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Here’s how to use DNA to find elusive sharks

Genetic traces in seawater reveal an unseen ‘dark diversity’ that divers and cameras miss

7:00am, May 7, 2018

SHARK SIGNS  A baited camera lures a tiger shark and gray reef shark into view, as part of a test to compare what works better to census the elusive fishes: cameras, divers or collecting DNA from seawater. 

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Pulling DNA out of bottles of seawater collected from reefs has revealed some of what biologists are calling the “dark diversity” of sharks.

Physicists have their dark matter, known from indirect evidence since humans can’t see it. Dark diversity for biologists means species they don’t see in some reef, forest or other habitat, though predictions or older records say the creatures could live there.

That diversity showed up in a recent comparison of shark sampling methods in reefs in the New Caledonian archipelago, east of Australia. An international team analyzed results from three approaches: sending divers out to count species, baiting cameras and analyzing traces of DNA the animals left in the environment.

Environmental DNA revealed at least 13 shark species — at least six of which failed to show up in the other surveys, the team reports May 2 in Science Advances. With environmental DNA, “you reach the inaccessible,” says marine biologist Jeremy Kiszka of Florida International University in Miami.

The six bonus species found only by DNA included a great hammerhead that might have just been passing through. But the bull shark, silky shark and three other kinds were all plausible as reef residents.

Environmental DNA complements rather than replaces other sampling methods, Kiszka says. The DNA method takes less collecting effort, in this case just 22 bottles of seawater.

Yet these genetic traces give no information about the number of individuals in an area. What’s more, the DNA failed to register three species — tiger, tawny nurse and scalloped hammerhead — that turned up in the other surveys. Even combining all the methods yielded only 16 kinds of sharks. Reports show that 26 shark species once lived in the shallow waters of the archipelago, so 10 remain in the shadows, either having vanished or escaped detection.  

Shark census

Scientists used three methods to spot shark species in New Caledonian reefs: environmental DNA (eDNA) from seawater, human divers and baited cameras. The DNA identified the most species, including six not captured by the other approaches. For one, the dusky shark (asterisk), the genetic evidence couldn’t distinguish between it and two other additional species. Combining all three methods revealed 16 species.

Shark nameeDNADiverBaited

Bull shark

Great hammerhead

Dusky shark*

Silky shark

Copper shark

Spottail shark

Sandbar shark

Silvertip shark
Gray reef shark

Gray reef shark
blacktip reef shark

Blacktip reef shark
whitetip reef shark

Whitetip reef shark
sharptooth lemon shark

Sharptooth lemon shark
zebra shark

Zebra shark

Tawny nurse shark

Scalloped hammerhead
tiger shark

Tiger shark

Source: G. Boussarei et al/Sci. Adv. 2018; Illustrations: M. Dando


G. Boussarie et al. Environmental DNA illuminates the dark diversity of sharks. Science Advances. Published online May 2, 2018. doi:10.1126/sciadv.aap9661.

Further Reading

S. Zielinski. Why we need predators. Science News Online, September 17, 2015.  

E. Conover. Shark jelly is strong proton conductor. Science News. Vol. 190, July 9, 2016, p. 4.

S. Milius. Study ranks Greenland shark as longest-lived vertebrate. Science News. Vol. 190, September 17, 2016, p. 13.

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