🐟 The fish on your plate may no longer belong to the group it was classified in for over a century. Japan's largest fish taxonomy group, Perciformes, has been dismantled by DNA analysis. Invisible nanoplastics are killing fish larvae through the food chain. And shortfin mako sharks "warm up" before diving deep — a behavior never seen in fish before. Here's how Japan's latest marine research is rewriting everything we thought we knew about fish.
Japan's Waters: A Marine Biodiversity Powerhouse
Japan's Exclusive Economic Zone (EEZ) covers approximately 4.47 million km². While this represents less than 1% of the world's ocean volume, roughly 34,000 marine species have been confirmed within these waters — about 15% of all known marine life on Earth. Some 3,700 species of saltwater fish alone inhabit Japan's seas, representing approximately a quarter of the world's estimated 15,000 marine fish species.
The reason for this extraordinary diversity lies in geography. The Japanese archipelago spans from subtropical to subarctic climate zones, and sits at the convergence of four tectonic plates. Deep ocean trenches, expansive continental shelves, and complex seafloor topography create a mosaic of habitats found in few other places on the planet. Researchers estimate that an additional 120,000 species may still await discovery.
And from these rich waters, a wave of surprising findings is emerging.
The Great Perciformes Breakup: Fish Taxonomy Turned Upside Down
For decades, the order Perciformes was the largest group in all of vertebrate taxonomy — containing over 10,000 species and accounting for more than half of all fish. Virtually every "fish-shaped fish" you can imagine belonged to this group, from gobies and hairtails to wrasses and sillagos.
Then came the revolution in molecular phylogenetics — the science of using DNA to trace evolutionary relationships. As researchers began comparing the genomes of thousands of species, they discovered that many fish placed together based on physical appearance were, in fact, only distantly related. Perciformes, it turned out, had been functioning as a kind of "taxonomic wastebasket" — a catch-all for species that didn't obviously belong elsewhere.
The result has been a dramatic dismantling. Grunts and stripeys moved to Centrarchiformes. Groupers and scorpionfish were reassigned to a restructured Perciformes (now informally called the "Perch order"). New orders such as Labriformes (wrasses), Gobiiformes (gobies), Carangiformes (jacks), and Scombriformes (mackerels) were established.
The biggest shock? The Japanese sea bass (suzuki) — the very fish that gave Perciformes its Japanese name "Suzuki-moku" — was itself removed from the group. DNA analysis revealed that suzuki is more closely related to tiny deep-sea fish in the family Acropomatidae (lanternbellies), placing it in the order Acropomatiformes. A one-meter predator sharing a branch with centimeter-long fish nobody has heard of — that's the kind of surprise molecular biology delivers.
The Ichthyological Society of Japan continues to announce reclassifications. In 2025 alone, a new species of stingray was described from Ariake Bay, and 16 species of anthias had their genus assignments changed. The family tree of fish is still very much a work in progress.
Nanoplastics: The Invisible Killer in the Food Chain
While taxonomic reshuffling is an academic matter, another line of research touches something far more urgent: fish survival.
In December 2025, a research team led by Associate Professor Mitsuharu Yagi at Nagasaki University published alarming findings in Science of the Total Environment. Their experiments showed that nanoplastics — particles smaller than 1 micrometer (one-thousandth of a millimeter) — dramatically reduced the survival rate of red sea bream (madai) larvae.
What made this study particularly significant was its focus on exposure pathways. When larvae absorbed nanoplastics directly from the water, the effects were concerning. But when the larvae consumed rotifers (tiny zooplankton) that had already accumulated nanoplastics in their bodies, the lethal effects were far worse. The food chain was amplifying plastic pollution.
Even surviving larvae showed elevated antioxidant enzyme levels and activated inflammatory genes — clear signs of severe physiological stress at the cellular level.
The research group noted that across hundreds of sampling expeditions using university research vessels, they have never once failed to find microplastics in their nets. Japan's surrounding waters, fed by the Kuroshio Current and the Tsushima Warm Current, collect plastic debris from across East Asia. Some areas have recorded microplastic concentrations 27 times the global average.
Mako Sharks Warm Up Before Diving: A World First
Another remarkable discovery comes from a collaboration between the Okinawa Churashima Foundation, the Graduate University for Advanced Studies (SOKENDAI), and international partners. The study focused on shortfin mako sharks (Isurus oxyrinchus) and their thermoregulation behavior.
