Research publication and activity

Hydrophis stokesii found off of Okinawa Main Island in 2021

2025/Aug/17

The speciation mechanisms of organisms have been a mystery, particularly when, geographically, there are fewer barriers in the open seas. In this study, we conducted genome-wide analyses on 16 individuals (14 species) from the highly diverse sea snake genus Hydrophis, to study the process of their evolution and speciation.
The results showed that most Hydrophis sea snakes speciated simultaneously around one million years ago. After speciation, there was little hybridization between different species, and reproductive isolation.
The species Hydrophis stokesii was found for the first time in Japanese waters off of Okinawa Main Island in 2021. Okinawan specimens had a lot less genetic diversity than specimens of the same species in Australian waters. It suggests the possibility that it may belong to a new and extremely small group.
This study was conducted in collaboration with a research team led by Professor Takushi Kishida, College of Bioresource Sciences, Nihon University.
For more information, please read the scientific paper below.

Authors: Takushi Kishida, Rina Keboushi, Takahide Sasai, Mamoru Toda　Bold letters : Foundation staff
GenPaper title: Genomics Reveals Recent Rapid Speciation of Sea Snakes of the Genus Hydrophis (Reptilia, Squamata, Elapidae)
Journal: Ecology and Evolution Link to Scientific
Paper: https://doi.org/10.1002/ece3.71627

2025/Aug/11

In recent years, environmental DNA (eDNA) metabarcoding has attracted attention as a method for assessing biodiversity. Aquatic organisms release trace amounts of DNA into the environment through excretion, mucus, and skin fragments. By extracting and analyzing this DNA from water samples, researchers can identify the species present in a given area. A key feature of eDNA metabarcoding is its ability to amplify specific DNA regions and analyze them using next-generation sequencing, enabling the comprehensive detection of numerous species in a short time. Compared to traditional survey methods such as diving or capture surveys, this approach is non-invasive and highly efficient, making it widely applicable to marine ecosystem research and biodiversity monitoring.
However, in coastal areas, water flow constantly changes due to tidal movements, and how this affects the distribution of eDNA and influences survey results has not been fully understood. Since tidal fluctuations may cause the dilution or dispersion of DNA, it is crucial to determine the extent to which this impacts the accurate detection of fish communities. This study aimed to clarify these effects.
To investigate this, we collected water samples at different tidal stages in two regions of Japan with distinct climatic conditions: the Boso Peninsula in Chiba Prefecture (temperate zone) and the Motobu Peninsula in Okinawa Prefecture (tropical zone). We then conducted DNA analysis to quantitatively evaluate the impact of tidal changes on fish eDNA samples. Our findings revealed that while tidal effects were observed to some extent, their influence was relatively limited compared to other factors. These results suggest that, in many cases, tidal conditions do not need to be excessively considered when conducting eDNA-based fish community surveys.
This study contributes to the further refinement of eDNA-based survey methods and the realization of more accurate biodiversity monitoring. Future research should focus on understanding the dynamics of eDNA under different environmental conditions and optimizing survey designs accordingly.

【Authors】 Shin-ichiro Oka, Masaki Miya, Tetsuya Sado, Masayuki Ushio（Bold names indicate foundation-affiliated researchers）
【Title】Assessing the impact of tidal changes on fish environmental DNA metabarcoding in temperate and tropical coastal regions of Japan
【Journal】Metabarcoding and Metagenomics
【Link（Available for free）】 https://doi.org/10.3897/mbmg.8.135461
 

Seminar members

Research presentation

2025/Aug/11

The 8^th Okinawa Fish Seminar was held at the University of the Ryukyus on March 8^th, 2025. The Okinawa Fish Seminar is an annual event where researchers and students engaged in fish research in the Ryukyu Islands present their latest research and exchange information.
This year, around 30 participants from Okinawa Prefecture and Kagoshima Prefecture gathered to present their research on taxonomic and ecological studies, primarily focusing on fish species that inhabit the waters of the Ryukyu Islands. This event has provided a significant opportunity for the exchange of ideas, which may lead to advancements in fish research in the Ryukyu Islands.

