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DNA barcoding takes on the world

The real power of the fast-growing science of DNA barcoding, according to its supporters, is in describing and cataloguing the 98 percent or so of biological life that has yet to be named.

Researchers have relied on the technique to trace a dead warbler found in the lettuce of a Canadian salad bar back to California. Other scientists have used the strategy to identify China as the true origin for a mouse head unexpectedly starring in a TV dinner and a deadly pufferfish posing as benign monkfish.

DNA barcoding can readily point out birds or mice or fish that don’t belong, just like a Universal Product Code can determine where a sack of flour should or shouldn’t go in a supermarket. But the real power of the fast-growing science, according to its supporters, is in describing and cataloguing the 98 percent or so of biological life on Earth that has yet to be named.

“Two hundred and fifty years after we began the organization of life, we can’t identify the organisms around us,” said Paul Hebert, an evolutionary biologist at the University of Guelph in Canada. If we are to overcome our biological illiteracy before extinction permanently removes our neighbors, he told attendees at last month’s European Science Open Forum in Barcelona, “we need to look for a technology assist, and it is based on DNA barcoding, reading the stream of information underpinning organisms.”

A DNA barcode, or a short standardized sequence that enables researchers to distinguish among many species, works the same way as the 12-number UPC identifies brands of flour or sugar. To systematically sort through the various inhabitants of the natural world, though, Hebert introduced the idea of reading a 650-letter fragment from the front end of a gene encoding the enzyme cytochrome oxidase I, which is shared by virtually all higher organisms. A feather, a scale or a piece of skin can all provide the DNA necessary for an identification, and with it, valuable information about a species’ relative numbers in a given locale, its geographic origins and even its evolutionary age.

In 1758, Swedish biologist Carl Linnaeus introduced his two-part naming system to classify the world’s biological flora and fauna and in so doing launched the field of taxonomy. Since then, about 1.7 million species have been formally described. But with up to 100 million inhabiting the planet and an estimated one-third facing extinction in the coming decades, researchers are scrambling to catalogue Earth’s remarkable biodiversity before much of it disappears.

In the five years since Hebert’s first publication introducing DNA barcoding as a potential boost for taxonomy, the movement has generated plenty of controversy even as it has spawned an alphabet soup of international collaborations and barcoding records representing more than 46,000 species. A proposed 5-year, $150 million multinational effort called the International Barcode of Life Project, or iBOL, could help ramp up the process even more.

An international collaboration
Starting as early as next year, iBOL’s leaders aim to sequence DNA from 5 million specimens representing 500,000 species over a five-year period. Canada, the U.S., China and Europe would be the primary partners, with nearly two dozen other countries participating. Among the project’s specific goals, the alliance would try to obtain DNA barcodes for all known backboned animals, one-fourth of the world’s plants, all disease-causing organisms, and a good representation of the world’s pollinators and polar inhabitants.

Complementary projects would try to obtain DNA barcodes for representatives of every living thing on the Polynesian island of Moorea and in the town of Churchill on northern Canada’s Hudson Bay, nicknamed the “Polar Bear Capital of the World.” The collaborators would also spend about $15 million on new bioinformatics, better positioning the researchers to be able to do once-unheard of science, like collecting a few pounds worth of insects from the Amazon, dumping them all in a blender and creating a sort of bug smoothie, and shortly thereafter acquiring the DNA barcodes from all representative species in the goop.

Another dreamed-of technology that could become a reality in the not-so-distant future and provide greater accessibility in infrastructure-poor locations has been readily likened by Hebert to the fictional tricorder of “Star Trek” fame. The handheld DNA barcoder, Hebert said, will integrate the DNA extraction and sequencing steps for each sampled bug or bird or fish and match the resulting barcode sequence against a reference library of known species.

“Presto, you will gain an identification or a declaration that you’ve encountered something new that is close to species ‘X’ in the reference library,” he said later. “OK, it’s not going to be quite presto — with current analytical approaches, it will take five minutes.”

Even that may be too long for Hebert, who frequently declared at the conference that time is running out for cataloguing and conservation efforts. “This is science that cannot wait,” he told attendees. “We need to do this now.”

Another group called the Consortium for the Barcode of Life, or CBOL, is helping to lead the charge. CBOL, based at the Smithsonian Institute in Washington, D.C., exists primarily to promote DNA barcoding as a new scientific standard, said its executive secretary, David Schindel. Speaking at the conference, Schindel said the consortium now boasts more than 170 members from 50 countries. Borrowing a common refrain from conservationists, he told attendees that species that haven’t been registered or described cannot be protected.

