How losing genes made the pygmy seahorse a master of disguise
Paul Arnold
contributing writer
Stephanie Baum
scientific editor
Robert Egan
associate editor
Pygmy seahorses are remarkable creatures. These tiny marine vertebrates, often no bigger than two centimeters in size, are masters of camouflage, able to match the texture and color of the coral in which they live. Some species even have tiny bumps on their skin that mimic the polyps of gorgonian sea corals. Blending into the background makes them almost invisible to predators and divers trying to spot them.
So how did they evolve to be so good at avoiding detection? A team of Chinese and German scientists decided to find out. First, they created a detailed map of the pygmy seahorse's entire genetic code, or genome. Then they compared it to the genomes of other seahorses and similar fish. This allowed them to pinpoint the specific genes that contribute to making pygmy seahorses so unique. The researchers also looked at which genes are active and how the DNA is organized as the seahorse develops.
One particular gene of interest was the hoxa2b gene, which is involved in craniofacial development. It's a member of a family of master control genes called homeotic selector genes that are responsible for organizing the overall body plan in most animals, from insects to humans.
Missing genes
The researchers found that pygmy seahorses lost 438 complete genes that are present in other seahorses and 635 genes with mutations that render them nonfunctional. They also discovered that the tiny creatures had lost many important genetic "switches" near genes that control growth and development.
In their paper in the Proceedings of the National Academy of Sciences, the researchers argue that these genetic losses are responsible for the distinctive traits in pygmy seahorses.
"Our study shows that the pygmy seahorse's extraordinary adaptations are the result of extensive gene and regulatory element loss, tightly linked to its symbiotic lifestyle," they write.
One clear example is the hoxa2b gene, which was found to be nonfunctional. This most likely stunted the growth of the pygmy seahorse's head, the scientists believe, giving it a miniature, knob-like snout, resembling a coral knob.
The study also revealed that pygmy seahorses have significantly weaker immune systems than other fish. They are missing MHC genes (major histocompatibility genes) that make proteins involved in fighting off pathogens. The researchers speculate this isn't a problem because their coral hosts produce antimicrobial compounds that protect both the corals and the seahorse.
The reduced immune system may also be responsible for another unique trait of the pygmy seahorse—male pregnancy. Bringing embryos inside the body could potentially trigger the immune system to attack, but losing some of its genes may have been an adaptation that allowed males to carry their young.
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More information: Meng Qu et al, Symbiosis with and mimicry of corals were facilitated by immune gene loss and body remodeling in the pygmy seahorse, Proceedings of the National Academy of Sciences (2025).
Journal information: Proceedings of the National Academy of Sciences
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