Versuriga anadyomene

Versuriga anadyomene (Inside the tank)

2025/Jul/29

In 2022, a jellyfish specimen was collected off the coast of Yomitan. It was identified as a species of true jellyfish called Versuriga anadyomene. This was the first time it had been recorded in Japanese waters. This species has a beautiful color with distinctive mesh patterns on the surface of its bell. These patterns are similar to a traditional Japanese textile called chirimen. Its Japanese name was proposed as chirimen kurage, meaning chirimen jellyfish. Versuriga anadyomene had been reported in Southeast Asia, Australia, and Palau, and has now been recorded in Okinawan waters. Versuriga anadyomene is the only species in its genus, and Versugia is the only genus in the family Versurigidae. The species Versuriga anadyomene, the genus, and the family are therefore all given the Japanese name chirimen kurage. This study was a collaboration between Okinawa Churaumi Aquarium and the Kuroshio Biological Research Institute.


【Authors】Sho Toshino, Miyako Tanimoto
【Title】First Japanese record of Versuriga anadyomene (Scyphozoa: Rhizostomeae) from the Ryukyu Archipelago
【Journal】Biogeography
【Link】 https://doi.org/10.11358/biogeo.27.86
 

 

 

2025/Jun/17

Reef-building corals are vulnerable due to climate change and human activities. An accurate assessment of their status in each region is needed for future conservation. Until now, coral research required specialist divers and underwater imaging techniques, however, the effectiveness of this approach was limited in terms of efficiency and scope. Environmental DNA metabarcoding (eDNA-M) is an effective method to detect existing corals, but requires optimized primers for PCR amplification of eDNA, and then comparison to libraries with complete mitochondrial genome sequences. There are 85 genera of reef-building corals known in Japan, only 60 of which had been sequenced. Of the remaining 25 coral genera, the mitochondrial DNA of 22 have now been sequenced, and an additional 12 genera were re-sequenced. Okinawa Churashima Foundation has contributed by creating the genome sequence data of 7 genera. By integrating this new data, future studies of eDNA-M will now be able to detect 83 of 85 known genera. This allows for comprehensive genus-level detection of nearly all Japanese reef-building corals in a single glass of seawater. This research was conducted in cooperation with a research team led by Professor Noriyuki Satoh of the Marine Genomics Unit at the Okinawa Institute of Science and Technology (OIST).

Authors name:
Kanako Hisata, Tomofumi Nagata, Megumi Kanai, Frederic Sinniger, Fumihiko Nagata,
Mayuki Suwa1,Yuki Yoshioka1, Saki Harii, Masanori Nonaka, Hironobu Fukami, Seiji Arakaki,
Manabu Fujie, Nana Arakaki, Yuna Zayasu1, Haruhi Narisoko, Takeshi Noda1, Aya Koseki,
Koki Nishitsuji1, Jun Inoue, Chuya Shinzato, and Noriyuki Satoh

Paper Title:
An eDNA metabarcoding system for detecting scleractinian corals to the generic level along the Japanese coast

Journal Name: Galaxea, Journal of Coral Reef Studies
Link:  https://www.oist.jp/ja/news-center/news/2025/5/22/discovering-rich-biodiversity-coral-reefs-using-comprehensive-new-system

 

Stages of growth from eggs

2025/Jun/10

sea anemone, live in symbiosis with anemonefish species. Both are highly popular for ornamental aquaria, and their capture is a cause of decreases in wild populations. In the 1970s and 1980s, captive breeding techniques for anemonefish developed. However, captive breeding of the host sea anemones has been limited, and knowledge of their reproduction was also limited. 
 From 2019 to 2022, Okinawa Churaumi Aquarium conducted research to shed light on the reproductive ecology of gigantic sea anemones, and to develop captive reproduction with the aim of conservation. Using a puncture needle to distinguish sex, mixed genders of anemones were kept in outdoor tanks. We succeeded in capturing footage of reproductive behaviors and collected fertilized eggs. Breeding of the gigantic sea anemone took place between June and July (in water temperatures from 26.1 to 27.2 ℃). Six to nine days after a full moon, sperm were released one hour before sunset, and egg spawning began after sunset.  
 In 2023, the same methods were used for the successful captive breeding of the leathery sea anemone, and in 2024, for the successful captive breeding of the Merten's sea anemone. The techniques are expected to contribute to the ex situ conservation of numerous host sea anemone species.  


