Chemicals in fish ear bones help researchers track winter flounder

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Researchers at the University of New Hampshire are turning to an unusual source – otoliths, the inner ear bones of fish — to identify the nursery habitats of winter flounder in hopes of restoring their populations along the U.S. Eastern Seaboard.

Much like the rings in the cross-section of a tree, otoliths provide information about the age of a fish. Chemical elements like magnesium, sodium and barium found in a fish’s watery surroundings are also imprinted on the ear bones. New research indicates that juvenile winter flounder born in estuaries within 12 km (about 7.5 miles) of one another share similar chemical “signatures” on their otoliths, influenced by unique geology and water chemistry from the watersheds that empty into estuaries.

Results from this study indicate that otolith chemistry can be used to trace juvenile winter flounder back to their birthplace with 73% accuracy, offering scientists a new technological tool in their quest to monitor the species. The N.H. Sea Grant funded study, “Microchemical signatures in juvenile winter flounder otoliths provide identification of natal nurseries,” was recently published in the journal Transactions of the American Fisheries Society.

microscoping view of otolith cross-section

Above: Cross-section of a winter flounder inner ear bone, called an "otolith," that is used to determine age and origin of the fish. Photo by: Dave Bailey.

Winter flounder populations all along the East Coast have plummeted in the last decade, but despite strict regulations that have limited fishing pressure, their numbers are not rebounding, said Elizabeth Fairchild, UNH research assistant professor of biology. Many estuaries — the nursery grounds of winter flounder — are experiencing warming waters and land development pressures that may impact the number of juveniles that can survive and make their way out to deeper offshore waters, she explained. The connectivity between the two environments has been a missing piece of the puzzle for scientists and fisheries managers trying to improve winter flounder populations.

“We don’t know where the adults actually come from, which specific bay,” Fairchild said. “We wanted to know if the estuaries where winter flounder are born or reside in their first year of life impart a unique chemical tag on the fish’s otolith so we could say, yes, that’s a Great Bay fish, or that’s a Narragansett Bay fish, or a Boston Harbor fish. If we can figure that out, we can determine which estuaries in the Northeast are the most essential in terms of providing valuable habitat for winter flounder and protect those places.”

Close-up of juvenile winter flounder in man's hand.

Above: Juvenile winter flounder. Photo by: Dave Bailey

For this study, otoliths from juvenile winter flounder were collected at 12 locations in estuaries and shallow coastal waters ranging from the Navesink River in New  Jersey northward to N.H.’s Great Bay. Lead author David Bailey (UNH ’13), currently a research assistant at the Marine Biological Lab in Woods Hole, Mass., ran the samples through a mass spectrometer to determine the chemical make-up of otoliths from each location.

Juvenile winter flounder from the three study sites in N.H., including Great Bay, Little Harbor and Hampton-Seabrook Harbor, were able to be traced back to their birthplace with reasonable (73%) accuracy and had slightly different otolith chemistries among sites, despite the relative proximity of the estuaries to one another, Bailey said. Looking at the data on a larger scale, the research results indicated regional groupings for winter flounder stocks from Cape Cod, the Gulf of Maine and New Jersey, he added.

Although their research indicates a 12 km geographic range for similarity in otolith chemical signatures, the study was unable to include otolith samples from adult winter flounder to definitively make the connection between estuary and offshore stocks. Fairchild recently received a research grant from NOAA’s Saltonstall-Kennedy Grant Program to continue the research and address this lingering question.

“There’s a lot of money riding on what winter flounder are doing,” Fairchild said. “Fishermen would like to see the stocks rebound so they can harvest them again. The Wampanoag Tribe on Martha’s Vineyard would like to see them make a comeback because of the cultural importance this species has played in their history. The Army Corps of Engineers cannot dredge navigable water channels during several months each year when winter flounder eggs may be present.”

“I think this research is important in terms of environmental protection, trying to figure out which estuaries are producing the most number of fish for the population where people can actually fish for them, and trying to protect those estuaries so we don’t harm the winter flounder,” Bailey added. “You wouldn’t want to dredge an area if you know that’s the prime area that produces fish for a Gulf of Maine winter flounder fishery.”

For more information or to obtain a full copy of the journal article, please contact Elizabeth Fairchild at or 603.862.4475.

N.H. Sea Grant promotes the wise use, conservation and sustainable development of marine and coastal resources in the state, the region and beyond. Located at the University of New Hampshire, NHSG is part of a national network of programs located in our coastal and Great Lakes states as well as in Puerto Rico and Guam.

Rebecca Zeiber, N.H. Sea Grant Science Writer