Download - BIOLOGICAL SCIENCE FUNDAMENTALS · PDF fileBIOLOGICAL SCIENCE FUNDAMENTALS AND SYSTEMATICS CONTENTS VOLUME I Biological Science Fundamentals (Systematics) 1

CONTENTS

BIOLOGICAL SCIENCE FUNDAMENTALS AND SYSTEMATICS

Biological Science Fundamentals and Systematics Volume 1 eISBN : 978-1-84826-304-8 (eBook) ISBN : 978-1-84826-754-1 (Print Volume) No. of Pages: 493 Biological Science Fundamentals and Systematics Volume 2 eISBN : 978-1-84826-305-5 (eBook) ISBN : 978-1-84826-755-8 (Print Volume) No. of Pages: 322 Biological Science Fundamentals and Systematics Volume 3 eISBN : 978-1-84826-306-2 (eBook) ISBN : 978-1-84826-756-5 (Print Volume) No. of Pages: 369 Biological Science Fundamentals and Systematics Volume 4 eISBN : 978-1-84826-189-1 (eBook) ISBN : 978-1-84826-639-1 (Print Volume)

No. of Pages: 346 For more information of e-book and Print Volume(s) order, please click here Or contact: [email protected]


CONTENTS

VOLUME I Biological Science Fundamentals (Systematics) 1 Giancarlo Contrafatto, School of Life and Environmental Science, University of Natal Durban, Durban, South Africa Alessandro Minelli, Department of Biology, University of Padova, Padova, Italy 1. Introduction 2. Life on Earth 3. The Geological Scenario and the Major Evolutionary Transitions

3.1. Some Fundamentals of Geology 3.2. Geological Changes, Evolutionary Transitions, and Extinctions

3.2.1. Major Evolutionary Transitions 4. The Cell

4.1. The Procaryotic Cell 4.2. Autotrophs and Heterotrophs 4.3. The Eucaryotic Cell 4.4. The Emergence of Eucaryotes and the Kingdoms of Life

5. Routes to Multicellularity 5.1. Aggregative 5.2. Plasmodial 5.3. Clonal 5.4. Soma and Germ Plasm

6. Growth and Development 7. Life-Cycles

7.1. Direct and Indirect Development 7.2. The Life-Cycles of Cnidarians, Rotifers, and Aphids 7.3. Plant Life-Cycles

8. Individual, Colony, Society 9. Populations, Species, and Communities 10. The Continuity of Life

10.1. Descent with Modification 10.2. Mutations 10.3. Gene Assortment: Inheriting Variation 10.4. Selection, Random Change

11. Adaptation 12. Life Forms

12.1. Living In the Sea 12.2. Nutrition 12.3. From the Sea to the Internal Waters 12.4. Water to Land

13. Biodiversity 14. The Science of Taxonomy History and Scope of Biological Sciences 51 Alberto Mario Simonetta, Dipartimento di Biologia Animale e Genetica "L.Pardi", Università di Firenze, Italy 1. Ancient and Medieval Times up to the 16th Century 2. Post-Renaissance Developments 3. Paleontology and Evolution 4. Morphology and Physiology 5. Genetics 6. Behavior

©Encyclopedia of Life Support Systems (EOLSS) i


7. Ecology and Applied Ecology History of Biology 66 Alberto Mario Simonetta, Dipartimento di Biologia Animale e Genetica, “L. Pardi,” University of Firenze, Italy 1. Introduction 2. Antiquity 3. The Medieval and Renaissance Periods 4. The Development of Morphology 5. Palaeontology 6. Taxonomy and Evolution 7. Hystology, Reproduction and embryology 8. Physiology 9. Genetics 10. Ecology and Ethology 11. Pathology Characteristics of Living Beings 84 Pietro Omodeo, Department of Evolutionary Biology and Department of Environmental Sciences, University of Siena. Italy 1. Introduction

1.1. Epistemology of Biology 2. Former Conceptions of Life

2.1. The Birth of Biology 2.2. Metabolism, 'Irritability' and Cellular Organisation 2.3. The Becoming of Individuals and Species 2.4. Inadequacy of Mechanistic Interpretations and the Revival of Vitalism 2.5. The Gestation of the Concept of Biological Information 2.6. Information Flux is an Endowment of Every Living Being 2.7. First Conclusions on Living Beings

3. Current Conceptions About Living Beings 3.1. The Rise of Genetics 3.2. The Mighty Advance of Dynamic Biochemistry 3.3. The Sources of Information Flux and the Self-Control in Living Beings 3.4. Limits and Peculiarities of the Sensory Flux 3.5. Self Regulation of Genetic Information 3.6. Information and Needs 3.7. Death and Life 3.8. Ontogeny and Morphogenesis

4. Evolution 4.1. Is it Conceivable that a Living Being May Not Evolve? 4.2. The Darwinian Assumptions 4.3. The Subjects of Darwin's Evolution

5. Conclusion 5.1. Summary of the Properties of Living Beings 5.2. Final Definition

Levels of Biotic Organization 107 Alberto Mario Simonetta, Dipartimento di Biologia Animale e Genetica, “L. Pardi,” University of Firenze, Italy 1. Introduction 2. The Development of Organization at the Individual Level

©Encyclopedia of Life Support Systems (EOLSS) ii


3. The Development of Organization: Embryology and Cycles 4. The Paleontological Account 5. The Intertaxa Organization and Evolution 6. Symbiosis and Parasitism 7. Conclusion Population, Species and Communities 118 Juergen Tomiuk, Institute of Anthropology and Human Genetics, University of Tübingen, Germany Lutz Bachmann, Zoological Museum, University of Oslo, Norway 1. Introduction 2. Populations and Species

2.1. The Species Concept 2.2. The Population Concept

2.2.1. Population Size 2.2.2. Constant Reproduction of Populations 2.2.3. Variation in Population Size

3. Species Communities 3.1. General Aspects 3.2. Composition of Communities 3.3. Island Biogeography 3.4. Biological Invasions 3.5. Interaction

