The Key to Protecting Life on Earth May Be Barcoding It
An easier way to read DNA is helping scientists tease apart species and ecosystems in nuanced ways
The herbivores that roam the African savannah are massive, and they eat a lot. Yet somehow, they all manage to live in roughly the same place, supported by the same sparsely vegetated environment. In 2013, ecologists wanted to know exactly how this worked. However, because elephants, zebra, buffalo, and impala roam many miles to feed and aren’t fond of nosy humans watching them eat, it was nearly impossible to figure out their diets.
The researchers were left, as they so often are, to scrutinize poop. But the digested plants were impossible to identify by human eyes alone. So for this puzzle, they turned to what was a relatively new genetic technique: DNA barcoding.
Ecologists took samples to the lab and scoured the DNA of the plant remains, looking for one specific gene known as Cytochrome c oxidase I. Due to its location in the cell’s mitochondria, the gene, known as COI for short, has a mutation rate roughly three times that of other forms of DNA. That means it will more distinctly show the genetic differences between even very closely related organisms, making it a useful way to tease apart species in groups from birds to butterflies—like the tag on the inside of your shirt, or a grocery store barcode.
For this ingenious method, aptly referred to as DNA barcoding, we can thank one geneticist who found himself fed up with the “stressful” and time-consuming methods of traditional taxonomy. Paul Hebert, a molecular biologist at the University of Guelph in Canada, recalls one wet, cloudy night that he spent spent collecting insects in a sheet as a postdoctoral researcher in New Guinea.
“When we sorted them morphologically the next day, we realized there were thousands of species that had come in,” Hebert says. Many, as far as he could tell, had never been described by science. “I realized on that one night I’d encountered enough specimens to keep me busy for the rest of my life," he says.
Hebert continues: “It was at that moment that I pretty much … realized that morphological taxonomy couldn’t be the way to register life on our planet." He gave away his specimen collections, and moved on to other research in Arctic evolutionarily biology—the “lowest species diversity habitats I could find,” in his words—but the topic of measuring the Earth’s biodiversity always lingered in the back of his mind.
Technology continued to advance in the mid-1990s, allowing researchers to isolate and analyze smaller and smaller bits of DNA. Hebert, who was working in Australia as a visiting researcher, decided to start “playing around” sequencing the DNA of different organisms and searching for a single sequence that could be easily isolated and used to quickly distinguish species. “I settled upon this one mitochondrial gene region as being effective in many cases,” he says. That was COI.
Hebert decided to test his method in his own backyard, by collecting scores of insects and barcoding them. He found that he could distinguish the bugs easily. “I thought ‘Hey, if it works on 200 species in my backyard why won’t it work on the planet?”
And, with some exceptions, it has.
Using this technique, the researchers in the 2013 savannah study were able to piece together the varied diets of these coexisting animals. "We could tell everything the animals were eating from barcoding their scats," says W. John Kress, botany curator at the Smithsonian's National Museum of Natural History, who collaborated on the study. By informing wildlife managers and scientists exactly what grasses each animal feeds on, these results “could have direct impact on designing new conservation areas for these animals,” Kress says.
It also gave ecologists a bigger picture of how the entire ecosystem works together. "Now you can see how these species are actually coexisting in the savannah," says Kress. Today the very idea of what makes a species is changing, thanks to DNA barcoding and other genetic techniques.
Since the days of Darwin, taxonomists have sifted out species based on what they could observe. I.e. if it looks like a duck, walks like a duck, and sounds like a duck—throw it in the duck pile. The advent of DNA sequencing in the 1980s changed the game. Now, by reading the genetic code that makes an organism what it is, scientists could glean new insights into species’ evolutionary history. However, comparing the millions or billions of base pairs that make up the genome can be an expensive and time-consuming proposition.
