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Discovering Mammals in Insect Soup and Leech Stew

Posted by Richard Conniff on August 7, 2013

The land leech as conservationist

The land leech as conservationist

By Richard Conniff/Takepart.com

Wandering through the forest in Madagascar a while back, I quickly became accustomed to having land leeches turn up on various parts of my body. “Filthy little devils,” iHumphrey Bogart called them, in The African Queen. The leeches were mainly annoying because anticoagulants in their saliva caused the wounds to bleed long after I had flicked the leeches themselves back into the underbrush. It  never occurred to me that I was tampering with one of the most sophisticated and cost effective biological monitoring tools ever invented.

Imagine your mission is to visit a remote protected area and determine the presence of the Annamite striped rabbit (Nesolagus timminsi), first discovered in the Annamite Mountains of Vietnam and Laos in the 1990s, and rarely seen since then. You have tried using camera traps in likely habitats for 2000 nights—that’s more than five years—without success. Monitoring on foot has also failed to produce results, as rare mammals are often nocturnal and have typically managed to survive because they live in steep, wet, densely vegetated places. They also tend to be heavily hunted. So they naturally flee from humans. What to do?

Go out and ask the leeches what they’ve been eating.

Resarchers recently tested the method in the Central Annamite region of Vietnam, using the time-honored technique of picking the leeches—25 of them—off their own  

legs. “We let them hunt us,” says researcher Tom Gilbert. “So basically stand in likely spots, and keep our eyes very wide open.” The team had already determined in a preliminary experiment that DNA from a leech’s meal can survive in its digestive tract for at least four months. So they sent off the 25 leeches from the field for DNA barcoding, a technique that sequences a small fragment of mitochondrial DNA as a quick way of identifying species, both the leeches themselves and the species on which they have been feeding. (The study used a sequencing technique designed to ignore any human DNA from the time of capture.) When the results came back from the lab, 21 of the leeches contained mammal DNA—and four of them had been feeding on the elusive Annamite striped rabbit. Bingo.

That kind of genetic monitoring and discovery, called iDNA, for invertebrate DNA, or sometimes “metabarcoding,” is rapidly becoming a standard tool in the conservation world. Researchers have already collected, but not yet sequenced, leeches from the same region of Vietnam in an attempt to find the saola (Pseudoryx nghetinhensis), a remarkable antelope-like bovine, sometimes called the Asian unicorn, also discovered in the 1990s. Despite weighing almost 200 pounds, it has proven almost impossible to find by conventional means.

Other researchers are applying the iDNA technique by sequencing an “insect soup” of mosquitoes, ticks, carrion beetles, and other blood sucking or meat-eating invertebrates. In an article this week in the journal Ecology Letters, Douglas Yu and his co-authors describe a study comparing this technique with the conventional “gold standard” method for sampling a habitat by hand, and with standard trapping techniques.

The traditional methods took highly-trained experts more than 2,500 hours to assemble 55,000 arthropod and bird specimens. For iDNA sampling, says Yu, “We collected lots of insects and other creepy-crawlies, ground them up into an ‘insect soup,’ and read the DNA using sequencers that are now cheap enough to use weekly or even daily.” The soup turned out to deliver “the same biodiversity information as the gold-standard datasets. They are also more comprehensive, many times quicker to produce, less reliant on taxonomic expertise, and they have the added advantage of being verifiable by third parties.”

That last bit is important, said Yu, when I reached him this week at the Kunming Institute of Zoology in southern China. (Yu, an American tropical ecologist, holds a joint appointment there and at the University of East Anglia in England.) Right now, he says, if you buy natural products certified as sustainable, you are essentially taking the seller’s word that the landowner is actually following the rules in between visits by monitoring groups like the Forest Stewardship Council. If a mining company says it will not damage local habitat, or a country says it is designating an area for protection, you need to have a certain faith, or perhaps gullibility, to believe that they mean what they say.

But iDNA monitoring makes it cheap and quick enough to routinely monitor the reality on the ground. Yu gives the example of certain protected areas in China where each ranger is responsible for 500 hectares of forest, and if a ranger fails to alert authorities to illegal logging in the area, he goes to jail. Now iDNA makes it possible to determine if a ranger fails to report illegal hunting, or if a mining company fails to live up to its promises: Are the same species present this month as last? Does an area have the same diversity of species at the end of the mining project as at the beginning? Researchers are already using the technique in northern Canada, to monitor species in Wood Buffalo National Park, the world’s second largest protected area, as it faces threats from mining, hydroelectric projects, climate change, and other human intrusions.

For biologists, these techniques promise to revolutionize the way they look at the natural world. (A sister technique, eDNA, or environmental DNA, does the same sort of thing for aquatic species by sequencing DNA from a water sample. Researchers have already used it in the United States to locate the hellbender, a rare amphibian, and will soon attempt it in China to find remaining wild populations of the Chinese giant salamander.)

Insect soup and other methods are also good news for animals. Other than the insects, leeches, and other sample invertebrates, these techniques don’t actually require killing animals, or even handling them. In one case in the Annamite Mountains, DNA from a leech enabled researchers to identify one mammal species that they could otherwise distinguish from an essentially identical species only by handling it. Because DNA can identify animals not just by species, but individually, it also becomes possible to release captive-bred animals into the wild and monitor their survival without ever having to recapture or even see them again.

Finally, says Yu, genetic monitoring is rapidly becoming even faster and less expensive. A British company, Oxford Nanopore Technologies, is already developing a portable sequencing device. So researchers will soon be able to go into the field, whip up their insect soup, then plug the sequencing device into their laptop computers, and almost instantly see a panoramic view of the species hidden all around them.

It is as if someone handed Charles Darwin a Star Trek tricorder.

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2 Responses to “Discovering Mammals in Insect Soup and Leech Stew”

  1. […] Insect soup: It’s not a new meal, but a way to measure biodiversity. (Mongabay) [RC note: And for the same story, five months ago on Strange Behaviors click here.] […]

  2. […] while back, I reported on use of DNA in the blood meals of mosquitoes to identify species in a habitat. That technique is called iDNA (for invertebrate DNA).  Now the Smithsonian Tropical […]

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