3.5.1. Interspecific Competition 3.5.2. Mutualism 3.5.3. Host-parasite Relations 3.5.4. Predator-prey Relations

4. Conclusion The Philosophy of Biological Sciences 137 Alberto Mario Simonetta, Dipartimento di Biologia Animale e Genetica“L. Pardi,” University of Firenze, Italy 1. Introduction 2. Basic Issues in the Philosophy of Biology: Is Biology an Experimental or a Historical Discipline? 3. Methodological Debates 4. Realism versus Nominalism 5. The Population Concept: Problems and Inferences 6. Bioethics: Some Sample Problems The Origin and Evolution of Early Life 149 Martino Rizzotti, Department of Biology, University of Padova, Italy 1. Introduction 2. The Need for Organic Molecules 3. Asymmetry in Organic Molecules 4. The Need for Suitable Energy 5. The Rise and Fall of Organic Chemistry of Galaxies 6. Organic Chemistry on Orbiting Bodies 7. The Need for Liquid Water 8. The Evolution of Hydrospheres 9. Self-organization and Self-replication 10. Encapsulation and Translation 11. The First Ecosystems 12. The Probability and Stability of Biospheres

©Encyclopedia of Life Support Systems (EOLSS) iii


Formation of the Building Blocks of Primitive Life 181 Andre Brack, Centre de Biophysique Moléculaire, CNRS, Rue Charles Sadron, F-45071 Orléans cedex James P. Ferris, Department of Chemistry, Rensselaer Polytechnic Institute, Troy NY 12180-3590, USA 1. Introduction 2. The role of water 3. Possible environments for the production of prebiotic organic molecules

3.1. Production of CHONS in the atmosphere 3.2. Submarine hydrothermal systems 3.3. Delivery of extraterrestrial CHONS

4. Availability of the primitive building blocks 5. Production of homochiral building blocks 6. Conclusion From The Building Blocks to Life 194 Andre Brack, Centre de Biophysique Moléculaire, CNRS, Rue Charles Sadron, F-45071 Orléans cedex , FranceJames P. Ferris, Department of Chemistry, Rensselaer Polytechnic Institute, Troy NY 12180-3590, USA 1. Introduction 2. A Primitive Cellular Life

2.1. Prebiotic RNA 2.1.1. The Montmorillonite Clay-catalyzed Synthesis of RNA 2.1.2. Metal Ion Catalysis of RNA Synthesis 2.1.3. Template-directed RNA Synthesis

2.2. Prebiotic Polypeptides 2.2.1. Polypeptide Formation on Clay Minerals 2.2.2. Peptide Elongation on Minerals 2.2.3. Polypeptide Formation via N-Carboxyanhydrides 2.2.4. Proteinoids 2.2.5. Polypeptide Formation Using Simulated Hydrothermal Conditions 2.2.6. Thermal Conversion of Amino Acid Amides to Polypeptides 2.2.7. Prebiotic Polypeptide Structure and Stability 2.2.8. Prebiotic Polypeptide Catalysis

3. Primitive Life Based on RNA: The RNA World 3.1. RNA Analogs and Surrogates

3.1.1. Nucleotides with a Pyrophosphate Backbone 3.1.2. Pyranosyl-RNA, a Hexose Nucleic Acid, and Threose-RNA, a Tetrose Nucleic Acid 3.1.3. Peptide Nucleic Acid

4. Autocatalysis Preceding RNA 5. Conclusion The Earliest Anaerobic and Aerobic Life 212 Martino Rizzotti, Department of Biology, University of Padova, Italy 1. The First Cells 2. From Heterotrophy to Autotrophy 3. Ancient Oxygen-producing Photosynthesis 4. The First Aerobic Microorganisms 5. Origin of the Organelles of Bacterial Cells 6. Origin of the Nucleus 7. Origin and Evolution of the Mitochondrion 8. Origin and Evolution of Plastids 9. Origin of the Cilium 10. The Rise of Highly Differentiated Organisms

©Encyclopedia of Life Support Systems (EOLSS) iv


Evolution 231 Saverio Forestiero, Department of Biology, University of Rome “Tor Vergata,” Italy 1. Introduction: The Nature of Evolution

1.1. Differentiating Replicators and Interactors 1.2. The Historical Nature of Evolution 1.3. Evolution Does Not Necessarily Mean Progress

2. Major Transitions in Evolution 2.1. Natural Selection and Levels of Organization

3. Different Approaches to the Study of Evolution 4. Microevolution

4.1. The Causes of Evolution 4.2. Natural Selection

5. Adaptive Evolution 5.1. Adaptation 5.2. Adaptations and Adaptive Responses 5.3. Adaptation and Exaptation 5.4. Coevolution

6. Neutral Evolution 7. Species and Speciation 8. Macroevolution 9. Phylogeny 10. Evolution, Complexity, and the Information Content of Living Beings History of Evolutionary Theory 254 Barbara Continenza, Dipartimento di Ricerche Filosofiche, Facoltà di Lettere e Filosofia, Università di Roma "Tor Vergata", Roma, Italia 1. Introduction 2. Scientific Historiography and the Analysis of the Theoretical Concepts 3. The Definition of "Species" 4. The Problem of Classification 5. Linneus, the "System" and the "Methods" 6. Buffon and the nuance of Nature 7. The Historical Dimension and the Re-orientation of Natural History 8. Lamarck and Transformism 9. Paleontology and Geology The Darwinian View of Life 270 Barbara Continenza, Dipartimento di Ricerche Filosofiche, Facoltà di Lettere e Filosofia, Università di Roma "Tor Vergata", Roma, Italia 1. Introduction 2. Evolutionism and Darwinism 3. What are the Laws of Life? 4. The Structuring of a New Theoretical Picture 5. The Origin of Species and its Critics 6. Toward a Natural History of Mind Evolution and the Species Concept 289 Peter John Taylor, Durban Natural Science Museum, South Africa 1. Introduction 2. Historical Aspects

2.1. Pre-Darwin

©Encyclopedia of Life Support Systems (EOLSS) v


2.2. Darwin's View 2.3. Post-Darwin (Modern Synthesis)

3. Current Paradigms and Challenges 3.1. Philosophical Perspectives: The Individual Species Concept 3.2. Current Paradigm: The Biological Species Concept

