Scanning Species

On June 26, 1974, merchandise tracking was revolutionized with a 10-pack of Wrigley’s Juicy Fruit chewing gum. The gum package, today sequestered in the Smithsonian, was the first nationally barcoded item to be scanned at a supermarket checkout (in Troy, Ohio) and the result of a quarter-century-long effort to reduce product information to a little rectangle of stripes that a machine could read instantaneously. The new technology could identify an item anywhere in the country, regardless of its shape or brand.

A group of scientists at Harvard and other universities now think that a version of this system could help keep track of the planet’s biodiversity, too. The Consortium for the Barcode of Life (CBOL), which counts Harvard’s Museum of Comparative Zoology (MCZ) as a member, is promoting a technique known as DNA barcoding to build a database that could identify most species immediately from a short stretch of DNA. Begun in May 2004, CBOL already includes nearly 70 member institutions in more than 30 countries and has begun collecting data for birds and marine fish, which are relatively straightforward to barcode.

Supporters of DNA barcoding say that every species on the planet, like every brand of macaroni, bears a tag distinguishing it from every other species: the DNA found in every cell. That’s not a novel idea in itself. (A similar premise is used to identify individuals whenever a suspect’s DNA is tested against a crime scene.) One of the things that makes barcoding new—and controversial among biologists—is that it aims to make this analysis using less than a single gene. An animal’s “barcode” is the stretch of mitochondrial DNA in the cytochrome c oxidase I (COI) gene, which is among the genes that code for protein.

James Hanken, seen in his laboratory, uses a thermocyler and DNA sequencing equipment in his work on species identification.
Photograph by Jim Harrison

Barcoders have chosen this sequence of about 650 base pairs because it’s easy to isolate, differs significantly among species, and tends to be relatively consistent. Mitochondria also have many more copies of the genetic sequence than do cells’ nuclei, making it easier to obtain the necessary data. (Plants, which have a slower rate of mitochondrial evolution, currently present a problem; researchers hope to use a gene from their chloroplasts instead.) Identifying a species by a fragment of one gene—faster and cheaper than analyzing an entire DNA sequence—resembles distinguishing two novelists on the basis of a single sentence. It isn’t hard to differentiate Faulkner from Hemingway, but what about Wodehouse and Waugh? Yet for those who hope to record the planet’s biodiversity, time is of the essence. Many of the least documented species are also among those vanishing most rapidly, perhaps even before being discovered.

Barcoding’s critics say that closely related species could present misleading obstacles for the technique. Barcoding works only if genetic variation within a given species is significantly less than genetic variation between species. This is not the case among prokaryotic organisms—it currently takes at least six genes to distinguish most bacteria—and it’s sometimes untrue even of more complex life forms. Hybrid species and amphibians, whose genes tend to differ by location, also present barcoding challenges. These concerns, in fact, impelled James Hanken, professor of biology as well as Agassiz professor of zoology and director of the MCZ, to get involved in the project: herpetology, the study of reptiles and amphibians, is his specialty. Three years ago, when barcoding was still in its embryonic stages, he wrote a lengthy critique “of the specific proposal as it was presented,” he says. “But I also felt that the idea that they were proposing—of using a short molecular gene sequence from a particular gene to identify species—actually had merit.”

To his surprise, he was invited to the next symposium on the topic, and then to another, where he suggested barcoding couldn’t succeed without support from the existing community of taxonomists and museums of natural history. “If your ultimate goal is to use barcoding to discover new species, then it had better work to recognize already named species,” he explains. “It should be based, operationally and logistically, in museums and herbaria, because that’s where there’s expertise.” The organization has taken his advice. Hanken, meanwhile, was invited to coordinate what became the formative conference for CBOL, sponsored by the Sloan Foundation. Today he serves on the group’s executive committee (although he plans to step down shortly to make space for more foreign scientists).

CBOL’s motivation in compiling a library of gene sequences is partly democratic and partly economic. The democratic part has to do with giving people like border guards and agricultural specialists, many of whom don’t have extensive taxonomy backgrounds, a tool to help flag possible hazardous organisms. The economic fillip comes from enabling researchers in the field to identify specimens cheaply and within a matter of minutes.

