Fish Diversity of Japan: Evolution, Zoogeography, and Conservation

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