3.2.1. Isolating Barriers 3.2.2. Limitations of the Biological Species Concept

3.2.2.1. Non-universality 3.2.2.2. Inapplicability to Multi-dimensional Situations 3.2.2.3. Incomplete Speciation

3.3. Challenges, Extensions and Alternatives to the Biological Species Concept 3.3.1. Evolutionary Species Concepts 3.3.2. Phenetic Species Concept 3.3.3. Ecological Species Concept 3.3.4. Recognition Species Concept 3.3.5. Cohesion Species Concept 3.3.6. Phylogenetic Species Concepts

4. A Case Study 5. The Future: Towards a Holistic Approach?

5.1. Which Criteria? 5.2. Monism versus Pluralism

6. Conclusions Speciation and Intra-specific Taxa 311 Peter John Taylor, Durban Natural Science Museum, South Africa Giancarlo Contrafatto, School of Biological and Conservation Sciences, University of KwaZulu-Natal Durban,South Africa 1. Introduction 2. Time frame for speciation 3. Ecological considerations 4. Genetic models of speciation

4.1. Speciation by natural selection 4.2. Wright’s shifting balance theory 4.3. Founder-effect models 4.4. How many "speciation genes"? 4.5. Genetic properties of species

5. Modes of speciation 5.1. Allopatric speciation

5.1.1. Intra-specific taxa 5.1.2. Clinal variation 5.1.3. Vicariance model 5.1.4. Peripatric model 5.1.5. Reinforcement

5.2. Parapatric speciation 5.3. Stasipatric speciation: the role of chromosomes

5.3.1. Chromosome rearrangements and meiotic segregation 5.3.2. Post-zygotic isolation: two case studies

5.4. Sympatric speciation 6. Speciation in plants

6.1. Speciation by polyploidy 6.2. Speciation by hybridization

7. Conclusions

©Encyclopedia of Life Support Systems (EOLSS) vi


Natural Selection and the Effects of Ecological Interaction on Populations 338 Piero Cervella, Dipartimento di Biologia Animale e dell'Uomo, Università di Torino, Torino, Italy Massimiliano DelPero, Dipartimento di Biologia Animale e dell'Uomo, Università di Torino, Torino, Italy Giampaolo Zampicinini, Dipartimento di Biologia Animale e dell'Uomo, Università di Torino, Torino, Italy 1. Introduction

1.1. Adaptation and Evolution 2. Natural Selection

2.1. The Different Aspects of Natural Selection 2.1.1. Stabilizing Selection 2.1.2. Directional Selection 2.1.3. Disruptive Selection 2.1.4. Frequency-dependent Selection 2.1.5. Density-dependent Selection 2.1.6. Sexual Selection 2.1.7. Kin Selection 2.1.8. Indirect Selection

3. Non-selective Aspects of Population Biology 3.1. Genetic Drift

3.1.1. Founder Effect 3.1.2. Bottleneck Effect 3.1.3. Gene Flow

4. Deterministic and Stochastic Concerns in Population Biology 4.1. Interactions between Genotypes and Environment 4.2. Metapopulations

4.2.1. Local Extinction 4.2.2. Recolonisation

5. Conclusions Cell and Tissue Structure in Animals and Plants 359 Michael K. Richardson, Institute of Evolutionary and Ecological Sciences, Leiden University, Kaiserstraat 63,Postbus 9516, 2300 RA Leiden, The Netherlands L. Goosen-de Roo, Institute of Molecular Plant Sciences, Clusius Laboratory, Leiden University, Wassenaarseweg 64, 2333 AL, Leiden, The Netherlands 1. Introduction

1.1. Scope of the Article 2. Cell and Tissue Development

2.1. Development of Animal Cells and Tissues 2.2. Developmental Processes in Higher Plants

2.2.1. Tissue Origins in Higher Flowering Plants 2.2.2. Cell Division, Growth and Differentiation 2.2.3. Initials in Meristems

2.3. The Size of Cells 2.4. Methods in Histology and Cytology

3. Cell Ultrastructure 3.1. Cell Membrane 3.2. Plant Cell Wall

3.2.1. Cellulose and Other Cell Wall Substances 3.2.2. Cell Wall Formation 3.2.3. Middle Lamella, Primary Cell Wall and Secondary Cell Wall 3.2.4. Communication between Cells

3.3. Cytoplasm 3.4. The Nucleus of Eukaryotic Cells

3.4.1. Nuclear Membrane 3.4.2. Genetic Material

©Encyclopedia of Life Support Systems (EOLSS) vii


3.5. Other Structures in the Cytoplasm 3.5.1. Mitochondria 3.5.2. Plastids 3.5.3. Endomembrane System (Lysosomes, Golgi Complex, ER, Vacuoles) 3.5.4. Ribosomes 3.5.5. Cytoskeleton (Microtubules, Actin Filaments) 3.5.6. Projections from the Animal Cell Surface (Flagella, Cilia, Microvilli)

4. Selected Examples of Differentiated Cell Types 4.1. Pigment Cells 4.2. Muscle Cells 4.3. Plant Root Hairs 4.4. Vessel Elements in Plants

5. General Organisation of Tissues 5.1. Tissue Systems in Plants 5.2. Animal Extracellular Matrix (ECM)

6. Some Examples of Specialised Tissue Types 6.1. Plant Epidermis 6.2. Xylem 6.3. Animal Cartilage and Bone 6.4. Epithelia 6.5. Nervous Tissue

Biological Homeostasis 387 Pietro Omodeo, Department of Evolutionary Biology and Department of Environmental Sciences, University of Siena. Italy 1. Introduction 2. Stabilization 3. Homeostasis

3.1. Logic and Structure of the Homeostat 3.2. The Components of the Homeostat: the Measuring Unit 3.3. The Components of the Homeostat: The Effector 3.4. The Control of Controllers 3.5. The Control of Stores

4. Homeorrhesis, the Automatic Control of Behavior 4.1. Trajectory Control 4.2. Smooth Control 4.3. Coordinate Control in Homeostasis and Homeorrhesis

5. Control of Development and Reproduction 5.1. Exogenous and Endogenous Clock and the Calendar 5.2. Embryonic Regulation 5.3. Control of the Flux of Genetic Information

6. Conclusion Patterns and Rates of Species Evolution 401 Michael James Benton, Department of Earth Sciences, University of Bristol, Bristol, BS8 1RJ,UK 1. Introduction 2. Biological and morphological species concepts 3. Evidence from ecology and palaeobiology

