sole Water Conductors in Gymnosperms 7.4 Angiosperm Tracheids, Fiber Tracheids, and Libriform Fibers Represent a Continuum of Imperforate Tracheary Element Design and Function 7.5 Vessel Elements Are Perforate Cells and the Main Water Conductors in Angiosperms 7.6 Vessel Element Side Walls Are Patterned for Strength and Water Movement 7.7 Most Vessel Elements End in a Perforation Plate and Are Connected to Another Vessel Element 7.8 Xylem Parenchyma Are Living Cells Involved in Xylem Metabolism and Protection 7.9 Chapter Review References and Additional Readings 8 Phloem 8.1 Phloem Is a Complex Tissue Containing Multiple Cell Types, Each with a Specific Structure and Function 8.2 Phloem’s Main Function Is Photosynthate Translocation 8.3 Sieve Tube Elements Are Living Cells Responsible for Translocation 8.4 Companion Cells Support the Sieve Tube Element and Are Involved in Phloem Loading and Unloading in Angiosperms 8.5 Phloem Parenchyma Cells Are Involved in Radial Translocation, Xylem/Phloem Coordination, and Storage 8.6 Phloem Fibers Protect the Delicate Sieve Tubes 8.7 Secondary Phloem Typically Only Functions for One Growing Season 8.8 Gymnosperm Phloem Is Simpler Than An

Note: Contents Part I Introduction Predictive Environmental Indicators in Metal Mining / Bernd Lottermoser Part II Waste Quality Principles of Sulfide Oxidation and Acid Rock Drainage / Anita Parbhakar-Fox and Bernd Lottermoser Prediction of Sulfidic Waste Characteristics / Anita Parbhakar-Fox and Bernd Lottermoser Micro-analytical Technologies for Mineral Mapping and Trace Element Deportment / Ron F. Berry, Leonid V. Danyushevsky, Karsten Goemann, Anita Parbhakar-Fox and Thomas Rodemann Predicting Waste Properties Using the Geochemistry-Mineralogy- Texture-Geometallurgy Approach / Anita Parbhakar-Fox Chemical Staining Techniques for Drill Core Characterization / Anita Parbhakar-Fox, Nathan Fox, Jake Moltzen and Bernd Lottermoser Prediction of Acid Rock Drainage Using Field-Based Testing Tools / Anita Parbhakar-Fox, John Aalders, Laura Jackson and Bernd Lottermoser Prediction of Acid Rock Drainage from Automated Mineralogy / Anita Parbhakar-Fox, Bernd Lottermoser, Richard Hartner, Ron F. Berry and Taryn L. Noble Predictive Waste Classification Using Field-Based and Environmental Geometallurgy Indicators, Mount Lyell, Tasmania / Anita Parbhakar-Fox and Bernd Lottermoser Predictive Waste Classification Using the Geochemistry-Mineralogy- Texture-Geometallurgy (GMTG) Approach at a Polymetallic Mine / Anita Parbhakar-Fox and Bernd Lottermoser Part III Water Quality pH Testing Methods for Sulfidic Mine Wastes / Taryn L. Noble, Bernd Lottermoser and Anita Parbhakar-Fox Modified Abrasion pH and NAGpH Testing of Minerals / Taryn L. Noble and Bernd Lottermoser Prediction of Leachate Quality for a Gossan Dump, Angostura, Spain / Anita Parbhakar-Fox, Julie Hunt, Bernd Lottermoser, Eleanor M. van Veen and Nathan Fox Prediction of Metal Mobility from Sulfidic Waste Rocks Using Micro-analytical Tools, Baal Gammon, Northern Australia / Nathan Fox, Anita Parbhakar-Fox and Bernd Lottermoser Prediction of Metal Mobility from Sulfidic Waste Rocks Using Micro-Analytical Tools, Spray, Tasmania / Nathan Fox, Anita Parbhakar-Fox and Bernd Lottermoser Part IV Air Quality Mineral Dust Emissions at Metalliferous Mine Sites / Taryn L. Noble, Anita Parbhakar-Fox, Ron F. Berry and Bernd Lottermoser Mineral Dust Properties at the Mt Lyell Cu-Au Mine Site, Australia / Taryn L. Noble, Ron F. Berry and Bernd Lottermoser Assessing Mineral Dust Properties Using Passive Dust Samplers and Scanning Electron Microscopy / Taryn L. Noble, Ron F. Berry, Karsten Goemann and Bernd Lottermoser Prediction of Mineral Dust Properties at Mine Sites / Taryn L. Noble, Ron F. Berry, Karsten Goemann and Bernd Lottermoser Part V Land Quality Bioaccessibility Testing for Metals at Mine Sites / Eleanor M. van Veen and Bernd Lottermoser Prediction of Plant Metal Bioaccessibility in Mineralized and Sulfidic Rocks / Eleanor M. van Veen, Bernd Lottermoser and Taryn L. Noble Predicting Plant Metal Bioaccessibility at the Historic Wheal Maid Tailings Lagoons, Cornwall, UK / Eleanor M. van Veen, Bernd Lottermoser, Anita Parbhakar-Fox and Julie Hunt Index

