Fish Diversity of Japan: Evolution, Zoogeography, and Conservation

Description

This book reviews and summarizes the studies on the fish diversity of Japan. It covers the present knowledge of ichthyofauna, habitat distribution, phylogeography, ecology, morphology, and conservation, as well as the history of ichthyology and fish collections in Japan. The book comprises five parts: I. Fish Diversity and Ichthyology of Japan, II. Habitat Distribution and Species Diversity, III. Diversity within Species: Phylogeographic Perspective on Japanese Fishes, IV. Morphological and Ecological Diversifications, and V. Conservation of Fish Diversity in Japan.  The Japanese Archipelago is surrounded by two major warm and one cold currents. It is located in the western North Pacific and encompasses several climatic regimes from north to south. Although the land area of Japan is small, the Exclusive Economic Zone (EEZ) of Japan ranks as the sixth largest in the world, including several marginal seas (Sea of Okhotsk, Sea of Japan, and East China Sea), and deep trenches (Izu-Ogasawara, Japan, and Kurile Trenches). Owing to a variety of marine habitats and a complex geological history, Japan has a rich fish species diversity, representing over 4,500 species in 370 families. The richness of fish species diversity has attracted many scientists since the late 1700s, and continuous studies have led to the development of ichthyology in Japan. With chapters written by leading experts in the field, the book will provide a stimulating and reliable resource for future research and contribute to the progress of ichthyology of the world.  Contents 1: Introduction References Part I: Fish Diversity and Ichthyology of Japan 2: Geography, Currents, and Fish Diversity of Japan 2.1 Introduction 2.2 Geography 2.3 Currents 2.4 Species Diversity of Fishes of Japan References 3: Origins and Present Distribution of Fishes in Japan 3.1 Overview of the Fish Fauna of Japan 3.2 Distributional Pattern in the Pacific Ocean 3.3 Distributional Patterns in the Seas of Japan and Okhotsk 3.4 Origins from Disjunct Distributions 3.5 Future Perspectives References 4: Ichthyology and Collection Building in Japan 4.1 Introduction 4.2 History of Ichthyology in Japan 4.2.1 Dawn of Ichthyology in Japan 4.2.2 Ichthyology Before World War II 4.2.3 Ichthyology After World War II 4.2.4 History of the Ichthyological Society of Japan 4.3 Major Fish Collections in Japan 4.3.1 National Museum of Nature and Science 4.3.2 Hokkaido University Museum 4.3.3 Kyoto University: Maizuru Fisheries Research Station and Kyoto University Museum 4.3.4 Kagoshima University Museum 4.3.5 Kanagawa Prefectural Museum of Natural History 4.3.6 Department of Zoology, University Museum, University of Tokyo 4.3.7 Faculty of Science and Technology, Kochi University References Part II: Habitat Distribution and Species Diversity 5: Fish Diversity Along the Kuroshio Current 5.1 Physical Characteristics 5.2 Fish Dispersal by the Kuroshio Current 5.3 Vicariance Due to the Kuroshio Current 5.4 Southern Japan Ichthyofaunal Boundary 5.5 Unique Ichthyofauna of Yaku-shima Island References 6: What Is Known of Fish Diversity in the Sea of Japan? Flatfishes: A Case Study 6.1 Sea of Japan 6.2 Fishes of the Sea of Japan 6.3 Review of the Flatfish Fauna in the Sea of Japan 6.3.1 Species Checklist: What Species and Where? 