3.1. The cichlid fishes of the African rift valleys 3.2. Sticklebacks and speciation by natural selection 3.3. Ice ages and species migrations 3.4. The punctuated equilibrium revolution 3.5. Stasis 3.6. Speciation and ecophenotypic change: the rift valley snails

©Encyclopedia of Life Support Systems (EOLSS) viii


4. Fossil evidence of speciation. 4.1. Microfossils 4.2. Shallow marine invertebrates 4.3. Terrestrial vertebrates

5. Species diversification through time 5.1. Biodiversity today 5.2. Biodiversity through time - patterns of increase 5.3. Biodiversity through time - land and sea compared 5.4. Explanations for patterns of diversification

6. Evolutionary patterns and processes Index 427 About EOLSS 433

VOLUME II

Classification and Diversity of Life Forms 1 Alessandro Minelli, Department of Biology, University of Padova, Padova, Italy Giancarlo Contrafatto, School of Life and Environmental Science, University of Natal, Durban, South Africa 1. Natural vs. artificial classifications 2. Classification vs. system 3. Nomenclature

3.1. The international codes of nomenclature 3.2. Nomenclatural stability: problems and solutions 3.3. Ethnotaxonomy

4. The diversity of life 4.1. Nature and origin of biological diversity 4.2. Species known and estimated 4.3. Big genera

5. Taxonomy and nomenclature of domesticated animals and cultivated plants 6. The tools of classification Historical Review of Systematic Biology and Nomenclature 27 Alessandro Minelli, Department of Biology, Via U. Bassi 58B, I-35131, Padova,Italy 1. The Origins 2. From Classical Antiquity to the Renaissance Encyclopaedias 3. From the First Monographers to Linnaeus 4. Concepts and Definitions: Species, Homology, Analogy 5. The Impact of Evolutionary Theory 6. The Last Few Decades 7. Nomenclature 8. Natural History Collections Metabolic Diversity in Prokaryotes and Eukaryotes 40 Aharon Oren, Department of Plant and Environmental Sciences, The Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel. 1. Introduction 2. The Thermodynamic and Mechanistic Basis of Cellular Metabolism

©Encyclopedia of Life Support Systems (EOLSS) ix


2.1. Dissimilatory Metabolism 2.1.1. The Phototrophic Way of Life 2.1.2. The Chemheterotrophic Way of Life 2.1.3. The Chemoautotrophic Way of Life

2.2. Assimilatory Metabolism 2.2.1. Autotrophy 2.2.2. Heterotrophy

3. Metabolic Diversity Within the Three Domains of Life: Archaea, Bacteria and Eucarya 4. Phototrophy - The Use of Light as Energy Source

4.1. Oxygenic Photosynthesis of Plants and Cyanobacteria 4.2. Anoxygenic Photosynthesis in Bacteria 4.3. Retinal Pigment-Based Phototrophy

5. Heterotrophy 5.1. Aerobic Respiration 5.2. Anaerobic Respiration 5.3. Fermentation

6. Chemoautotrophy 6.1. Nitrification 6.2. Oxidation of Reduced Sulfur Compounds 6.3. Oxidation of Reduced Iron and Manganese 6.4. Aerobic Oxidation of Hydrogen 6.5. Anaerobic Oxidation of Hydrogen: Methanogens and Homoacetogens

7. Metabolic Diversity and the Cycles of Carbon, Nitrogen, Sulfur and Other Elements Diversity of Form, Function and Adaptation in Microorganisms 77 Aharon Oren, Department of Plant and Environmental Sciences, The Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel. 1. Introduction 2. Cell Size and Cell Shape in the Procaryotes

2.1. Small is Powerful 2.2. Appendages and Other Strategies to Increase Cell Surface 2.3. The Largest Procaryotes

3. The Outer Layers of the Procaryotic Cell 3.1. The Cell Wall and the Cytoplasmic Membrane 3.2. Fimbriae and Pili 3.3. Exopolysaccharides

4. Special Intracellular Structures 4.1. Intracellular Membrane Structures 4.2. Storage Materials

5. Motility Organelles 5.1. Flagella 5.2. Magnetosomes 5.3. Gas Vesicles

6. Survival and Dispersal Forms 7. Multicellular Differentiation and Special Life Cycles in Procaryotes

7.1. Heterocysts and Other Specialized Cells of Cyanobacteria 7.2. Bdellovibrio, the Intracellular Predator of Bacteria 7.3. The Life Cycle of Caulobacter and Hyphomicrobium 7.4. The Life Cycle of Myxobacteria

8. Diversity of Form, Function, and Adaptation - The Lower Eucaryotes and the Procaryotes Compared Diversity of Form, Function and Adaptation in Fungi 97 Silvano Onofri, Department of Environmental Sciences, University of Tuscia in Viterbo, Italy Alessandra Belisario, Plant Pathology Research Institute, Rome, Italy

©Encyclopedia of Life Support Systems (EOLSS) x


1. Introduction 2. Diversity of Form

2.1. Hyphae and Mycelium 2.2. Fungal Cells 2.3. Colonization of Substrates

3. Reproduction 3.1. Sexual Reproduction 3.2. Asexual Reproduction 3.3. Spore Dispersal

4. Diversity of Function 4.1. Nutrition 4.2. Saprobic Fungi 4.3. Parasitic Fungi 4.4. Symbiotic Fungi

4.4.1. Mycorrhizas 4.4.2. Lichens 4.4.3. Endophytes

5. Adaptation 5.1. Adaptation to Terrestrial Habitats 5.2. Temperature

6. Economic Relevance of Fungi 6.1. Plant diseases 6.2. Food Spoilage 6.3. Mycotoxins 6.4. Drugs 6.5. Food Production 6.6. Edible Mushrooms

Evolutionary and Molecular Taxonomy 116 Eric H. Harley, Department of Chemical Pathology, University of Cape Town, South Africa. 1. Introduction 2. Basic Concepts

2.1. Metabolism, Proteins, and Nucleic Acids 2.2. Nuclear and Organellar Genomes 2.3. Inheritance of Genomes 2.4. Mutation and Molecular Evolution

3. Molecular Methods used in Systematics 3.1. Allozymes 3.2. DNA/DNA Hybridization 3.3. Restriction Fragment Length Polymorphisms (RFLP) 3.4. Restriction Site Mapping 3.5. DNA Sequencing

