User Guide
Purpose and How to Use This Atlas
- When you access Coral Atlas Japan, the [Home] page will appear. At the top of this page are six menu items: [Home], [User Guide], [What is Environmental DNA?], [Coral eDNA Atlas of the Ryukyu Islands], [Mesophotic Coral eDNA], and [Coral Photo Collection of the Ryukyu Islands].
- The [Home] page provides a brief introduction to the purpose and overview of this atlas. In coral research, visual surveys by scuba diving have traditionally been the primary survey method. To complement direct [SA1.1]underwater observations, environmental DNA metabarcoding (eDNA-M) has been developed and is now widely used. This atlas presents coral eDNA data collected throughout the Ryukyu Islands. It also introduces the remarkable ability of corals to build coral reefs and explains how coral reefs provide habitat for approximately 30% of marine organisms, forming highly complex ecosystems together with small fishes, echinoderms, crustaceans, and many other marine organisms. Furthermore, it describes how coral reefs not only support exceptional biodiversity, but also contribute to fisheries, tourism, local culture, etc.
- This page explains how to use this atlas and the terms governing its use. Before using the [Coral eDNA Atlas of the Ryukyu Islands], [Mesophotic Coral eDNA], or [Coral Photo Collection of the Ryukyu Islands], please read this User Guide.
- Clicking on the [Coral eDNA Atlas of the Ryukyu Islands] first displays the 12 islands currently available for viewing.
You may browse them in sequence or jump directly to an island of interest. For example, selecting "(1) Okinawa Island and Surrounding Islands" will take you to the data for that region. The "(1) Okinawa Island and Surrounding Islands" page begins with an overview of Okinawa Island, followed by a map showing the eDNA sampling sites (sites), each identified by a number. Surveys on Okinawa Island were conducted in 2021–2022 simultaneously with the Ministry of the Environment's Monitoring Sites 1000 visual coral reef surveys. Because surface seawater could not be collected at one location (Site 29) due to rough seas, eDNA data are available for 62 sites, while visual observations were conducted at 63 sites. Thus, eDNA data are available from 62 observation sites on Okinawa Island. Clicking on any site number (1–62) opens the data for that particular site. For example, clicking Site 14 opens the page for Ikei Island East Reef Slope. First, an aerial photograph shows the approximate location of the site. Below this, the top 10 coral genera detected by eDNA are presented. Dominance is expressed as the percentage of coral-derived DNA sequences assigned to each genus. At this site, Montipora is the dominant genus, accounting for approximately 60% of the sequences, followed by Acropora at about 20%. Below the graph, as many photographs of the reef as possible, taken in 2023, are provided. Finally, a map of the entire island illustrates the distribution of the dominant coral genus across the island. For example, Acropora is particularly abundant along the west coast of Okinawa Island, especially around Onna Village. At the bottom of each page, a "Notes" section summarizes observations and interesting features identified by the researchers from the eDNA data. - This atlas analyzes eDNA from 83 genera of zooxanthellate scleractinian corals found in Japan. Target genera are based on the list of 84 genera presented in the "Comparison of the Old and New Classification Systems of Japanese Zooxanthellate Scleractinian Corals" available in the Illustrated Guide to Japanese Zooxanthellate Corals. However, although Boninastrea is included in the classification, it is excluded from this atlas because no reference DNA sequence is currently available for the genus.
Table. 84 genera of zooxanthellate scleractinian corals recorded from Japan. This atlas analyzes 83 genera, excluding Boninastrea (underline). - • Some coral genera are closely related and possess identical DNA sequences in the genetic region analyzed in this study. Consequently, the genera below cannot be distinguished by eDNA analysis.
Anacropora / Montipora
Gardineroseris / Leptoseris / Pavona
Duncanopsammia / Turbinaria
Ctenactis / Polyphyllia
Danafungia / Lithophyllon
Herpolitha / Podabacia / Sandalolitha
Homophyllia / Micromussa
Caulastraea / Oulophyllia
Coelastrea / Dipsastraea
Goniastrea / Merulina
Leptoria / Platygyra
Mycedium / Pectinia / Physophyllia - You are free to download and use the eDNA data from individual survey sites for your own purposes.
However, if you intend to analyze data at the island level or combine data from multiple survey sites, please contact the Marine Genomics Unit, Okinawa Institute of Science and Technology (OIST), in advance.
Last Updated: July 2026