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Is Your Dinner Endangered? DNA Detectives Investigate

Scientists deploy genetic forensics to protect overhunted animals
November 05, 2010

Popular Science

By Laura Allen

Dr. Demian Chapman was interviewed for the following story:

To better understand how scientists are attempting to trace contraband animal products back to their source, I invited Kolokotronis to another meal, this time with more guests. Joining us would be Demian Chapman, a geneticist at the Institute for Ocean Conservation Science at Stony Brook University, and his wife, Debra Abercrombie, a fisheries consultant. We met at Congee Bowery, one of the dozens of restaurants in Manhattan that serve sharkfin soup. As we crowded around a table, Chapman explained that demand for the soup threatens several dozen of the more than 400 species of sharks, which, like bluefin tuna, remain largely unprotected. Regulating the industry, he said, requires legislation at the source—where the sharks are pulled out of the water. “The problem with the shark-fin trade is that so many different countries are participating,” Chapman said, picking up his menu. “Anyone can do whatever they want. It’s a Wild West show.”

DemianGlancing around the dining room, I spotted a stuffed deer and a net bulging with plastic fish. On display inside a clear case was a pair of dried, bone-colored shark fins the size of banquet platters. “Those are probably worth 15 grand,” Chapman said. Abercrombie identified them in seconds: “basking shark.”

We ordered a $40 bowl of “Braised Supreme Shark Fin in Broth.” Shark fin is mostly cartilage, which swells and separates into needle-like strands when cooked. Finding usable DNA in hot soup would be challenging. The main genetic marker for species identification, which scientists refer to as a DNA barcode, is only 650 nucleotides long, and cooking can break that marker into even shorter fragments. Chapman and Kolokotronis were eager to see if their techniques were good enough to isolate the DNA from such heavily degraded samples. Kolokotronis transferred a limp fin sample into a baggie as I gingerly tried a few spoonfuls. The needles were almost crunchy. “I just don’t see the hype,” Kolokotronis said after he nibbled a piece. I offered a taste to the shark scientists, who had ordered the General Tso’s chicken instead, and they politely declined.

As we picked at our fins, Chapman explained his method for pinpointing shark origins. Every species has a unique DNA barcode, but other genetic markers can reveal regional variations—the genetic equivalent of a ZIP code. Step one was to perfect a test that could identify the species, even in fins that had been cut, dried, and boiled. Step two was to identify the shark’s genetic ZIP code. And the final step—a multiyear endeavor— was to develop a DNA database of sharks in the wild, a map whereby scientists could compare sample data against known regional characteristics and make a determination. Accurate geographic data could help authorities intercept the hunters and ensure that trade in certain regions was sustainable.

Owing to the remarkable breakthrough of one of Chapman’s colleagues, a fisheries scientist named Shelley Clarke, the technique has already given scientists a better picture of the market for shark fins. In 2001, when Clarke was living in Hong Kong near the fish market that sold more than half of the world’s shark fins, she convinced the market’s major shark-fin traders to let her snip nearly 600 samples of their product. (“It was amazing that I got the access that I did,” she wrote in an e-mail, “given the value of the product, the fact that I didn’t pay for any samples, and that the shark-fin traders are known for being closed and secretive.”)

DNA tests revealed that the majority of Clarke’s shark fins derived from overfished blue shark. But Chapman said he was particularly interested in the small group identified as scalloped hammerhead shark, an endangered species that lives worldwide and is among the most prized in the fin trade. So he drilled deep into the Hong Kong samples, located their unique regional markers, and matched them to a reference map. His results showed that that one fourth of the scalloped hammerhead fins came from sharks in the western Atlantic, where ecological surveys reveal a 75 to 80 percent decline since 1972. Chapman could even specify the exact regions of the sharks’ capture, such as in the Gulf of Mexico and off the coast of Brazil.

The species in my soup bowl proved to be a tougher challenge. The first step—species identification—was difficult yet doable. Chapman reported an extremely weak DNA signal, and Kolokotronis had to run his procedure several times, but both scientists produced the same results: Prionace glauca, the near-threatened blue shark. Unfortunately, the last two steps necessary to determine P. glauca’s geographic origin are not yet possible. Scientists have only just begun to establish a DNA reference map for blue shark. “Since blue sharks are highly mobile, finding distinguishing markers for populations is much more challenging than for hammerheads,” Chapman says.

The reference maps for sharks need more time, but geographic tracing is already exposing countries that are lax about protecting other rare animals from trade, and in some cases the technique is even helping authorities arrest poachers. Scientists at the University of Washington’s Center for Conservation Biology are using geographic tracing to track massive ivory seizures back to where the elephants were killed. They were able to show, for instance, that a 2002 seizure of 532 large tusks and 42,000 hankos (ivory seals used in China and Japan) came from protected elephants in Zambia, Mozambique and Angola. The group also found that 1,094 tusks seized in Taiwan and Hong Kong in 2006 were poached from game reserves in Tanzania and Mozambique. The findings have already enabled multiple prosecutions, including the 2009 arrest of six officials from Tanzanian customs who accepted bribes from the smugglers.

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