4. Phylogenetic Analysis 4.1. Distance Methods 4.2. Parsimony Methods 4.3. Maximum Likelihood Methods 4.4. Relative Merits of the Three Approaches 4.5. Reliability of Inferred Trees 4.6. Questions and Precautions

5. Future Developments Systematics of the Microbial Kingdom(s) and Fungi 139 John C. David, CABI Bioscience, Egham, England, Surrey, UK Gerry S. Saddler, Scottish Agricultural Science Agency, Edinburgh, Scotland, UK

©Encyclopedia of Life Support Systems (EOLSS) xi


1. Introduction 2. The Emergence of the Microbial World

2.1. Timetable of Events 2.2. Universal Ancestor and Early Eucaryotes

3. Microbial Systematics 3.1. Higher Order Classification 3.2. Different Approaches to the Study of Microbial Diversity

3.2.1. The Study of Procaryotes 3.2.2. The Study of Eucaryotes

4. Microbial Species Concepts 4.1. Eucaryotic Species 4.2. Procaryotic Species

5. Rules of Nomenclature 6. The Microbial Tree of Life

6.1. The Procaryotes 6.2. The Eucaryotes

7. Conclusions Systematics of Archaea and Bacteria 162 Aharon Oren, Department of Plant and Environmental Sciences, The Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel. 1. Introduction 2. Systematics, Taxonomy and Nomenclature of Procaryotes - A Few Definitions 3. Procaryote Systematics - A Historical Overview 4. The Formal Framework of Description and Nomenclature of Procaryotes 5. Approaches to the Classification of Procaryotes

5.1. Experimental Tools of Procaryote Taxonomy 5.2. The Species Concept in the Procaryote World 5.3. The Number of Described Procaryote Species

6. Bacteria and Archaea, the two Domains of the Procaryotic World 6.1. The Recognition of the Archaea as a Separate Domain 6.2. The Differences between Archaea and Bacteria 6.3. Systematics of Archaea and the Properties of the Main Groups of Archaea 6.4. Systematics of Bacteria and the Properties of the Main Groups of Bacteria

7. How Many Procaryote Species are there in Nature? 8. Conclusions Protoctista 187 Carolina Mudespacher Ziehl, Departamento de Biología. Universidad Autónoma Metropolitana-Iztapalapa. México. Irma E. Lira-Galera, Departamento de Biología. Universidad Autónoma Metropolitana-Iztapalapa. México. 1. Introduction 2. Classification

2.1. Archamoeba 2.2. Neomonada 2.3. Rhizopoda 2.4. Mycetozoa 2.5. Foraminifera 2.6. Heliozoa 2.7. Radiozoa 2.8. Percolozoa 2.9. Euglenozoa 2.10. Dinozoa

©Encyclopedia of Life Support Systems (EOLSS) xii


2.11. Metamonada 2.12. Parabasala 2.13. Apicomplexa

3. Ciliophora Systematics of Fungi 217 Silvano Onofri, Department of Environmental Sciences, University of Tuscia in Viterbo, Italy Alessandra Belisario, Institute for Experimental Plant Pathology, Rome, Italy 1. Introduction 2. Kingdom Fungi

2.1. Phylum Chytridiomycota 2.2. Phylum Zygomycota

2.2.1. Class Zygomycetes 2.2.2. Class Trichomycetes

2.3. Phylum Ascomycota 2.3.1. Class Archiascomycetes 2.3.2. Class Saccharomycetes 2.3.3. Class Ascomycetes

2.3.3.1. Group Plectomycetes 2.3.3.2. Group Pyrenomycetes 2.3.3.3. Group Discomycetes 2.3.3.4. Group Loculoascomycetes 2.3.3.5. Lichenized Ascomycetes

2.4. Conidial or Mitosporic Fungi 2.5. Phylum Basidiomycota

2.5.1. Class Urediniomycetes 2.5.2. Class Ustilaginomycetes 2.5.3. Class Hymenomycetes

Lichens 237 Mauro Tretiach, Dept. of Biology, University of Trieste, Italy Pier Luigi Nimis,Dept. of Biology, University of Trieste, Italy 1. Introduction 2. Biology 3. Lichen compounds 4. Evolution 5. Classification

5.1. Historical background 5.2. Diagnostic characters 5.3. Orders of Ascomycetes with lichen-forming fungi 5.4. Orders of Basidiomycetes with lichen-forming fungi 5.5. "Imperfect lichenized fungi"

6. Geographical distribution 7. Ecological role 8. Declining lichens

8.1. Pollution 8.2. Loss of habitat

9. Future investigations Index 255 About EOLSS 261

©Encyclopedia of Life Support Systems (EOLSS) xiii


VOLUME III

Systematic Botany 1 Ashley Nicholas, School of Life & Environmental Science, University of Durban~Westville, Durban, South Africa 1. Introduction 2. Aims and Philosophy of Plant Systematics

2.1. The Role of Plant Classifications in Life Support Systems 2.2. Philosophical Basis of Plant Classification

3. History and Development of Plant Systematics 3.1. The First Empirical Plant Classificatory Systems 3.2. The Herbals 3.3. The First Plant Taxonomists 3.4. Natural Plant Classifications 3.5. Phylogenetic Classifications 3.6. Modern Phylogenetic Plant Classifications 3.7. Plant Molecular Systematics

4. Plant Diversity 4.1. Is There a Plant Kingdom? 4.2. Evolution of Photosynthesis 4.3. Endosymbiotic Origin of Plastids 4.4. The Plant Kingdom 4.5. The First Land Plants 4.6. Plants with Vascular Tissue 4.7. The First Terrestrial Ecosystems 4.8. The Lycopod-line 4.9. The Sphenofern-line 4.10. The First Forests 4.11. The Evolution of Seeds 4.12. The First Seed Plants 4.13. The Pine-line 4.14. Ancient Mesozoic Floras 4.15. The Anthophyte Clade 4.16. Evolution of the Flower and Flowering Plants

4.16.1. Why Did Angiosperms Evolve? 4.16.2. What Did the First Angiosperms Look Like? 4.16.3. When Did the Angiosperms Evolve? 4.16.4. Where Did the Angiosperms Evolve? 4.16.5. From What Gymnosperm Ancestor Did the Angiosperms Evolve?