6.3.2 Faunal Characteristics 6.3.3 Temporal Changes in Flatfish Community Structures in Wakasa Bay 6.4 Conclusion Appendix: Checklist of Flatfishes in the Sea of Japan Order Pleuronectiformes Family Citharidae Family Paralichthyidae Family Bothidae Family Pleuronectidae Family Poecilopsettidae Family Samaridae Family Soleidae Family Cynoglossidae References 7: Fish Diversity of Subarctic Waters in Japan 7.1 Physical Characteristics 7.2 Fish Fauna of Hokkaido 7.3 Endemic Species 7.4 Distributional Pattern 7.4.1 Shallow-Water Fishes 7.4.2 Deep-Sea Fishes References 8: Diversity and Distribution Patterns of Deep-Sea Demersal Fishes of Japan: A Perspective from Grenadiers 8.1 Introduction 8.2 Materials and Methods 8.2.1 Study Area 8.2.2 Data Sources and Treatment 8.2.3 Elucidating Bathymetric and Biogeographical Boundaries 8.2.4 Data Analyses and Visualization 8.3 Results and Discussion 8.3.1 Taxonomic Diversity and Biogeographical Characteristics of Total Regional Fauna 8.3.2 Vertical Distribution Patterns 8.3.3 Horizontal Distribution Patterns 8.4 Conclusions and Future Perspectives References 9: Fish Diversity of Estuaries Revealed by Environmental DNA 9.1 Introduction 9.2 What Is eDNA? 9.3 Estuarine Fish Species Composition 9.4 Anthropogenic Impacts on the Estuarine Fish Community 9.5 Conclusion Appendix References Part III: Diversity Within Species: Phylogeographic Perspective on Japanese Fishes 10: Deep-Sea Fishes 10.1 Introduction 10.2 Intraspecific Diversity of Deep-Sea Fishes 10.3 Phylogeographic Assumptions in Japanese Seas 10.3.1 Geography and its History in the Japanese Seas 10.3.2 Glacial-Induced Climate Changes and Their Impacts on Japanese Seas 10.4 Deep-Sea Intraspecific Diversity Around Japan 10.4.1 Mesopelagic Fishes 10.4.2 Deep-Demersal Fishes I: Zoarcidae 10.4.3 Deep-Demersal Fishes II: Liparidae 10.4.4 Deep-Demersal Fishes III: Other Instances 10.4.5 Benthopelagic Fishes 10.5 Conclusion References 11: Phylogeography of Coastal Fishes of Japan 11.1 Introduction: Characteristics and Factors Affecting the Population Structure of Coastal Fishes of Japan 11.2 Population Structure of Fishes Distributed Around the Main Islands of Japan, and the Roles of the Warm Kuroshio Current a... 11.2.1 Two Major Intraspecific Groups: the Pacific Group and the Sea of Japan Group 11.2.1.1 Phylogeographic Patterns 11.2.1.2 Mechanisms Underlying the Formation and Maintenance the Two Major Lineages 11.2.1.3 Historical Demography 11.2.2 Contact Zones Between the Two Major Lineages 11.2.2.1 Northeastern Pacific Coast 11.2.2.2 The Seto Inland Sea 11.2.3 Population Structure within the Two Major Groups 11.2.4 Phylogeographic Characteristics of Fauna from the East China Sea Coast of Mainland Kyushu 11.2.5 Phylogeographic Characteristics of Hokkaido Island 11.3 Population Structure of Coastal Fishes in the Ryukyu Islands-Japanese Mainland-Ogasawara Islands Region and the Effects o... 11.3.1 Phylogeographic Relationships Between the Ryukyu Islands and the Main Islands of Japan 11.3.1.1 Biogeographic Characteristics of the Ryukyu Islands 11.3.1.2 Transportation of Larvae by the Kuroshio Current 11.3.1.3 The Kuroshio Current as a Barrier to Larval Dispersal 11.3.1.4 Lineage Divergence and Historical Migration 11.3.2 Phylogeographic Relationships Between the Ogasawara Islands and the Main Islands of Japan 11.3.2.1 Biogeographic Characteristics of the Ogasawara Islands 11.3.2.2 Phylogeographic Patterns in the Region from the Ogasawara Islands to the Main Islands of Japan 11.3.2.3 Historical Demography of Populations in the Ogasawara Islands 11.3.3 Phylogeographic Relationships Between the Ogasawara Islands and the Ryukyu Islands 11.4 Phylogeographic Relationships Between the Japanese Coast and the Continental Coast 11.4.1 Population Structure around the East China Sea and the Surrounding Waters: Several Patterns of Genetic Population Struc... 