A mixed reception
Not everyone is jumping on the DNA barcoding bandwagon.

Many taxonomists, for example, agree that the gene chosen for differentiating animals is a relatively poor choice for distinguishing among plants and fungi, a point that barcoding supporters concede.

“You have to find a chunk of DNA that varies at the proper level to differentiate things that appear to be similar,” said Fred Hrusa, Senior Plant Taxonomist for the California Department of Food and Agriculture, in a telephone interview.

Hrusa, in fact, blasted the barcoding initiative as a “dangerous threat” to science that ignores how plant populations evolve in complex communities and may further erode support for taxonomy research through its “we know all the answers” mindset. Plants, he said, don’t have the same species barriers as animals and exchange genetic material too often for a method that samples only a handful of specimens to be of any use in distinguishing close relatives.

“DNA barcoding is an attempt to oversimplify a very complex problem,” he said, “and I really think it’s an attempt to put taxonomists out of business.”

Rob DeSalle, curator of invertebrate zoology at the American Museum of Natural History in New York, stressed that barcoding is not a replacement for taxonomy. In an e-mail, he said initially chilly relations between the two groups of scientists have warmed over the last five years as barcoding’s definition has become clearer. “Some taxonomists have found ways to hitch themselves to barcoding proposals and in this context are quite happy with the endeavor.”

As a way of identifying organisms, DeSalle said, barcoding’s main value is in its ability to centralize information and to allow any remains of an animal, plant or other organism to be identified so biodiversity can be regulated and protected (thus helping to enforce bans on exporting rare cats, elephant ivory or tropical birds, for example). In the future, he said, the technique may even help automate the naming and identification of biodiversity around the world.

Pilot projects
In the meantime, a range of collaborations have sprung up to barcode the world’s fruit flies, mosquitoes, birds, butterflies and moths, fish, hardwood trees, and endangered species. South Africa wants to use DNA barcoding to identify agriculture-damaging scale insects, Kenya wants it for safeguarding the commercial fisheries in its Rift Valley lakes, and Brazil would like a more accessible identification system to help protect its vanishing trees.

Buttressing the technique’s growing support, the Food and Drug Administration, Environmental Protection Agency, National Oceanic and Atmospheric Administration and Federal Aviation Administration all have launched pilot projects exploring DNA barcoding as a viable alternative to more traditional species identifications.

For the FAA’s pilot project, CBOL's Schindel said, the technique is being used to identify birds involved with aircraft collisions, a dangerous and costly phenomenon that has spurred officials to gather more information about the types of birds most often involved. “Can we change the habitats around airports to keep the birds out of flight paths of planes?” he said.

The FDA is using barcodes to monitor the problem of seafood mislabeling, like last year’s pufferfish-monkfish switcheroo, which sickened two people who ate fish soup before the case was solved. NOAA and the National Marine Fisheries Service are testing barcoding as a way of enforcing the Endangered Species Act with a joint pilot project in the Gulf of Maine. And the EPA’s pilot project is using DNA barcoding to identify the number and kinds of invertebrate animals living in Maryland streams as part of the agency’s water-quality monitoring activities. DNA barcoding also enabled EPA researchers to confirm the presence of the invasive quagga mussel in Lake Superior — positively identifying one specimen from among over 20,000 mussels.

Documenting biodiversity can be daunting when a country lacks the funding or infrastructure to do so on its own but bans the removal of any specimens beyond its borders. In India, which strictly controls the export of biological material, officials have announced plans for a new barcoding facility that would process samples acquired within the country. In other cases, researchers have negotiated agreements in which specimens are lent to more established foreign labs for DNA analysis in exchange for technological help that promotes self-sufficiency for the lending country. An upcoming workshop will try to set global standards to ensure that no samples are collected illegally.

Eventually, barcoding’s supporters hope, some of the remaining resistance will fade away when they demonstrate the technique’s benefits for applications such as border control and pest eradication. When, for example, should a port’s safety officers require fumigation before allowing in a ship that may harbor disease-carrying mosquitoes?

The answer, Schindel said, depends on the mosquito species — a not-so-simple calculation given the 3,000 known types. The difference, he said, “means using insecticides in large areas or not, so it has large environmental implications.”