Turning corpse-eaters and blood-suckers into census-takers

An antelope falls in a forest and there’s no one around to hear it. But there are plenty of things that will eat it. Blowflies and flesh flies land upon the carcass and start to feed on it. They also lay eggs, which hatch into maggots that also start devouring the dead flesh. The antelope will eventually disappear, but fragments of its DNA still exist inside the guts of the insects that feasted upon it.

And that’s great news for conservationists who are trying to work out what lives in this particular forest. They don’t have to hack their way to undergrowth in search of a skittish and elusive antelope. They just have to catch the flies.

That’s exactly what Sebastien Calvignac-Spencer from the Robert Koch Institute did. He captured carrion flies at two tropical forests—the Tai National Park in Côte d’Ivoire and the Kirindy Forest in Madagascar—and used the DNA in their guts to get a snapshot of the mammals in each area. He found a surprising proportion of the local species, including many that are hard to track and some that are highly endangered.

It was census-taking via corpse-eating, and one of several quick and cheap alternatives to the hard slog of traditional monitoring schemes. Typically, large teams of experts, including taxonomists and indigenous trackers, have to work for long periods of time under difficult conditions just to work out which species live in an area, much less measure their numbers or density. Such work is especially hard in thick tropical forests, which hold the greatest diversity of animal life.

But in recent years, scientists have developed several new approaches for detecting the presence of animals through their DNA, without having to actually find them.

From anthrax to antelopes

As I reported for Nature News, Calvignac-Spencer’s fly technique began with sick chimpanzees. Around a decade ago, his boss, Fabian Leendertz, had discovered a type of rainforest anthrax that was killing chimps in the Tai National Park.

Where was this infection coming from? Leendertz knew that the bacteria behind the more familiar version of anthrax can grow in the guts of some flies, so he wondered if the rainforest insects were harbouring the chimp-killing infection. His team captured several flies that emerged from carcasses found in the forest, and that were lured to bottle traps baited with meat. That work is still going on, but in the process, the team realised that they could use mammal DNA inside the flies to measure the forest’s biodiversity.

Obviously, DNA breaks down in the guts of flies but not to the extent you’d imagine. Unlike us, these insects don’t churn their food in a highly acidic stomach, so large fragments of DNA still remain—up to 300 ‘letters’ in length and occasionally up to 700. It’s “not gorgeous, but still usable,” says Calvignac-Spencer.

If you mush up a fly, you get a soup that contains its own DNA and that of its mammalian meals. The team pulled out the sequences they were interested in using primers that recognise the signatures of mammalian or vertebrate DNA.

Around 40 percent of the captured flies yielded mammalian DNA, and they had clearly fed on a broad menagerie. In the Tai National Park, the flies carried DNA from 16 species including six of the nine local primates, two bats, a porcupine, a hippo, and a shrew. They also revealed the presence of Jentink’s duiker, an extremely endangered antelope with fewer than 3,500 individuals left in the wild.

In Madagascar, the team found the DNA of two lemurs, a tenrec (a creature that looks like a hedgehog but isn’t one) and a meat-eater, probably a fossa. That’s four of Madagascar’s 31 mammal species, revealed through the guts of flies.

They now want to see if they can use the flies to get precise information about one species, rather than broad information about many of them. Could they work out a species’ distribution? Could they detect rapid population crashes, including those that traditional methods would never see? For example, Calvignac-Spencer mentions that between 2002 and 2003, thousands of gorillas were killed by the Ebola virus in the Republic of Congo. “But only 44 carcasses were found, in spite of active monitoring,” he says. “And these were gorillas! Just imagine how hard it might be to monitor die-offs of bats or rodents,” which are important reservoirs for infections that could jump into humans. “Flies could really be precious in this context.”

This technique sucks

Corpse-eaters aren’t the only indirect source of animal DNA—blood-suckers could also be a monitoring goldmine. Last year, a team led by Thomas Gilbert from the University of Copenhagen studied the mammals of a dense Vietnamese rainforest, by extracting their DNA from the bellies of leeches.

His team collected 25 leeches in Vietnam’s Central Annamite region, and found that 21 of them carried mammalian DNA. These included the Ammanite striped rabbit, which was only found in 1996, and the Truong Son muntjac, a small deer that was identified in 1997. Both are extremely rare. We know so little about them that the International Union for Conversation of Nature classifies them as “data deficient”. The rabbit had never been seen in that particular area, even though camera-traps had snapped photos of the forest’s residents for more than 2,000 nights. And the muntjac is still only known from its skull—a living specimen has never been seen by Western scientists.

And yet, just by collecting 25 leeches, Gilbert had uncovered clear evidence that both animals were alive, roaming the forests, and getting drained by parasites. His leeches had also recently sucked the secretive Chinese ferret-badger and the Chinese serow, a rare goat-like creature whose populations are falling. Perhaps other leeches will reveal the presence of the soala or ‘Asian unicorn’—an antelope that was described in 1992 but has rarely been seen alive.

The mountainous forests of the Annamite region are a treasure trove of undiscovered life. Including the rabbit and muntjac, five new mammals have recently been discovered here. But once found, they are hard to find again. The terrain is dense, rugged and humid, and many of the remaining mammals are understandably wary of humans.

Leeches could provide and easy way to assess what’s living in these forests and others. They’re found in fewer parts of the world than Calvignac-Spencer’s flies, but they preserve DNA in their stomachs for a lot longer—at least four months, according to Gilbert. They’re also keen on human blood, which makes them extremely easy to collect—just walk through the forest and get ready to remove them from your limbs and clothes. As Gilbert says, “Unlike camera trapping and dung-searches, leech data collection is simple, inexpensive and can be conducted by untrained personnel.”

A world of genetic litter

These techniques are just the tip of the iceberg. Throughout their lives, animals spread genetic litter throughout their surroundings, and this so-called environmental DNA (eDNA) is a boon to scientists. So far, groups have used eDNA to discern the presence of: bullfrogs in French ponds; frogs and giant salamanders in fast-moving mountain streams, invasive carp in American canals and lakes; and fish, whales and dolphins in Danish seas.

They have identified whales from DNA in skin that gets sloughed off while diving; large mammals like elephants and antelopes from DNA in the earth beneath their feet; and earthworms from DNA in the soil that they burrow through.

So, if an antelope falls in a forest, it doesn’t matter if there’s no one around. Its DNA inches through the undergrowth in the body of an engorged leech. It falls to the ground in pats of faeces. It zooms through the air in the guts of a well-fed flesh fly.

Animals aren’t just localised sacks of skin-bound flesh. They also cast a vast genetic shadow upon their environment, one that scientists are learning how to spot.

References: Calvignac-Spencer, Merkel, Kutzner, Kuhl, Boesch, Kappeler, Metzger, Schubert & Leendertz. 2013. Carrion fly-derived DNA as a tool for comprehensive and cost-effective assessment of mammalian biodiversity. Molecular Ecology http://dx.doi.org/10.1111/mec.12183

Schnell, Thomsen, Wilkinson, Rasmussen, Jensen, Willerslev, Bertelsen & Gilbert. 2012. Screening mammal biodiversity using DNA from leeches. Current Biology http://dx.doi.org/10.1016/j.cub.2012.02.058

Taberlet, Coissac, Hajibabaei & Rieseberg. 2012. Environmental DNA. Molecular Ecology http://dx.doi.org/10.1111/j.1365-294X.2012.05542.x