【Award recipients】 Shohei matsuzaki, Mayu suzumura, Miyako Tanimoto, Mariko Omata, Eeri Nakashima, Kiyomi Murakumo （Okinawa Churaumi Aquarium）
【title】Original Research Paper: Method of Sex Identification and Captive Breeding of the Gigantic Sea Anemone
【Journal publishing article】Journal of the Japanese Association of Zoos and Aquariums, Vol. 66, No. 3, 57–66, 2024.

Artificial substances excreted from a black sea turtle
(Length of scale line is 50 mm)

2025/May/17

Man-made marine debris affects many marine animals, and has become a global problem. Man-made objects, when ingested by sea turtles, negatively impact their growth and survival. An understanding of the extent of this problem is important for sea turtle conservation around Okinawa Main Island.
From 1999 to 2023, we conducted the first quantitative survey of ingested marine debris in the Western Pacific, with the study of five black sea turtles. Three black sea turtles were found alive, cared for at Okinawa Churaumi Aquarium, and they excreted soft plastics and other artificial materials over 2 to 72 days. The other two black sea turtles were found deceased and washed ashore. Necropsies showed that one of these turtles had artificial objects in their digestive tract.
Of this sample, four of the five turtles (80%) had consumed man-made marine debris. This is a higher percentage than seen in other species of sea turtles inhabiting the same area. A higher rate of marine debris consumption, especially if caught in their digestive tracts, will cause a deterioration in health of the black sea turtle population. The researchers suggest that black sea turtles, when found in distress near Okinawa Main Island, should undergo emergency rescue to quickly remove artificial objects using medication and endoscopy.
For more information, please read the scientific paper below.


Authors:Takahide Sasai・Kei Yamazaki・Ken Maeda・Kaho Mizuochi・Masakatsu Kino・Isao Kawazu
Paper Title:Marine debris ingestion of black sea turtles Chelonia agassizii around Okinawajima Island, Japan
Journal Name:Umigame Newsletter of Japan
For further details, please see the paper here

whale sharks (Rhincodon typus)

2025/Apr/5

It takes many years for whale sharks (Rhincodon typus) to reach maturity, and long-term observation is necessary to study their reproduction and conservation. For this reason, understanding how environmental factors impact behavior is important for conducting appropriate rearing. In this study, we attached a data logger to a male whale shark that has been reared at Okinawa Churaumi Aquarium for over 29 years. We wanted to see how water temperatures and light might influence its swimming behavior.
The data logger showed the whale shark’s tail beat frequency, swimming speed, and level of activity, decreased between 4% to 20% when comparing day and night in all seasons. Its activity decreased by as much as 20% on nights when water temperatures were lower than 23.6℃.       In addition, approximately 90% of “clasper crosses” (movement of male genitalia), a reproductive behavior of male sharks, occurred during daytime.
These results indicate that the current rearing environment is appropriate for the whale sharks, as it has a diurnal rhythm with higher activity during the day, while at night it beats its tail more slowly to conserve energy. The results of this research will deepen our understanding of the behavioral characteristics of whale sharks, and will be useful in future rearing management and conservation activities.


【Authors】
Tomoki Kanna, Sayaka Takahashi, Eundeok Byun , Atsushi Yamashiro , Rui Matsumoto , Shinsuke Torisawa , Yasushi Mitsunaga （太字：財団職員）

【Title】
Seasonal behavioral changes of a captive whale shark (Rhincodon typus) under variable temperature and light conditions

【Journal】 Fishery Bulletin

hawksbill sea turtles (Eretmochelys imbricata) 

Selenium is a trace element that exists naturally in marine environments. In oviparous (egg-laying) animals, when the concentration of selenium is low within the blood, there is a risk of hatching rates dropping. In this study, the serum selenium concentration of 45 wild and captive endangered hawksbill sea turtles (Eretmochelys imbricata) were compared, and changes in serum selenium concentration were monitored during the captive period. The results showed that the serum selenium concentration is significantly higher in wild hawksbill sea turtles than captive hawksbill sea turtles. The decline was particularly noticeable after one to two years in captivity. This result suggests that this may lead to lower rates of hatching in captivity. 
The Okinawa Churashima Foundation that manages Okinawa Churaumi Aquarium will continue to promote conservation research and will work toward finding a solution to this challenge.

【Authors】
Kino Masakatsu, Isao Kawazu, Konomi Maeda
（All authors are staff of the Churashima Foundation）

【Title】
Relationship between Serum Selenium Concentration and Rearing Period in Hawksbill Turtles

【Journal】 Current Herpetology