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Barcoding life
Short stretch of DNA sequence is a fast, accurate method for identifying species
BY BETSY HANSON
“For humans, birds are probably the easiest species to identify. They’re big, they’re colored differently, and they sing different songs. Yet even in that easy to identify group, there are hidden species that have been difficult to distinguish,” says Mark Y. Stoeckle, M.D., guest investigator in the Program for the Human Environment at Rockefeller University.
If Stoeckle gets his way, different bird species — in fact, all species of plants and animals — may be as simple to recognize as apples and oranges. Stoeckle, working with scientists at two other institutions, has shown that small stretches of DNA can be read like grocery-store barcodes to identify species.
Taxonomists traditionally have classified organisms on the basis of their physical characteristics. They use DNA too, but current techniques are labor intensive and difficult to compare.
Zoologist Paul Hebert, at the University of Guelph, last year proposed that a short DNA sequence from a gene found in all animals can be used to identify species because in each species the sequence varies slightly. He coined the term DNA barcode for this idea.
The technique depends on analyzing a portion of a gene called cytochrome c oxidase I (COI) that is found in the power sources of cells. Most DNA is found in the nucleus of a cell. Mitochondria, however, the organelles within cells that are responsible for energy production, also contain DNA. Mitochondrial DNA (mtDNA) is known to accumulate mutations three to five times faster than DNA in the nucleus. As a result, the mtDNA of closely related species differs more than the nuclear DNA of those species.
When the researchers analyzed COI sequences from 260 bird species that breed in North America, they found that each had a distinct COI sequence. For 130 of these species, the researchers looked at the DNA of two or more individuals.The variation in sequences between species — even closely related ones — was on average 18 times higher than the variation among individuals within the same species.
In a few cases, however, the scientists found two distinct COI barcodes within the species. In fact, the DNA barcoding technique has led to the discovery of four new species of North American birds. In the case of the solitary sandpiper, eastern meadowlark, marsh wren and warbling vireo, the scientists say there are actually two distinct species where there used to be one.
Based on traditional species identification methods such as morphology and behavior, some taxonomists had already suspected that these species should be split.The DNA barcode data confirmed the suspicions.
“New species won’t be determined by DNA analysis alone,” says Stoeckle, whose results are published in the September 28 issue of Public Library of Science Biology. “Morphology, behavior and vocalization, for example, will still need to be taken into account. But barcoding will enable rapid screening of large numbers of organisms and highlight those that are likely to be new species.”
Beyond the intellectual satisfaction of naming species, DNA barcoding has practical applications. It requires only a small sample of tissue so that wildlife biologists could use it to identify the stomach contents of animals and reconstruct food cycles. Other uses include identifying birds that fly into airplane engines and testing for protected fish species, for example, that sometimes make their way to market. It also works for identifying organisms at different stages of life, such as the eggs and larvae of insects. And it can easily distinguish between species that look alike.
As the cost of DNA sequencing goes down, the scientists envision developing a hand-held device that could be used for species identification in the field.They also picture building a library of barcodes to help taxonomists stay on the same page (see phe.rockefeller.edu/barcodeconference).“The first step toward a library is to show scientifically that a uniform approach can work.Then museums, ecologists and others can adopt it as a standard,” says Stoeckle.

October 15, 2004



 

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