DNA from flies helps survey mammal species

Who needs drones when you have flies?

Traditional survey methods can be expensive and difficult to conduct, but a team of researchers found studying carrion flies can reveal which mammals live in a given habitat. By catching these insects and sequencing DNA from their guts, researchers in Panama found they could assess what the flies were feeding on to paint a picture of the unseen animals living in the ecosystem.

“It worked well in characterizing the mammal community,” said Torrey Rodgers, first author on the paper published last month in Molecular Ecology Resources. “It performed better than camera trapping or transect counts in terms of number of species detected.”

Carrion flies are a widespread family of insects that feed on decaying flesh and scat. A few years ago, research in Africa showed that extracting DNA from these bugs could shed light on an ecosystem’s poorly studied mammal species. The technique involved analyzing the DNA in individual carrion flies from the carcasses and feces they’d fed off. Scientists compared the genetic sequences one at a time to a library of known DNA barcodes to identify the species the material had come from.

Samples of an animal’s DNA obtained not from its body but from its surroundings, such as from water, air or — in this case — another animal, are referred to as environmental DNA, or eDNA. Rodgers, a research associate with Utah State University, wanted to test the effectiveness of using carrion fly eDNA to detect mammals in a place where the mammal community had already been well described.

On Panama’s Barro Colorado Island, Rodgers collected more than 1,000 carrion flies by baiting them with rotting pork during a month of sampling in 2015. He spent another month in the lab grinding them up, extracting the DNA and using an advanced approach called “metabarcoding” to simultaneously sequence DNA from all the species represented in the genetic soup he was left with.

“Metabarcoding is a way you can sequence DNA from tons of species at once from a single sample that has DNA from many different organisms,” Rodgers said.

Initially used to describe bacterial communities, metabarcoding has only recently been applied to vertebrate species and eDNA, he said.

“We ended up detecting 20 mammal species,” Rodgers said. “We compared this to eight years of visual census and camera trap data and got about 70 percent of those species. This included some rare species only detected a few times with the other techniques.”

Some wildlife the researchers found include four monkey species, two sloth species, ocelots (Leopardus pardalis), kinkajous (Potos flavus), anteaters, peccaries and several rodents, marsupials and bats.

Because carrion flies exist around the globe, this method has the potential to help biologists monitor biodiversity in ecosystems worldwide, Rodgers said.

“Say you have a new nature reserve and want to see how effective conservation in that area is,” he said. “You can collect data using this technique.”

Increasing capacity to quickly generate enormous amounts of data and the declining price of sequencing equipment over the past five years has made metabarcoding a cost-effective alternative to transect surveys and camera traps, Rodgers said.

“Camera traps are expensive and visual transects require expert knowledge of the animal community to make sure you’re getting identifications correct,” he said. “Hopefully, this metabarcoding approach will be a more economical way to survey mammal species.”