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Bar-coding biodiversity

By Stuart Pimm Braga, Portugal–We don’t have names for perhaps 90 percent of all the species on Earth–and even when we do have names for them, we can’t readily identify many of them. In some cases we may encounter only fragments of specimens, making it even more challenging to identify them. A small piece of DNA, however, is enough to provide a ”bar...

By Stuart Pimm

Braga, Portugal–We don’t have names for perhaps 90 percent of all the species on Earth–and even when we do have names for them, we can’t readily identify many of them. In some cases we may encounter only fragments of specimens, making it even more challenging to identify them. A small piece of DNA, however, is enough to provide a ”bar code” that is unique to every species.

2010 is the International Year of Biodiversity. “And how many species are there?” We don’t have an answer!

Science has names for about 1.5 million species, but that’s only a small fraction of the total. We know almost all birds and mammals, and most flowering plants. Scientists and amateurs alike express considerable passion for these species.

For insects, fungi, nematode worms, and the like, not only are most species unknown, but very few scientists know how to identify them. And what we don’t know may hurt us economically–many insects are pests, so we should know who they are. Getting the right parasitic wasp to control that pest may be essential.

In any case, while I can identify a cod or a tilapia with a fish book–that’s only true when I see the whole fish, not a fillet in the supermarket. I won’t eat any fish that isn’t sustainably harvested. Am I getting the right fish with my chips?

Well, every species has unique DNA–but that’s a lot of information to read. Just a small piece of it would do, something that could be easily extracted. That’s the idea behind bar-coding species.

Since I care about how many species there should be, where they are, and what we do to them, I gladly accepted the chance to talk to an international conference on bar coding in Portugal this week. (It also gave me the chance to visit the birthplace, in Oporto, of Prince Henry the Navigator, who invented modern exploration. I’ll blog about that another time.)

Why bar codes for species?

“The idea behind taxonomic bar codes came from the ones familiar on the products we buy,” David Shindel told me.

David is the executive secretary for the Consortium for the Barcode of Life at the Smithsonian Institution in Washington, D.C. It coordinates the various international activities and different projects.

“Paul Hebert, a Canadian geneticist, was at a supermarket checkout, and wondered how many products were in the store, given they could all be diagnosed by a scanner that’s using a 12-digit code. The typical supermarket has about 30,000 ‘species’–that is products.”

“The mathematics of combinations means that a few hundred base pairs of the familiar A,T,C, and G that go into DNA’s genetic code would be enough to uniquely identify the 20 million or perhaps 200 million species that might be out there.”

Once a species has been bar-coded and the sequence put into an online database, one can check a piece of species–say a fish filet–to see if it’s really what it’s supposed to be.

Something smelly about fish

That’s what Bob Hanner, a professor at the University of Guelph has been doing.

“With more than 200 fish biologists around the world, we’ve bar-coded over 50,000 specimens and developed a reference library of over 8,000 species,” Hanner said. 

“With my graduate students and high school students in the USA and Canada, we began to collect fish fillets from the markets and bar-coded them. What was shocking was that one in four was mislabeled. This is a systemic problem, it happens with many different species.

“Every sample of “red snapper” was, in fact, tilapia–a fish that can be readily farmed. That’s market fraud–and nobody likes to be ripped off.

“There are more insidious problems. Sometimes endangered fish are passed off as sustainably harvested fish.”

Hundreds of new species

On a happier note, I also spoke to Sophie Vanmaele of the Museum of Natural History, Paris. Her Master’s work was on a family of small marine snails called Triphorids.

They are small–typically only a few millimetres long (1/4 inch)–very diverse and very poorly known. As such, they help make the case that the diversity of the oceans may be a lot greater than usually accepted–which is what the Census of Marine Life is trying to determine.

Sophie analyzed 20,000 individuals, containing about 500 live specimens. The rest were just the shells. “Of the 20,000 specimens they correspond to 257 morphospecies, of which only one or two are known–and probably all the rest are new species,” she told me.

Morphospecies are simply individuals that look different, based on their morphologies.

Of the 500 specimens, she grouped them into 73 morphospecies. She had analyzed about half of them using bar codes. Morphospecies are uncertain–they could just be different forms of the same species. Sophie’s work was showing that, from the genetic bar codes, they were all different species.

“There are many other places across the Pacific, where there is at least this much diversity, perhaps more,” she said.

What’s in a name?

Linneaus invented the standard two-part name for species some 250 years ago. That name gives access to all the information about the species–it’s metadata, as the bar-coding crowd insist on calling it. But in my closing remarks, I made this suggestion:

“Perhaps it’s time for a better tag–the bar code, perhaps compressed by that computer program than makes tiny URLs out of much longer ones. Traditional taxonomists will take a very long time to name Sophie’s Triphorid snails. Why bother, when the bar code works and its so much easier to obtain.”

In response, I only expect those taxonomists to create a Facebook page of “a million taxonomists who want to burn Stuart Pimm at the stake.” But you read it here first: As these techniques become ever cheaper and faster, the compressed bar code may eventually become the name of choice.

“Mqyzx7a” may lack the elegance of “Lophorina superba,” but for one of the hundreds of thousands of as yet unnamed nematodes, who would care?

Stuart Pimm.jpg

Professor Stuart L. Pimm is a conservation biologist at Duke University, North Carolina. A former member of the National Geographic Committee for Research and Exploration, Pimm is the author of dozens of books and research papers, including the book “The World According to Pimm: A Scientist Audits the Earth.”


 Earlier blog posts by Stuart Pimm>>

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Meet the Author

Author Photo Stuart Pimm
Stuart Pimm is the Doris Duke Chair of Conservation Ecology at the Nicholas School of the Environment at Duke University. He is a world leader in the study of present day extinctions and what we can do to prevent them. Pimm received his BSc degree from Oxford University in 1971 and his Ph.D from New Mexico State University in 1974. Pimm is the author of nearly 300 scientific papers and four books. He is one of the most highly cited environmental scientists. Pimm wrote the highly acclaimed assessment of the human impact to the planet: The World According to Pimm: a Scientist Audits the Earth in 2001. His commitment to the interface between science and policy has led to his testimony to both House and Senate Committees on the re-authorization of the Endangered Species Act. He has served on National Geographic’s Committee for Research and Exploration and currently works with their Big Cats Initiative. In addition to his studies in Africa, Pimm has worked in the wet forests of Colombia, Ecuador and Brazil for decades and is a long-term collaborator of the forest fragmentation project north of Manaus, Brazil. Pimm directs SavingSpecies, a 501c3 non-profit that uses funds for carbon emissions offsets to fund local conservation groups to restore degraded lands in areas of exceptional tropical biodiversity. His international honours include the Tyler Prize for Environmental Achievement (2010), the Dr. A.H. Heineken Prize for Environmental Sciences from the Royal Netherlands Academy of Arts and Sciences (2006).