The cost of finding the DNA sequence of a given COI gene is relatively inexpensive—about two dollars a sample—and much faster than shipping off unknown specimens or bringing in specialists. What can be more costly and logistically challenging is getting the DNA sample itself: isolating the gene requires equipment, travel, and expertise. As species’ DNA sequences are collected, they are entered in the Barcode of Life’s database, which holds 36,000 genetic barcodes as of this writing. The database enables researchers collecting beetles in Brazil—or examining specimens in a Cambridge lab—to enter a sequence they’ve derived from a sample and, ideally, pinpoint the species it came from.

Barcoding doesn’t claim to be a taxonomical panacea, though; it’s a tool that might not always be necessary or sufficient. Hanken gives an example: “Say somebody’s walking toward you, dragging an elephant.…You don’t need to sequence it.” Barcoding is useful, according to supporters, for dealing with plants and animals that—like most of the globe’s 1.7 million known species—don’t have two tusks and a gray trunk. “Somebody is digging underground and comes up with a larval insect, which is nondescript, doesn’t have any distinguishing features,” Hanken offers. “At that point, the gene sequence is probably one of the easiest ways to identify it.”

The technique’s strictly genetic approach to identification, in other words, is ideal where visual or behavioral clues are absent or misleading. It may eventually help to identify untagged specimens, in the MCZ and elsewhere, that have puzzled scientists for years. (Because some barcoding will be done from museum specimens, in which aldehyde preservatives may have decomposed DNA material, CBOL researchers are also working with commercial chemical companies to find ways of salvaging preserved genes.) Even so, its proponents say they don’t believe it should replace current taxonomical science. “What barcoding can do is help flag potentially new species—and quickly,” Hanken says. “At that point, though, it requires a specially trained taxonomist to examine the specimen and take into account all of the things used to describe species—morphology, behavior, color, where it’s found.” Barcoding can suggest approximately where on the tree of life a new species belongs, but it can’t point to a particular twig.

Under Hanken’s aegis and with support from a handful of other faculty members, barcoding is slowly becoming the norm in some of the MCZ’s highest-profile research. Hessell professor of biology Naomi Pierce, the MCZ’s curator of Lepidoptera, and Pellegrino University Professor emeritus E.O. Wilson have started barcoding specimens they collect in the course of their work. Professor of biology Brian D. Farrell is incorporating the technique into his work on the Boston Harbor Islands All Taxa Biotic Inventory, which aims to compile a record of all invertebrate life on the islands.

Some hope to get their students involved. “Many high-school students—and certainly undergrads here at Harvard—are using the [DNA sequencing] technique that goes into this barcoding effort,” reports professor of organismic and evolutionary biology Scott V. Edwards, the MCZ’s curator in ornithology, who is helping coordinate a bird-barcoding initiative. “What will be more exciting, I think, is…to obtain feathers, egg-shells, droppings of birds from the field and actually see what species have been there using the barcoding database.” Indeed, barcoding should be ideal for ornithology: birds often have to be tracked by their biological detritus, which contains genetic material. The technique might even be useful for what Edwards calls “forensics.” “When you get air strikes—when a bird hits an airplane—you may end up just with a bag of feathers,” he explains. “Whodunnit, so to speak? Was it Mr. Crow or Mr. Laughing Gull?”

Still, Edwards admits the “actual field logistics”—tracking down and sequencing specimens from all corners of the globe—“could be formidable.” The effort is already underway, though, and he expects that all North American birds will be entered into the database by the time the first workshop of the MCZ’s Barcoding All Birds project, which he is co-organizing, occurs in September. The meeting will officially kick off CBOL’s campaign to amass genetic barcodes for all 10,000 known species of birds. “I think this workshop will be crucial for establishing legitimacy in ornithology,” Edwards says. “We’ve been fortunate to recruit, one, some of the leading ornithological scientists in the country and, two, some of the most skeptical ornithological scientists. And we said, ‘Look, here’s your chance to define the tenor of this project.’”

Hanken says that even though the technique probably won’t produce an infallible gold standard for species identification, he’s optimistic. “These early efforts of barcoding are as much to validate the concept as to keep a file,” he explains. “It remains an open question as to whether barcoding will work on a global scale. That being said, the initial results, as they’re coming in, are very promising.”

Read more articles by: Nathan Heller

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