4.17. Flowering Plants 5. Conclusion Algae 49 Francisco F. Pedroche, Departamento de Hidrobiología, Universidad Autónoma Metropolitana –Iztapalapa,Mexico and University Herbaria, University of California, Berkeley, USA 1. Introduction 2. Cyanobacteria 3. Glaucophyta 4. Rhodophyta 5. Chlorophyta 6. Heterokontophyta 7. Dinophyta 8. Haptophyta 9. Cryptophyta

©Encyclopedia of Life Support Systems (EOLSS) xiv


10. Euglenophyta 11. Final Remarks Bryophyte Systematics 74 Claudio Delgadillo-Moya, Universidad Nacional Autónoma de México, Mexico 1. Introduction 2. Morphology

2.1. Anthocerotae (Hornworts) 2.2. Hepaticae (Liverworts) 2.3. Musci (Mosses)

3. Distinguishing Features Among Groups 4. Sources of Systematic Data

4.1. Ontogeny 4.2. Cytology 4.3. Chemistry 4.4. Paleobotany

5. Phylogenetic Relationships 6. Classification 7. Future Research Systematic Zoology: Invertebrates 93 Ronald Adam Jenner, Zoological Museum, University of Amsterdam, The Netherlands. Frederick Robert Schram, Zoological Museum, University of Amsterdam, The Netherlands. 1. Introduction to the systematic zoology of the Metazoa (Animalia) 2. Animal phylogeny: data sources and interpretation

2.1. Morphology 2.2. Molecules 2.3. Fossils

3. Systematic zoology of the Metazoa 3.1. Porifera, Placozoa, Cnidaria, Ctenophora 3.2. Platyhelminthes, Nemertea 3.3. Mollusca, Sipunculida, Entoprocta, Cycliophora 3.4. Annelida, Pogonophora, Myzostomida, Echiura 3.5. Onychophora, Tardigrada, Arthropoda 3.6. Rotifera, Acanthocephala, Gnathostomulida, Micrognathozoa 3.7. Priapulida, Kinorhyncha, Loricifera 3.8. Nematoda, Nematomorpha, Gastrotricha, Chaetognatha 3.9. Ectoprocta, Phoronida, Brachiopoda 3.10. Urochordata, Cephalochordata 3.11. Enteropneusta, Pterobranchia, Echinodermata 3.12. Some extant "problematica"

4. Alternative hypotheses of metazoan relationships 4.1. Morphology 4.2. Molecules

5. Reconciliation and pathways to future progress Porifera, Cnidaria, and Ctenophora 129 Giorgio Bavestrello, Istituto di Scienze del Mare University of Ancona, Italy Michele Sara, Dipartimeto per lo studio del Territorio e delle sue Risorse, University of Genoa, Italy 1. Introduction 2. Porifera

2.1. General Remarks

©Encyclopedia of Life Support Systems (EOLSS) xv


2.2. Importance 2.3. Form and Function

2.3.1. Size and Shape 2.3.2. Color, Consistency, and Surface 2.3.3. Water Current System 2.3.4. Cell Types 2.3.5. Skeleton

2.4. Life Cycle 2.4.1. Sexual Reproduction 2.4.2. Embryonic Development and Larvae 2.4.3. Asexual Reproduction 2.4.4. Regeneration, Individuality, and Life Span

2.5. Ecology 2.6. Evolution and Paleontology 2.7. Phylogeny and Systematics

3. Cnidaria 3.1. General Remarks 3.2. Importance 3.3. Form and Function

3.3.1. Body Structure 3.3.2. Size 3.3.3. Color 3.3.4. Cell Types

3.4. Life Cycle 3.4.1. Sexual Reproduction and Development 3.4.2. Asexual Reproduction 3.4.3. Coloniality and Polymorphism 3.4.4. Metagenetic Cycles

3.5. Ecology 3.6. Phylogeny and Systematics

4. Ctenophora Platyhelminthes, Nemertea, and "Aschelminthes" 154 Andreas Schmidt-Rhaesa, University of Bielefeld, Germany 1. Introduction 2. General Morphology 3. Platyhelminthes, the Flatworms 4. Nemertea (Nemertini), the Ribbon Worms 5. “Aschelminthes”

5.1. Gnathifera 5.1.1. Gnathostomulida 5.1.2. Micrognathozoa (Limnognathia maerski) 5.1.3. Rotifera 5.1.4. Acanthocephala 5.1.5. Cycliophora (Symbion pandora)

5.2. Nemathelminthes 5.2.1. Gastrotricha 5.2.2. Nematoda, the Roundworms 5.2.3. Nematomorpha, the Horsehair Worms 5.2.4. Priapulida 5.2.5. Kinorhyncha 5.2.6. Loricifera

Annelida 177 Greg W. Rouse, University of Sydney, Australia

©Encyclopedia of Life Support Systems (EOLSS) xvi


1. Introduction 2. Basic Annelid Organization

2.1. Coelom 2.2. Metamerism 2.3. Chaetae

3. Annelid Anatomy 3.1. Body wall 3.2. Parapodia 3.3. Nervous System 3.4. Sense Organs 3.5. Circulation and Respiratory Structures 3.6. Segmental Organs

4. Annelid Diversity 4.1. Polychaeta 4.2. Clitellata 4.3. Unusual or Controversial Groups Placed in Annelida

4.3.1. Echiura 4.3.2. Myzostomida 4.3.3. Siboglinidae (Pogonophora and Vestimentifera)

5. Annelid Behavior and Physiology 5.1. Locomotion 5.2. Feeding 5.3. Osmoregulation 5.4. Symbiosis

6. Reproduction and Development 6.1. Asexual Reproduction in Polychaeta 6.2. Sexual Reproduction in Polychaeta 6.3. Sexual Reproduction in Clitellata

7. Annelid Phylogeny 7.1. Fossil Annelida

Arthropods Other than Insects 203 Frederick Robert Schram, Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, Netherland Sven Lange, Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, Netherland Alessandro Minelli, Department of Biology, University of Padova, Italy 1. Introduction 2. Myriapoda