Certain fish — including tunas, marlins, and some sharks — possess "regional endothermy," the ability to maintain body temperatures above ambient water temperature. This was long assumed to be an adaptation for cold-water hunting. But for shortfin makos, which prefer warmer seas, the advantage was unclear.
By attaching data loggers to wild makos off southeastern Taiwan, the team found that body temperature dropped slowly in cold deep water but rose rapidly at the warm surface — at more than 10 times the rate of cooling. This allows makos to extend hunting time in the prey-rich deep while efficiently reheating near the surface.
The true surprise was this: some individuals actively raised their body temperature above the surrounding water temperature before initiating a deep dive. This "pre-dive warm-up" had never been documented in any fish species. It suggests a level of behavioral flexibility and anticipatory decision-making that challenges our assumptions about fish cognition.
Environmental DNA: Reading the Ocean in a Cup of Water
Supporting these discoveries is a revolution in survey technology. Environmental DNA (eDNA) metabarcoding allows researchers to identify fish species from traces of DNA — shed through scales, mucus, and waste — floating in seawater.
A team led by Associate Professor Reiji Masuda at Kyoto University demonstrated that a single day of eDNA sampling could detect roughly 80% of fish species in a given area — far outperforming traditional methods like dive surveys that require multiple trained experts over several days.
At the Okinawa Institute of Science and Technology (OIST), researchers working with the Churashima Foundation developed an eDNA system capable of detecting 83 out of 85 known genera of reef-building corals in Japanese waters. The survey requires, quite literally, a cup of seawater.
This technology promises to transform marine conservation and fisheries management by making comprehensive biodiversity surveys faster, cheaper, and less invasive than ever before.
Evolutionary Dead Ends and New Species: The Mysteries Continue
In June 2025, a joint team from Science Tokyo (formerly Tokyo Institute of Technology) and Sophia University published a groundbreaking study in Molecular Ecology. By comparing the genomes of 240 fish species, they discovered that fish which evolved parental egg-guarding strategies had lost the genes responsible for producing tough egg membranes. Without those genes, these species cannot revert to non-guarding reproductive strategies — they are trapped in an "evolutionary dead end," confirmed at the molecular level for the first time.
Meanwhile, new species continue to emerge. In 2025, the Ariake stingray (Hemitrygon ariakensis) was formally described as a new species from Japan's Ariake Bay. ROV surveys off Okinawa uncovered two goby species never before recorded in Japan, revealing their living coloration for the first time. And a mullet long known as "Anpin-bora" was shown through molecular analysis to actually comprise two distinct species, with the name "Takitsubo-menada" proposed for the newly recognized one.
These discoveries underscore that even in one of the world's most studied marine environments, we have barely scratched the surface.
Conclusion: Fish Are Still Full of Surprises
DNA technology is rewriting fish classification from the ground up. Nanoplastics threaten the very first stages of fish life through invisible food-chain contamination. Deep-sea surveys keep revealing species unknown to science. And behavioral studies show that fish are far more sophisticated than we assumed.
Japan stands at the forefront of these discoveries, leveraging its extraordinary marine biodiversity and deep research tradition to push the boundaries of ichthyology.
Even the fish we eat every day still hold secrets. That familiar creature on your plate is far more mysterious than it appears.
What about your country? Are there surprising fish facts, new species discoveries, or unique marine research stories from your corner of the world? We'd love to hear about them!
References
- https://tsurinews.jp/fish_labo/
- https://www.fish-isj.jp/
- https://churaumi.okinawa/research/marine_organisms/
- https://www.isct.ac.jp/ja/news/y89gj0lh34jp
- https://www.nagasaki-u.ac.jp/ja/science/science426.html
- https://www.kyoto-u.ac.jp/ja/research-news/2017-01-13-1
- https://www.env.go.jp/nature/biodic/kaiyo-hozen/guideline/05-2.html
Reactions in Japan
Suzuki leaving the Suzuki order? Sounds like a comedy skit. But DNA doesn't lie. Science is merciless.
The Perciformes lecture was a staple in fisheries science classes. Can't use it anymore... Textbooks need a complete rewrite.
That nanoplastic study is terrifying. When larvae eat it through plankton, mortality skyrockets? The very base of the food chain is contaminated.
As an angler, I call it seabass anyway so the reclassification doesn't matter lol. But the evolution stories are genuinely fascinating.