With a marker like Cytochrome c oxidase I, you can pinpoint these distinctions faster and more efficiently. Barcoding can tell you in a matter of hours—which is how long it takes to sequence a DNA barcode in a well-equipped molecular biology lab—that two species that look exactly the same on the surface are substantially different on a genetic level. Just last year, scientists in Chile used DNA barcoding to identify a new species of bee that insect researchers had missed for the past 160 years.
Working with Hebert, experts like National Museum of Natural History entomology curator John Burns have been able to distinguish many organisms that were once thought to be the same species. Advances in the technique are now allowing researchers to barcode museum specimens from the 1800s, Burns says, opening the possibility of reclassifying long-settled species definitions. A year after Hebert outlined DNA barcoding, Burns used it himself to identify one such case–a species of butterfly identified in the 1700s that turned out to actually be 10 separate species.
Pinning down murky species definitions has ramifications outside of academia. It can give scientists and lawmakers a better sense of a species' numbers and health, crucial information for protecting them, says Craig Hilton-Taylor, who manages of the International Union for the Conservation of Nature's "Red List." While the organization relies on different groups of experts who can work from different perspectives on how best to define a species, DNA barcoding has helped many of these groups more precisely discriminate between different species.
"We ask them to think about all the new genetic evidence that's coming forward now," Hilton-Taylor says of the IUCN’s procedures today.
While innovative, the original barcoding technique had limitations. For instance, it only worked on animals, not plants because the COI gene didn’t mutate fast enough in plants. In 2007, Kress helped expand Hebert's technique by identifying other genes that mutate similarly rapidly in plants, allowing studies like the savannah one to take place.
Kress recalls how, starting in 2008, he and a former colleague of his, University of Connecticut ecologist Carlos García-Robledo, used DNA barcoding to compare the various plants that different insect species fed on in the Costa Rican rainforest. They were able to collect insects, grind them up, and quickly sequence the DNA from their guts to determine what they were eating.
Previously, García-Robledo and other scientists would have had to tediously follow insects around and document their diets. “It can take years for a researcher to fully understand the diets of a community of insect herbivores in a tropical rain forest without the help of DNA barcodes,” Garcá-Robledo told Smithsonian Insider in a 2013 interview.
They've since been able to extend that research by looking at how the number of species and their diets differ at different elevations, and how rising temperatures from climate change could impact this as species are forced to move higher and higher. "We've developed a whole, complex network of how insects and plants are interacting, which was impossible to do before," Kress says.
"Suddenly, in a much simpler way, using DNA, we could actually track, quantify and repeat these experiments and understand these things in a much more detailed fashion," he adds. Kress and other researchers are now are also using barcoding to analyze soil samples for the communities of organisms that inhabit them, he says. Barcoding also holds promise for helping to identify remnants of genetic material found in the environment.
"For ecologists," Kress says, "DNA barcoding is really opening up a whole different way of tracking things in habitats where we couldn't track them before.”
By allowing scientists to scrutinize one specific gene instead of having to sequence entire genomes and compare them, Hebert had hoped his method would allow genetic analysis and identification to be performed much more rapidly and cheaply than full sequencing. "The past 14 years have shown that it works much more effectively and it's much simpler to implement than I anticipated," he says now.
But he still sees room for progress. "We're really grappling with inadequate data in terms of species abundance and distribution," Hebert says of conservationists now. Rapidly improving technology to analyze DNA samples faster and with less material required paired with DNA barcoding offers a way out, Hebert says, with modern scanners already able to read hundreds of millions of base pairs in hours, compared to the thousands of base pairs that could be read in that same time by earlier technology.
Hebert envisions a future where DNA is collected and sequenced automatically from sensors around the world, allowing conservationists and taxonomists to access vast amounts of data on the health and distribution of various species. He’s working now to organize a worldwide library of DNA barcodes that scientists can use to quickly identify an unknown specimen—something like a real-life Pokedex.
“How would you predict climate change if you were reading temperature at one point on the planet or one day a year?” Hebert points out. “If we're going to get serious about biodiversity conservation we just have to completely shift our views about the amount of monitoring that's going to be required.”