2.1. Chilopoda 2.2. Diplopoda 2.3. Symphyla 2.4. Pauropoda 2.5. General aspects of myriapod biology

3. Crustacea 3.1. Remipedia 3.2. Cephalocarida 3.3. Branchiopoda 3.4. Maxillopoda 3.5. Malacostraca

3.5.1. Phyllocarida 3.5.2. Hoplocarida 3.5.3. Eumalacostraca

3.6. General aspects of crustacean biology 4. Cheliceriformes [= Cheliceromorpha]

4.1. Pycnogonida 4.2. Chelicerata

©Encyclopedia of Life Support Systems (EOLSS) xvii


4.2.1. Merostomata 4.2.2. Scorpiones 4.2.3. Pseudoscorpiones 4.2.4. Solifugae 4.2.5. Opiliones 4.2.6. Palpigradi 4.2.7. Amblypygi 4.2.8. Uropygi 4.2.9. Schizomida 4.2.10. Araneae 4.2.11. Ricinulei 4.2.12. Acari

4.3. General aspects of cheliceriform biology Insects and Other Hexapodous Arthropods 232 Denis J. Brothers, School of Botany and Zoology, University of Natal, South Africa 1. Introduction 2. What are Insects? 3. Why are Insects so Successful? 4. Insect Life Cycles 5. Ecological Importance of Insects 6. Insect Diversity

6.1. Superclass: Hexapoda - Hexapods, Insects sensu lato (i.e., in the broad sense) 6.1.1. Class: Entognatha - Entognathans (may be a paraphyletic group) 6.1.2. Class: Insecta sensu stricto (= Ectognatha) - True Insects

Mollusca 271 Winston F. Ponder, Centre for Evolutionary Research, Australian Museum, Sydney, NSW 2010, Australia. 1. Introduction 2. Relationships and Higher Classification 3. General Morphology of the Mollusca 4. Gastropoda

4.1. Major Groups, Diversity and Adaptive Radiation 5. Bivalvia (=Pelecypoda)

5.1. Major Groups, Diversity and Adaptive Radiation 6. Cephalopoda

6.1. Major Groups, Diversity and Adaptive Radiation 7. Other Classes - Living and Extinct

7.1. Polyplacophora 7.2. "Aplacophora" (Caudofoveata and Solenogastres) 7.3. Monoplacophora (Helcionelloidea and Tergomya) 7.4. Scaphopoda 7.5. Extinct Groups that have been Suggested as Additional Classes

8. Current Knowledge 9. Geographic Diversity 10. Ecological Diversity 11. Conservation

11.1. Marine 11.2. Freshwater 11.3. Terrestrial

12. Economic Importance 12.1. Bivalvia 12.2. Cephalopoda 12.3. Gastropoda

©Encyclopedia of Life Support Systems (EOLSS) xviii


Index 303 About EOLSS 311

VOLUME IV

Echinodermata 1 Rich Mooi, California Academy of Sciences, San Francisco, California, USA 1. Introduction 2. General Morphology of the Echinodermata

2.1. Recognizing an Echinoderm 2.2. Organization of the Echinoderm Body

2.2.1. Morphological Pattern 2.2.2. Embryological Pattern

3. Classification and Relationships of the Echinodermata 4. Edrioasteroid-like Echinoderms

4.1. Morphology of Edrioasteroid-like Echinoderms 4.2. Paleoecology of Edrioasteroid-like Echinoderms

5. Blastozoans 5.1. Morphology of Blastozoans 5.2. Paleoecology of Blastozoans

6. Crinoidea 6.1. Morphology of Crinoids 6.2. Reproduction and Development of Crinoids 6.3. Ecology and Behavior of Crinoids 6.4. Economic Importance of Crinoids

7. Asteroidea 7.1. Morphology of Asteroids 7.2. Reproduction and Development of Asteroids 7.3. Ecology and Behavior of Asteroids 7.4. Economic Importance of Asteroids

8. Ophiuroidea 8.1. Morphology of Ophiuroids 8.2. Reproduction and Development of Ophiuroids 8.3. Ecology and Behavior of Ophiuroids 8.4. Economic Importance of Ophiuroids

9. Holothuroidea 9.1. Morphology of Holothuroids 9.2. Reproduction and Development of Holothuroids 9.3. Ecology and Behavior of Holothuroids 9.4. Economic Importance of Holothuroids

10. Echinoidea 10.1. Morphology of Echinoids 10.2. Reproduction and Development of Echinoids 10.3. Ecology and Behavior of Echinoids 10.4. Economic Importance of Echinoids

11. Ongoing and Future Research Other Invertebrate Taxa 21 Andreas Schmidt-Rhaesa, University of Bielefeld, Germany 1. Introduction 2. Mesozoa

2.1. Rhombozoa

©Encyclopedia of Life Support Systems (EOLSS) xix


2.2. Orthonectida 3. Xenoturbellida (Xenoturbella bocki) 4. Kamptozoa (Entoprocta) 5. Sipunculida 6. Tardigrada, the Water-bears 7. Onychophora, the Velvet Worms 8. Chaetognatha, the Arrow Worms 9. Tentaculata, or Lophophorata

9.1. Phoronida 9.2. Bryozoa (Ectoprocta) 9.3. Brachiopoda

10. Hemichordata 10.1. Pterobranchia 10.2. Enteropneusta

Tunicata and Cephalochordata 43 Loriano Ballarin, University of Padova, Italy Paolo Burighel, University of Padova, Italy 1. Introduction to Protochordata: General Characteristics 2. Tunicata

2.1. Ascidiacea 2.1.1. Tunic 2.1.2. Morphology and Physiology 2.1.3. Reproduction and Development 2.1.4. Larval Morphology and Metamorphosis 2.1.5. Ecology and Economic Relevance 2.1.6. Systematics

2.2. Thaliacea 2.2.1. Pyrosomes 2.2.2. Salps 2.2.3. Doliolids

2.3. Appendicularia 2.3.1. Morphology and Behavior 2.3.2. Relevance in Marine Ecosystems

3. Cephalochordata 3.1. Morphology and Physiology 3.2. Reproduction and Development

Pisces 68 Ofer Gon, South African Institute of Aquatic Biodiversity, Grahamstown, South Africa 1. Introduction 2. The Biology of Fishes