Note: Contents Part I Introduction to Harmful Algal Blooms and the GEOHAB Programme 1 Introduction to the Global Ecology and Oceanography of Harmful Algal Blooms (GEOHAB) Synthesis / Patricia M. Glibert, Elisa Berdalet, Michele A. Burford, Grant C. Pitcher, and Mingjiang Zhou 2 Harmful Algal Blooms and the Importance of Understanding Their Ecology and Oceanography / Patricia M. Glibert, Elisa Berdalet, Michele A. Burford, Grant C. Pitcher, and Mingjiang Zhou 3 Establishment, Goals, and Legacy of the Global Ecology and Oceanography of Harmful Algal Blooms (GEOHAB) Programme / Raphael M. Kudela, Robin Raine, Grant C. Pitcher, Patrick Gentien, Elisa Berdalet, Henrik Enevoldsen, and Ed Urban Part II Global Changes and Harmful Algal Blooms 4 Changing Land-, Sea-, and Airscapes: Sources of Nutrient Pollution Affecting Habitat Suitability for Harmful Algae / Patricia M. Glibert, Arthur H.W. Beusen, John A. Harrison, Hans H. Dürr, Alexander F. Bouwman, and Goulven G. Laruelle 5 Harmful Algal Blooms in a Changing Ocean / Mark L. Wells and Bengt Karlson Part III Adaptive Strategies and Harmful Algal Blooms 6 Nutrients and Harmful Algal Blooms: Dynamic Kinetics and Flexible Nutrition / Patricia M. Glibert, Cynthia A. Heil, Frances P. Wilkerson, and Richard C. Dugdale 7 Mixotrophy in Harmful Algal Blooms: By Whom, on Whom, When, Why, and What Next / Kevin J. Flynn, Aditee Mitra, Patricia M. Glibert, and JoAnn M. Burkholder 8 The Role of Life Cycle Characteristics in Harmful Algal Bloom Dynamics / Rhodora V. Azanza, Michael L. Brosnahan, Donald M. Anderson, Inga Hense, and Marina Montresor Part IV Harmful Algal Blooms in Specific Habitats and Biomes 9 Key Questions and Recent Research Advances on Harmful Algal Blooms in Stratified Systems / Robin Raine, Elisa Berdalet, Hidekatsu Yamazaki, Ian Jenkinson, and Beatriz Reguera 10 Key Questions and Recent Research Advances on Harmful Algal Blooms in Fjords and Coastal Embayments / Suzanne Roy, Marina Montresor, and Allan Cembella 11 Key Questions and Recent Research Advances on Harmful Algal Blooms in Eastern Boundary Upwelling Systems / Grant C. Pitcher, Francisco G. Figueiras, Raphael M. Kudela, Teresa Moita, Beatriz Reguera, and Manuel Ruiz-Villareal 12 Key Questions and Recent Research Advances on Harmful Algal Blooms in Relation to Nutrients and Eutrophication / Patricia M. Glibert, Adnan Al-Azri, J. Icarus Allen, Alexander F. Bouwman, Arthur H.W. Beusen, Michele A. Burford, Paul J. Harrison, and Mingjiang Zhou 13 Key Questions and Recent Research Advances on Harmful Algal Blooms in Benthic Systems / Elisa Berdalet and Patricia A. Tester Part V Spotlight on Harmful Algal Blooms in Asia 14 Overview of Harmful Algal Blooms in Asia / Ken Furuya, Mitsunori Iwataki, Po Teen Lim, Songhui Lu, Chui-Pin Leaw, Rhodora V. Azanza, Hak-Gyoon Kim, and Yasuwo Fukuyo 15 Harmful Algal Blooms in the Coastal Waters of China / Ren-Cheng Yu, Song-Hui Lü, and Yu-Bo Liang 16 Green Tides of the Yellow Sea: Massive Free-Floating Blooms of Ulva prolifera / Dongyan Liu and Mingjiang Zhou 17 Ecological Drivers of Green Noctiluca Blooms in Two Monsoonal-Driven Ecosystems / Joaquim I. Goes, Helga do R. Gomes, Khalid Al-Hashimi, and Anukul Buranapratheprat