Environmental DNA detecting 80% of fish species from a cup of seawater? Revolutionary. Could drastically cut survey costs and help marine conservation in developing countries too.
Charging for plastic bags at convenience stores is a drop in the bucket against microplastics. We need structural changes in industry itself for a real solution.
Mako sharks warming up before a dive is adorable? Even fish have that 'alright, let's go' moment of psyching themselves up.
120,000 potentially undiscovered species in Japanese waters? That's fantasy-level stuff. The deep sea really is like another world.
Proving an 'evolutionary dead end' by comparing 240 genomes is quietly incredible. Fish that guard eggs can never go back to not guarding. This is what irreversible evolution looks like.
My kid just learned at school that Perciformes is the biggest fish group, and now it's already wrong? Teachers have it tough.
I'm a fisherman and the species we catch are clearly changing. I can feel southern fish migrating north due to warming. It's not just classification — the ocean itself is transforming.
eDNA tech could also be applied to aquarium water quality management. Imagine knowing in real-time what microorganisms are proliferating — it would change how we manage captive fish.
Before plastics, fix Japan's fishing regulations first. Saury and squid catches are plummeting but science-based resource management hasn't advanced at all.
A new stingray species in Ariake Bay is exciting. Local fishermen apparently always said 'there's a different kind of ray here.' Love when traditional knowledge and science connect.
Honestly, hearing about nanoplastics makes me nervous about eating sashimi. What's the actual impact on humans? I want to see more research on this.
Finding new goby species via deep-sea ROV and seeing their living colors for the first time is amazing. Deep-sea creatures lose their color when they die, so this is truly special.
As a marine biologist, I'm deeply interested in Japan's environmental DNA work. We've started trialing eDNA tech on the Great Barrier Reef, but Japan's coral detection system achieving 83 out of 85 genera is remarkable precision.
Plastic pollution in the Baltic Sea is a serious issue in Sweden too. The Nagasaki study is important for demonstrating that the food chain pathway is more dangerous. We should replicate similar experiments in Nordic waters.
I work at Taiwan's Fisheries Research Institute. The mako shark study was conducted in our waters, and I'm proud this Japan-Taiwan collaboration produced such remarkable results. Sharks aren't just predators — they have astonishing physiology.
India has 7,500km of coastline but our marine taxonomy research is still in early stages. Seeing Japan rebuild fish classification through DNA analysis makes me wonder how many unknown species lurk in our waters.
American angler here. Japan's 'suzuki leaving suzuki-moku' is like if perch left Perciformes. Classification doesn't affect my fishing, but the science behind it is genuinely cool.
Microplastic concentrations along France's Mediterranean coast are already serious. But Japan's waters at 27 times the global average is shocking. The Kuroshio collecting plastic from across Asia is a structural issue.
From a fishing village in Mexico. Fish species in our area are changing year by year too. Scientific surveys are far from sufficient. If eDNA can survey efficiently like in Japan, please spread that technology to developing countries.
Russia's Far Eastern waters adjoin Japan's research area across the Sea of Japan. We're also observing fish distribution shifting northward due to warming. I wish there were more opportunities for joint research.
In Nigeria, fish is a primary protein source. Nanoplastic food chain contamination research is a global food security issue. I strongly feel such studies should be conducted more in Africa.
I'm an aquarist at a UK aquarium. Perciformes dismantlement means rewriting all our display panels. But visitors actually find DNA classification stories surprisingly engaging.
Fish species caught on Korea's East Sea side are changing too. Much of Japan's research is directly relevant to us. eDNA technology in particular should be considered for Korean coastal surveys.
The Netherlands is largely below sea level, so we're sensitive to marine changes. The finding that fish reproductive strategies can enter irreversible 'evolutionary dead ends' raises new concerns about fish adaptability under climate change.
Italian shark researcher here. The mako pre-dive warm-up genuinely surprised me. Evidence for decision-making behavior in sharks is mounting, and it's changing how we view shark cognition.
The Persian Gulf off Kuwait has extreme high temperatures and salinity, with far less fish diversity than Japan. But that's exactly why studying fish adapted to extreme environments matters. We'd like to adopt Japan's genome comparison methods.
Honestly, reading about nanoplastics makes the future seem bleak. But scientists making the problem visible is exactly what enables us to discuss solutions. Pessimism alone solves nothing, though.