Hakai Magazine

A portrait of a Japanese anchovy by Japanese artist Kawahara Keiga from the 1820s
Japanese scientists have analyzed DNA trapped in seafloor sediments from fish such as the Japanese anchovy—depicted in this 1820s painting by Japanese artist Kawahara Keiga—to chart changes in fish populations over time. Photo by Historic Images/Alamy Stock Photo

Decades of DNA in the Ocean Depths Could Help Track Fish Populations

Estimates of historical populations, reconstructed from ancient DNA, align with shifts in fisheries catch data.

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by Mara Johnson-Groh

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There may be plenty of fish in the sea, but how many did there used to be? The answer to that question is lurking in DNA hidden at the bottom of the ocean.

Japanese scientists who analyzed DNA trapped in seafloor sediments have now shown, for the first time, how this preserved genetic material can be used to chart changes in fish populations over centuries. The new technique, reported in a recent study, could be used to help understand population dynamics of marine species.

Just as humans shed hair and skin cells throughout their lives, fish similarly drop genetic material. Some of this gene-stocked debris inevitably ends up entombed in clays or organic matter in the water column before sinking to the ocean floor. Over time, the sediment builds up, creating a layered time capsule.

While previous studies have analyzed the DNA in sediment to identify which species are present in a region, none have tried to estimate population sizes. The Japanese team, led by Ehime University paleoceanographer Michinobu Kuwae, set out to see if it could be done.

“[Marine] sediments have lengthy records of fish DNA and little degradation over time,” Kuwae said by email. Under the right environmental conditions, DNA can be preserved for decades or even centuries. The cold muddy bottom of Beppu Bay, in southern Japan, is one such place. The deep bay has a relatively shallow mouth, which means incoming tides only interact with the top layer of the water column. This leaves the depths untouched and without oxygen—the perfect mix for DNA preservation.

From Ehime University’s R/V Isana, the scientists dropped instruments to fetch cores of sediment from the bottom of Beppu Bay. In the lab, bits of DNA extracted from the sediment showed which species were present in the bay and their relative population. Radiocarbon dating of the sediment and mollusk remnants therein allowed the scientists to see how those numbers changed.

The scientists focused their attention on three common species—Japanese anchovy, Japanese sardine, and jack mackerel—over a period of 300 years. They found changes in population sizes over time—for instance, the population of sardines had distinct peaks around 1850 and 1980.

Additionally, the reconstructed population sizes showed regular alternating peaks in the populations of sardine and anchovy—a well-known ecological shift related to multidecadal changes in ocean conditions.

To verify the validity of their paleogenetic analyses, the scientists compared their reconstructed population sizes with historical records of fish landings and sales around Japan. They found the peaks in population sizes were matched by increases in fish catches at that time.

Today, fisheries managers and conservationists depend on having accurate population counts to regulate the fishing industry and set conservation goals. While sonar and trawling surveys, and information from fishers’ catches, can help researchers estimate current population sizes, information on historical populations is key to knowing how a range of pressures—from climate change to human interference to natural factors—alters population sizes.

“You could definitely use this [technique] to learn something about how populations fluctuate with variations in environmental conditions,” says Louis Bernatchez, a population biologist at Université Laval in Quebec and a Canada Research Chair in Genomics and Conservation of Aquatic Resources, who was not involved with the new work. He adds that this sort of information can then help the management and conservation of marine species.

The ideal environmental conditions for the preservation of DNA in Beppu Bay likely played a role in the technique’s success. While similar conditions also exist in other places—such as the Santa Barbara Basin in California, Saanich Inlet in British Columbia, and Cariaco Basin in Venezuela—they are rare. However, Bernatchez believes the approach could be applied almost anywhere, though having ideal conditions certainly increases the chances of detecting well-preserved DNA.

“We’re still in the exponential wave of all sorts of environmental DNA applications,” Bernatchez says. “I’m sure we will see other similar studies in the near future.”