Part VI Observing and Predicting Harmful Algal Blooms: Tools and Predictive Approaches 18 Advancements and Continuing Challenges of Emerging Technologies and Tools for Detecting Harmful Algal Blooms, Their Antecedent Conditions and Toxins, and Applications in Predictive Models / Patricia M. Glibert, Grant C. Pitcher, Stewart Bernard, and Ming Li 19 Recent Advances in Modelling of Harmful Algal Blooms / Peter J.S. Franks Part VII Moving Forward: Emerging Issues and a New Global Programme 20 Emerging HAB Research Issues in Freshwater Environments / Michele A. Burford, David P. Hamilton, and Susanna A. Wood 21 Mitigation and Control of Harmful Algal Blooms / Zhiming Yu, Xiuxian Song, Xihua Cao, and Yang Liu 22 GlobalHAB: Fostering International Coordination on Harmful Algal Bloom Research in Aquatic Systems / Elisa Berdalet, Raphael M. Kudela, Neil S. Banas, Eileen Bresnan, Michele A. Burford, Keith Davidson, Christopher J. Gobler, Bengt Karlson, Po Teen Lim, Lincoln Mackenzie, Marina Montresor, Vera L. Trainer, Gires Usup, Kedong Yin, Henrik Enevoldsen, and Ed Urban Index

Note: Contents 1 Introduction 2 Time and Geological Periods 3 Rocks and the Geological Record 4 The Age of the Rocks 5 Plate Tectonics, the Unifying Theory 6 Tectonics Units of Europe 6.1 Ancestral Europe 6.2 Paleo-Europe 6.3 Meso-Europe 6.4 Neo-Europe 7 Overview of the Plate Tectonic History of Europe 8 The Dynamic Earth, Earthquakes in Germany 9 Early Geological Evolution of Germany 9.1 The Pre-variscan Basement 9.2 Occurrences of Proterozoic and Early Paleozoic Units 9.2.1 Harz Mountains 9.2.2 Rheinisches Schiefergebirge 9.2.3 Lusatia 9.2.4 Elbe Zone 9.2.5 Erzgebirge 9.2.6 Schwarzburg Anticlinorium, Vesser Zone 9.2.7 Bohemian Massif 9.2.8 Black Forest 10 Late Paleozoic of Germany 10.1 The Variscan Orogeny 10.1.1 Rhenohercynian Zone 10.1.2 Saxothuringian Zone 10.1.3 Moldanubian Zone 10.2 Development of the Variscan Orogeny Through Time 10.2.1 Devonian 10.2.2 Carboniferous 10.3 The Variscides in Germany 10.3.1 Regional Geology of the Rhenohercynian 10.3.2 Northern Phyllite Zone 10.3.3 Regional Geology of the Saxothuringian 10.3.4 Saxothuringian (excluding the Mid-German Crystalline Zone) 10.3.5 Regional Geology of the Moldanubian 11 Permian and Mesozoic Geology of Germany 11.1 Post-Variscan History 11.2 Permian 11.2.1 Rotliegend 11.2.2 Zechstein 11.3 Permian/Triassic Boundary 11.4 Triassic 11.4.1 Buntsandstein (Bunter Sandstone) 11.4.2 Muschelkalk 11.4.3 Keuper 11.5 Triassic/Jurassic Boundary 11.6 Jurassic 11.6.1 Early Jurassic 11.6.2 Middle Jurassic 11.6.3 Late Jurassic 11.7 Cretaceous 11.7.1 Early Cretaceous 11.7.2 Late Cretaceous 11.8 Cretaceous/Tertiary Boundary 12 The Evolution of the Alps 12.1 Overview of the Tectonic Structure of the Alps 12.1.1 Helvetic 12.1.2 Penninic 12.1.3 Austroalpine and Southern Alpine Units 12.2 Development of the Alpine Region During the Permian 12.3 The Alpine Triassic 12.4 The Alpine Jurassic 12.5 The Alpine Region in the Cretaceous and Early Tertiary 12.6 The Tectonic Evolution of the Alps 13 Tertiary Basins 13.1 Tertiary Brown Coal Deposits 13.2 The Upper Rhine Graben 13.3 The Northern Alpine Foreland Basin—The Molasse 14 Tertiary and Quaternary Volcanism 14.1 Volcanism in the Eifel 14.2 Westerwald, Siebengebirge, Vogelsberg, Rhön, and Heldburger Gangschar 14.3 Small Chimneys in the Odenwald and the Messel Pit 14.4 Kaiserstuhl 14.5 Tuff Chimneys of Bad Urach, Hegau 14.6 Eger Graben Area, Fichtel Mountains, Vogtland, and Lusatia 15 Asteroid Craters 16 Germany During the Glacial Periods 16.1 Glacial and Interglacial Periods 16.2 Deposits and Erosion Forms of the Glacial Periods 16.3 The Baltic Sea—A Relic from the Last Glaciation Period Appendix References Index