How the Pygmy Sea Horse Lost Its Snout

The New York Times, August 25, 2025

The pygmy sea horse is an inch-long fish that lives on corals in the Pacific. The corals, fan-shaped and knobby, are venomous, yet the sea horse can safely wrap its tail around a branch to feed on tiny animals passing by.

Some species of pygmy sea horse are pink, others are yellow, each a perfect match to the species of coral on which it lives. The sea horse also has knobs on its body to match the size and spacing of the knobs on its corals. Instead of the typical sea horse snout, the pygmy sea horse has a face like a pug; its snout resembles yet another coral knob.

By mimicking coral so well, the pygmy sea horse can hide from predators. And because it is also immune to the corals’ venom, it gains a kind of protective shield by living among them. (Each knob of coral houses a tiny animal called a polyp that kills prey by firing poisonous harpoons.)

If that wasn’t remarkable enough, pygmy sea horses flip the typical roles of the sexes. After a pair of pygmy sea horses mate, the female inserts the fertilized eggs into the male’s body, and the males, not the females, carry the embryos.

Male pregnancy occurs in all sea horses, but pygmy sea horses take it to the extreme. A typical male sea horse carries its eggs in a kangaroolike pouch on its tail. In male pygmy sea horses, the brood pouch is more like a uterus, growing deep inside his body cavity near his kidneys and intestines. The male nurtures his young with a special organ in the pouch that functions like a mammalian placenta. Once the baby sea horses hatch, they exit their father’s body through a tiny slit and swim away.

How did so extraordinary a creature evolve? To better understand, a team of Chinese and German scientists have sequenced the genome of a pygmy sea horse for the first time.

“They’re just something very odd and interesting and in need of explanation,” said Axel Meyer, an evolutionary biologist at the University of Konstanz in Germany and an author of the new study, which was published on Monday in Proceedings of the National Academy of Sciences.

Dr. Meyer and his colleagues compared the DNA of pygmy sea horses to that of other sea horses and more typical fish. Looking at the mutations in the different species, the researchers estimated that pygmy sea horses split off from full-sized ones about 18 million years ago.

Some of the mutations that pygmy sea horses gained altered single genetic letters in their DNA. Those alterations, in turn, caused subtle changes in the shape of certain proteins, including ones that are active in the sea horse’s nervous system. Dr. Meyer and his colleagues suspect that these changes stopped coral venom from locking onto nerve cells in the pygmy sea horses. The animal thus evolved to be immune.

Evolution can also unfold when old genes learn new tricks. Animal DNA contains millions of short sequences that proteins can grab in order to turn on nearby genes or turn them off. When these genetic switches mutate, genes can turn on in response to new signals.

The knobs on pygmy sea horses, which are unlike anything found on other sea horses, appear to have arisen this way. In the new study, the researchers found that cells in the knobs use genes that are typically active in the brain, eyes, kidneys and other organs.

But most striking was how much DNA had gone missing from the pygmy sea horse’s genome. DNA can disappear over the course of generations when mutations chop out hundreds or thousands of genetic letters at a time. Dr. Meyer and his colleagues discovered that pygmy sea horses had lost 438 entire genes that are found in other sea horses. Another 635 genes have lost enough DNA that they no longer work, and 5,135 genes have lost nearby genetic switches, so that they no longer turn on in response to certain signals.

These losses led to many of the most distinctive traits in pygmy sea horses, the scientists argue. For instance, it’s probably no coincidence that many of the lost genes and genetic switches are involved in the growth of cells, including the growth of the sea horse’s snout.

The effect of these losses, the researchers contend, was to halt the development of the pygmy sea horse’s head at an early stage. The result was a knob-like snout instead of a horse-like one.

Despite the loss of many genes in their immune system, pygmy sea horses don’t appear to have become more vulnerable to diseases. That might be thanks to the corals, which produce an arsenal of antibiotics and other molecules. These compounds protect the corals — and may rub off on the pygmy sea horses, too.

The loss of immune genes may have opened new avenues of evolution for pygmy sea horses. For one thing, it might explain their radical form of male pregnancy. Bringing embryos deep inside their bodies could potentially trigger the immune system to attack them as foreign tissue. Losing immune-system genes may have allowed fathers to tolerate their young.

Cristian Cañestro, a geneticist at the University of Barcelona who was not involved in the new study, noted that “gene losses are pervasive in all branches of the tree of life.” But, he added, pygmy sea horses are a striking demonstration that losing genes doesn’t always push evolution backward. “This beautiful work provides a clear example of how gene losses can be beneficial, leading to evolutionary innovations and adaptations,” Dr. Cañestro said.

In a sense, pygmy sea horses have been backed into an evolutionary corner: They have lost so many genes that they can no longer survive apart from their corals. But the corals are under threat, especially from heat waves driven by climate change. One species of pygmy sea horse has been declared critically endangered as a result, and more may follow.

“The research reveals a cruel irony,” said Richard Smith, an independent marine biologist. “The very traits that made these sea horses successful, such as their perfect mimicry, tiny size and specialized biology, are now their greatest vulnerability.”