2.1. Respiration 2.2. Osmoregulation 2.3. Buoyancy 2.4. Prey Detection and Predator Avoidance 2.5. Reproduction

3. The Emergence of Fishes 3.1. Agnatha (Jawless Fishes) 3.2. Gnathostomata (Jawed Fishes)

3.2.1. Placodermi (Armored Fishes) 3.2.2. Acanthodii (Spiny-Finned Fishes) 3.2.3. Chondrichthyes (Cartilaginous Fishes) 3.2.4. Sarcopterygii (Lobe-Finned Fishes)

©Encyclopedia of Life Support Systems (EOLSS) xx


3.2.5. Actinopterygii (Ray-Finned Fishes) 3.2.5.1. Basal (Pre-Teleostean) Actinopterygians 3.2.5.2. The Teleostei

Amphibia 100 Alan Channing, University of the Western Cape, Cape Town, South Africa 1. Introduction 2. Classification of Amphibia 3. Gymnophiona

3.1. Morphology 3.2. Life Cycle 3.3. Distribution 3.4. Feeding and Predators 3.5. Little-known Caecilians

4. Caudata 4.1. Morphology 4.2. Life Cycle 4.3. Distribution 4.4. Adult Variation 4.5. Feeding 4.6. Larval Variation

5. Anura 5.1. Morphology 5.2. Life Cycle

5.2.1. Variations in Life-history Strategies 5.3. Distribution 5.4. Adult Variation 5.5. Tadpole Variation 5.6. Food 5.7. Vocalization

5.7.1. Sound Production 5.7.2. Hearing

6. Metamorphosis 7. Ecological Role 8. Declining Amphibians

8.1. Implicated Factors 8.1.1. Ultraviolet Radiation 8.1.2. Loss of Habitat 8.1.3. Introduced Predators 8.1.4. Pollutants 8.1.5. Fungus 8.1.6. Long-term Drought 8.1.7. Human Consumption

9. Skin Secretions 10. Future Investigations Reptiles 120 Harold G. Cogger, Australian Museum, Sydney and Faculty of Science and Mathematics, University of Newcastle, Ourimbah, NSW, Australia 1. Introduction 2. Diversity and Systematics

2.1. A Brief Overview of the Families of Extant Reptiles 3. The Role of Reptiles in Ecosystems 4. Humans and Reptiles

©Encyclopedia of Life Support Systems (EOLSS) xxi


5. The Global Conservation Status of Reptiles 5.1. Threatening Processes

Birds 163 Walter J. Bock, Department of Biological Sciences, Columbia University, USA 1. Introduction 2. Basic attributes

2.1. Body 2.2. Feathers 2.3. Power production 2.4. Song 2.5. Life span

3. Structure and physiology 3.1. Outer shape 3.2. Integument

3.2.1. Feathers 3.2.2. Scales and claws 3.2.3. Bill covering

3.3. Wings 3.4. Legs 3.5. Tail 3.6. Feeding apparatus

3.6.1. Bill 3.6.2. Mouth and Tongue

3.7. Digestive system 3.8. Urinary system 3.9. Respiratory system 3.10. Circulatory system 3.11. Reproductive system 3.12. Sensory system

3.12.1. Hearing 3.12.2. Sight 3.12.3. Smell

3.13. Brain 3.14. Temperature regulation

4. Yearly cycle 4.1. Establishing territories 4.2. Courtship 4.3. Mating systems 4.4. Nests 4.5. Eggs 4.6. Incubation 4.7. Hatching 4.8. Care of the young 4.9. Molt 4.10. Fall migration 4.11. Direction finding 4.12. Navigation 4.13. Winter 4.14. Spring 4.15. Flocking behavior

5. Behavior 6. Distribution 7. Evolution and Classification

7.1. Origin and fossils 7.2. Classification

©Encyclopedia of Life Support Systems (EOLSS) xxii


7.2.1. Class Aves 7.2.1.1. Subclass Sauriurae (all extinct) 7.2.1.2. Subclass Ornithurae

7.2.1.2.1. Superorder Neornithae Mammals 199 Gary Neil Bronner, Department of Zoology, University of Cape Town, South Africa. 1. Introduction 2. Mammal characteristics

2.1. Hair 2.2. Epidermal glands 2.3. Lactation and parental care 2.4. Cardiovascular and respiratory specializations 2.5. Feeding specializations 2.6. Improved auditory acuity 2.7. An enlarged brain

3. Mammal evolution 3.1. Ancestors 3.2. Evolutionary trends during therapsid-mammal transition 3.3. The origin of mammals 3.4. Early mammals

4. Systematics 4.1. Traditional classification 4.2. Molecules remodel the eutherian phylogenetic tree 4.3. Modern mammal classification

5. Diversity and conservation priorities 5.1. Diversity 5.2. Global threats and conservation priorities

6. Future research Primate Evolution 226 Judith Masters, Natal Museum, Pietermaritzburg, South Africa 1. Introduction 2. Archaic Primates 3. Early Euprimates—“Primates of Modern Aspect”

3.1. Adapiforms and Omomyiforms 3.2. Early Simians

4. Later Simian Radiations 4.1. Early Monkeys 4.2. The Epoch of the Apes

5. The Origins of Modern Primate Groups 5.1. Nonhuman Primates 5.2. The Human Lineage

5.2.1. Early Hominins 5.2.2. The Genus “Homo”

Fundamentals of Biological Science: An Evolutionary Approach 253 Rem V. Petrov, Academician, RAN, Presidium of Russian Academy of Sciences, Moscow, Russia Emilia I. Vorobyeva, Correspondent-Member, RAS, Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia 1. Introduction 2. Evolutionary Theory and Evolutionary Synthesis

©Encyclopedia of Life Support Systems (EOLSS) xxiii


3. Structural Levels of Biosphere Organization 4. The Origin and Development of Life on Earth

4.1. The Origin of Life: History of the Problem 4.2. Stages and Factors of the Development of Life 4.3. Heterochrony as an Evolutionary Phenomenon 4.4. The Problem of Species and Speciation

5. Conclusion Index 281 About EOLSS 289

©Encyclopedia of Life Support Systems (EOLSS) xxiv

Download - BIOLOGICAL SCIENCE FUNDAMENTALS · PDF fileBIOLOGICAL SCIENCE FUNDAMENTALS AND SYSTEMATICS CONTENTS VOLUME I Biological Science Fundamentals (Systematics) 1

Top Related