A detailed genome of the snakelike gulf pipefish offers a new way to explore an ancient fish family that includes seahorses and sea dragons.
Genetic changes in this group have generated bodies with vastly different features. Comparing the genome with other vertebrate organisms may help scientists learn about basic aspects of human biology, such as how skulls develop and change shape and how the genome that people mostly share with other vertebrates can be tweaked to create new structures, says Susan Bassham, a senior research associate in the lab of University of Oregon biologist Bill Cresko where the research was done.
A paper detailing the genome appears in the journal Genome Biology. The gulf pipefish—abundant in seagrass beds of the Gulf of Mexico—has the species name of Syngnathus scovelli. It belongs to the family known as Syngnathidae, which dates back at least 50 million years.
“…they are so weird looking in terms of their unique body plans.”
“This group of species has novelties that are not well understood from an evolutionary genetic standpoint,” says Clay Small, one of the paper’s lead authors and a postdoctoral fellow in Cresko’s lab in the Institute of Ecology and Evolution.
“The family Syngnathidae is a very good model for studying these derived structural features because they are so weird looking in terms of their unique body plans. Ultimately, we are interested in identifying genetic changes that are related to the evolution of these novel features in this whole family.”
Species in the Syngnathid family have long snouts, which help their suction-like feeding behavior. They have bony body armor. They lack pelvic fins, ribs, and teeth and have evolved unique placenta-like structures in males for the brooding of developing offspring.
Tiger tail seahorses, too
The publication of the gulf pipefish genome comes less than a week after the genome of another family member, the tiger tail seahorse, appeared in the journal Nature.
“Having this pair of papers published almost simultaneously moved genomic analyses of this remarkable group of fish ahead tremendously,” says Cresko, a professor of biology.
The two genomes show that losses and changes in specific genes or gene functions may be responsible for evolutionary innovations, Small says. Through evolution, the pipefish and seahorse genomes have lost genetic elements compared to distant fish ancestors. These likely explain some changes in body alignment and the loss of pelvic fins, which correspond to legs in the human vertebrate lineage, he says.
A big part of Small’s efforts focused on the ability of male pipefish to gestate embryos in their brood pouch. The gulf pipefish, Bassham says, provides an example of one of the most elaborated placental structures found in the males of various pipefish species.
Some 1,000 genes are expressed differently in the pouch during a male’s pregnancy to control developmental processes, nutrient exchange, stability, and immunity, the researchers report.
In a comparative analysis between pregnant and nonpregnant male pipefish, Small found a family of genes that behaved unusually. This gene family, patristacins, contains some members that turn on during pregnancy and others that are suppressed during pregnancy. The group of genes is likely unique to Syngnathid fishes, and they behave similarly in seahorses.
The team also found that gulf pipefish have two chromosomes fewer than most ray-finned fish. “By looking at the patterns of where genes lie in the genome, it’s very likely this difference resulted simply from the fusion of four of the ancestral chromosomes into two,” Bassham says. “Most fish have 24 chromosomes, but the gulf pipefish has 22.”
How do we get these ‘novelties’?
“Fish are vertebrates. We are vertebrates,” she says. “We share large swaths of our biology with these fish. We’d like to understand how evolution occurs, and some of the most exciting aspects of evolution happen when novel features appear in an evolutionary lineage.
“Novelties can happen multiple ways,” Bassham says. “Sometimes it involves a loss of a structure that creates a new way of life. In other cases, it might be an evolution of a new body part that wasn’t there before. Where did that tissue come from? How did it come into being? What was modified to make it? Or what developmental gene pathways were changed to allow for it?”
Other coauthors are from University of Oregon, Oregon Health & Science University, and Texas A&M University. The National Institutes of Health and National Science Foundation supported the research.
Source: University of Oregon