11.4.1.1 Pattern 1: Geographic Population Structure Corresponding to Sea Regions 11.4.1.2 Pattern 2: Geographic Population Structure in the East China Sea 11.4.1.3 Pattern 3: Weak Genetic Differentiation Among Sampling Sites Within the East China Sea 11.4.1.4 Pattern 4: No Genetic Differentiation Around the East China Sea 11.4.2 Phylogeographic Characteristics of the Ariake Sound 11.5 Conclusion: Differences in Population Structure Among Species and Challenges for the Future 11.5.1 Differences in Population Structure Among Species 11.5.2 Challenges for the Future References 12: Lake Biwa and the Phylogeography of Freshwater Fishes in Japan 12.1 Geographical Regions Based on the Distribution of Japanese Freshwater Fishes 12.2 The Origin of Endemic Fishes in Lake Biwa 12.3 The History of Fishes in and Around Lake Biwa Based on Population Genetic Analysis and Phylogeographic Analysis References Part IV: Morphological and Ecological Diversifications 13: Migration of Fishes in Japan 13.1 Fish Migration 13.2 Types of Fish Migration 13.2.1 Oceanodromy 13.2.2 Potamodromy 13.2.3 Diadromy 13.2.3.1 Anadromy 13.2.3.2 Catadromy 13.2.3.3 Amphidromy 13.3 Migration Diversity of Fishes in Japan 13.3.1 Oceanodromy 13.3.2 Potamodromy 13.3.3 Anadromy 13.3.4 Catadromy 13.3.5 Amphidromy 13.4 Diversity of Migratory Fishes in Japan References 14: Adaptive Phenotypic Divergence in Fishes of Japan: Potential Model Systems for Ecological and Evolutionary Genomics 14.1 Introduction 14.2 Phenotypic Endemism in the Sea of Japan 14.3 Phenotypic Adaptation to the Lake Biwa Environment 14.4 Freshwater Threespine Stickleback in Japanese Spring-Fed Habitats 14.5 Phenotypic Divergence Among Populations of Medaka, a Model Fish from Japan 14.6 Highly Diverged Reproductive Traits in Two Japanese Fish Systems 14.7 Conclusion References 15: Ecological Diversity of Larval Fishes: Ontogeny of Deep-Sea Demersal Species 15.1 Introduction 15.2 Sampling Stations and Near-Bottom Layer Survey Method 15.3 Deep-Sea Demersal Fishes Collected from the Near-Bottom Layer 15.4 Characteristics of Larval and Juvenile Fishes in the Near-Bottom Layer and Water Column 15.5 Ontogeny of Deep-Sea Demersal Fishes 15.5.1 Leptoderma lubricum and L. retropinnum 15.5.2 Paraliparis Dipterus 15.6 Characteristics and Ecological Significance of the Ontogeny of Deep-Sea Demersal Fishes 15.7 Current Status of Larval Fish Taxonomy in Japan References 16: Morphological Diversity of the Lateral Line System in Teleostei 16.1 Introduction 16.2 Morphological Diversity of the Lateral Line System 16.2.1 Canal Topography on the Head 16.2.2 Morphology of Head Canals, and Canal Neuromasts 16.2.3 Canal Topography on the Trunk 16.2.4 Morphology of the Trunk Canal(s) and Canal Neuromasts 16.2.5 Distribution Pattern of Superficial Neuromasts on the Head 16.2.6 Distribution Pattern of Superficial Neuromasts on the Trunk and Caudal Fin 16.3 Innervation of the Lateral Line System 16.4 Ontogenetic Basis for the Morphological Diversity in the Lateral Line System 16.4.1 Lateral Line Canals and Neuromasts 16.4.2 Innervation Pattern of the Lateral Line System 16.5 Functional Significance of the Morphological Diversity in the Lateral Line System 16.6 Taxonomic Groups with Characteristic Lateral Line Systems 16.6.1 Apogonidae 16.6.2 Gobioidei 16.6.3 Kurtidae 16.6.4 Pleuronectiformes 16.7 Overview of the Morphological Diversity in the Lateral Line System References 17: Recent Distributional Shifts and Hybridization in Marine Fishes of Japan 17.1 Introduction 17.2 Distributional Shifts and Hybridization Under Ongoing Climate Change 17.3 Mass Occurrence of Natural Hybrids Between Two Pufferfishes 17.4 Increased Hybridization Among Yellowtails 17.5 Implications for Further Research References Part V: Conservation of Fish Diversity in Japan 18: Coastal Fishes in Sandy Beaches 18.1 What Is a Sandy Beach? 