Fishing for genes
Researchers study the underrated pipefish to shed light on evolution
By Nick Houtman
May 7, 2025

You won’t feed a family on pipefish. These snake-like sea animals, close relatives of seahorses and seadragons, graze in coral reefs and seagrass beds in the tropics and temperate waters, including the Oregon coast.
This group’s armor-plated bodies, which range in size from a few inches to two feet long, hold little nutritional value. But they are ripe for scientific discovery. University of Oregon researchers are examining the cells and gene networks behind unusual pipefish traits to gain insights into how evolution works.
First, there are the gender-bending sex roles. As with their seahorse relatives, male pipefish get pregnant. When they reproduce, they engage in an elaborate mating dance and entwine their bodies with females, who deposit eggs into a pouch on the male’s slender body. The males nurture the developing embryos and carry them to term.
Then there are traits that involve changes to bone, cartilage and muscles, such as the long body axis and bony armor. Pipefish, seahorses and sea dragons are all part of a family known as syngnathids, which roughly means “fused jaw” in ancient Greek. All members have an elongated head and fused jaws and feed by sucking in their prey.
For the researchers, pipefish attributes offer powerful clues to the complex machinery that drives biological development. Such knowledge can benefit human health. For example, about 5 percent of human births feature congenital birth defects, and head and jaw abnormalities comprise about three-quarters of them. Knowing which pipefish genes drive head and neck development could help shed light on this problem in humans.
Now the UO team has taken a big step in leveraging pipefish biology by developing the first “single-cell RNA sequencing atlas” for the organism, a kind of genetic roadmap to pipefish form and function.
The work was led by Hope Healey during her time as a graduate student in the lab of biologist Bill Cresko. She and her colleagues published a report detailing their findings in the journal eLife in February.
In the roadmap, researchers identified thousands of cells in pipefish embryos and the genes expressed in those cells. Those genes were sorted into gene networks, permitting each cell type to be examined through a lens of network interactions.
The research lays the foundation for what amounts to a whole pipefish catalog or parts list, which will enable other researchers to tease out exactly what makes the animals unique and how they grow. Knowing which genes are active in developing pipefish can reveal clues about other animals, including humans

Hope Healey uses a seine net to capture pipefish in a shallow inlet. Photo courtesy of Hope Healey.
Hope Healey uses a seine net to capture pipefish in a shallow inlet. Photo courtesy of Hope Healey.
“What makes them so interesting for understanding development is that they have so many alterations compared to other fishes,” Healey said. “They have exoskeletons, they don't have any scales, they've lost certain fins, they have elongated snouts and there are suspected changes to their nervous system as well.”
“Hope’s work has been a significant step forward in being able to study pipefish and other syngnathids,” said Cresko, who is a member of UO’s Institute for Ecology and Evolution and Lorry Lokey Chair and professor of bioengineering in the Phil and Penny Knight Campus for Accelerating Scientific Impact, where he also directs the Center for Biomedical Data Science.
Cresko has long been interested in how gene regulatory networks — essentially, genes that control the activity of other genes — evolve over time. Those networks help determine how cells and tissues develop into adult animals. He started studying syngnathids when he opened his lab in 2005 with the hope of discovering how their remarkable traits evolved.
Before Healey started her project, Cresko’s lab had published the complete genome of gulf pipefish, a species endemic to coastal estuaries in the Atlantic and the Gulf of Mexico. However, knowing that a gene is present doesn’t mean that it is active, so Healey’s goal was to investigate patterns of gene activity. To accomplish that, she and her team needed hundreds of embryos.
They could take advantage of a colony of gulf pipefish, also known by the Latin name Syngnathus scovelli, in Cresko’s lab, but breeding pipefish for research purposes can be difficult, Healey said.
“They are beautiful fish, but there are some challenges for using the colony for our studies,” he said. “Since development happens within the father’s brood pouch, fish must mate naturally, which can be challenging to time for experiments.”
In order to have an adequate supply of embryos, they had arranged for collaborators to mail more gulf pipefish overnight from Florida. And while some members of the team succeeded in breeding those fish in the lab, others did what many of us might do: They went fishing.

Bill Cresko and former lab member Tiffany Thornton use a seine net to catch pipefish off the Oregon Coast. Photo courtesy of Hope Healey.
Bill Cresko and former lab member Tiffany Thornton use a seine net to catch pipefish off the Oregon Coast. Photo courtesy of Hope Healey.
With nets and a permit from the Oregon Department of Fish and Wildlife, they traveled to Coos Bay to gather a local species known as bay pipefish, or Syngnathus leptorhynchus. Bay pipefish are larger and produce more embryos than their East Coast and Gulf Coast cousins.
“We could take sampling trips to the coast whenever we needed bay pipefish embryos,” Healey said.
In two shallow coves, they waded into knee-deep water, struggling not to let their boots get sucked into the sticky mud. They stretched, pulled and dragged their long nets through thick expanses of eelgrass, picking up everything from sticks and grass to crabs and pipefish.
On shore, the research team picked out the pregnant male pipefish and released everything else, including females and nonpregnant males.
For study in the lab, Healey collected embryos that were close to hatching from both gulf and bay pipefish. The goal was to identify the activated genes and cells that would develop into adult fish.
“We chose late-stage embryos because it is when many of the unique traits, such as the elongated snouts, of this family are set up,” she said.
Then the researchers began to analyze the genetic machinery behind those traits — toothless jaw, elongated head, armored skin and brood pouch — to understand how gene activity led to tissue development. They methodically identified how specific genes and cells lay the foundation for each trait, like the blueprints for a house.
“Pipefish allow us to understand the extent to which developmental gene networks are modified when a trait is modified,” Healey said. “For instance, is a gene network changed fundamentally, or are there only slight changes that lead to a highly altered trait?”
In part, they focused on the lack of teeth in the pipefish jaw. They wondered whether the predecessors of tooth cells, known as primordial tooth cells, were present but in a state of arrested development.
Surprisingly, they found that early tooth development genes were active, but no evidence of primordial tooth cells was found in the jaw. It’s possible, they wrote, that such cells existed in an earlier stage of development and that the genetic signals were too weak to initiate tooth development.

Hope Healey uses a dissecting microscope in the lab to remove embryos from the brood pouch of a male pipefish. Photo courtesy of Hope Healey.
Hope Healey uses a dissecting microscope in the lab to remove embryos from the brood pouch of a male pipefish. Photo courtesy of Hope Healey.
They pursued similar questions for the pipefish’s long head, brood pouch and armored skin.
“Hope was able to connect, for the first time in these fishes, gene regulatory network changes in cell types that likely contributed to these evolutionary innovations,” Cresko said. “The more we can learn about these evolutionary mutant models, the more we learn about ourselves.”
“Hope has now successfully defended her dissertation,” he said, “but her work is foundational for continuing research in our laboratory. We’re using similar approaches in additional syngnathid fishes and focusing on other amazing features of these beautiful and marvelous fish.
Healey received support for her research through a fellowship from the National Institute of Dental and Craniofacial Research at the National Institutes of Health. The broader project was funded by the National Science Foundation and the National Institute of General Medical Science at the National Institutes of Health.