18.2 Topography of a Sandy Beach 18.3 Morphodynamic Beaches 18.4 Sandy Beach Habitats 18.5 Fishes Inhabiting Sandy Beaches 18.6 Differences in the Use of Sandy Beaches by Fishes 18.7 Relationship Between Sandy Beach Type and Fish Species 18.8 Relationship Between Sandy Beach Environment and Fish Communities 18.9 Environmental Problems on Sandy Beaches 18.10 Conservation of the Sandy Beach Ecosystem References 19: Coastal Fishes in Rocky and Coral Reefs 19.1 Introduction 19.2 Regional Variability 19.3 Temporal Dynamics 19.4 Future Perspectives References 20: Fishes in Seagrass Habitats 20.1 Faunal Characteristics of Seagrass Fishes in Japan 20.1.1 Okinawa Region 20.1.2 Honshu, the Main Island of Japan 20.1.3 Hokkaido Region 20.2 Responses of a Seagrass Fish Assemblage to Habitat Degradation 20.2.1 Seagrass Fish Categories Based on Their Occurrence/Distribution Patterns 20.2.2 Transition of Fish Assemblage Structures with Progress of Seagrass Habitat Degradation 20.2.3 Brief Implications on Seagrass Habitat Restoration References 21: Coastal Fishes in Mangroves 21.1 What Are Mangroves? 21.2 Fishes Occurring in Mangrove Habitats 21.3 Factors Affecting Fish Diversity in Mangrove Habitats 21.4 Connection Between Mangrove Habitats and Coral Reefs as Fish Habitats 21.5 Mangrove Habitat Threats and Conservation References 22: Coastal Fishes in Tidal Flats and Salt Marshes 22.1 Introduction 22.2 Current Status of Tidal Flats and Salt Marshes in Japan 22.3 Ecological Role of Intertidal Habitats for Fishes 22.4 Threats for Fishes in Tidal Flats and Saltmarshes 22.5 Conservation 22.5.1 Mitigation and Restoration 22.5.1.1 Intertidal Flats 22.5.1.2 Wando Pools 22.5.1.3 Spawning Grounds 22.5.2 Selecting Conservation Areas Using Indicator Species 22.6 Conclusion References 23: Conservation of Freshwater Fish Diversity in Japan 23.1 Introduction 23.2 Freshwater Fishes in the Red Data Book 23.2.1 Publication of the Red Data Book 23.2.2 Definition of Threatened Species 23.2.3 Application of IUCN Criteria 23.3 Threats to Japanese Freshwater Fishes 23.3.1 Dam Construction and Crossing Work 23.3.2 Rice Paddy Field Remodeling 23.3.3 Invasion of Alien Species 23.3.4 Ornamental Fish Boom 23.3.5 Water Pollution 23.4 Red List Challenges 23.4.1 Insufficient Basic Data 23.5 Protection Measures 23.5.1 Three Basic Steps for Protection 23.5.2 In Situ Conservation 23.5.3 Ex Situ Preservation 23.5.4 Social Enlightenment References 24: Using Gyotaku to Reveal Past Records of Fishes Including Extinct Populations 24.1 Introduction 24.2 Using Gyotaku for Past Biodiversity Information 24.3 Identifications of Fishes Based on Gyotaku 24.4 Applications and Future Prospects References 25: Convention on Biological Diversity and Its Impact on Research, with Special Reference to Ichthyology 25.1 Introduction 25.2 Convention on Biological Diversity (CBD) 25.2.1 Pre-CBD 25.2.2 Outline of the CBD 25.2.3 Related Initiatives in Japan 25.3 Cartagena Protocol 25.4 Strategic Plan for Biodiversity 25.4.1 Strategic Plan 2002-2010, Including 2010 Biodiversity Target 25.4.2 Strategic Plan for Biodiversity 2011-2020, Including Aichi Biodiversity Targets 25.4.3 National Biodiversity Strategy of Japan 2012-2020 25.4.4 The Post-2020 Biodiversity Framework 25.5 Access to Genetic Resources and the Fair and Equitable Sharing of Benefits Arising from Their Utilization to the Conventi... 25.5.1 Background 25.5.2 Bonn Guidelines on Access to Genetic Resources and Fair and Equitable Sharing of the Benefits Arising Out of Their Util... 25.5.3 Nagoya Protocol on Access to Genetic Resources and the Fair and Equitable Sharing of Benefits Arising from Their Utiliz... 25.5.4 Scientific Research and Studies Under the Nagoya Protocol 25.5.5 Domestic ABS Measures in Japan (ABS Guidelines) 25.5.6 Other Laws, Regulations, and Guidelines to be Aware of When Accessing Fishes in Japan for Scientific Research 25.5.7 Summary of Procedures for Access to/Use of Fishes Existing in Japan for Scientific Research 25.5.8 Consultation Services on the ABS in Japan References Index