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DNA Barcoding I: Solving Old and New Problems in Biology

By David Micklos
DNA Learning Center (DNALC), Cold Spring Harbor Laboratory

Paul Hebert, of the University of Guelph, coined the term “DNA barcode” to mean a unique DNA sequence that identifies each living thing in the same way that the unique pattern of bars in a Universal Product Code (UPC) identifies each consumer product. DNA barcoding relies on short, highly variable regions of the mitochondrial and chloroplast genomes.

A region of the chloroplast gene rbcL—RuBisCo large subunit—is used for barcoding plants. The most abundant protein on earth, RuBisCo (ribulose-1,5-bisphosphate carboxylase oxygenase) catalyzes the first step of carbon fixation. A region of the mitochondrial gene COI (cytochrome c oxidase subunit I) is used for barcoding animals. Cytochrome c oxidase is involved in the electron transport phase of respiration. Thus, the genes used in DNA barcoding are involved in the key reactions of life: storing energy in carbohydrates and releasing it to form ATP.

Categorizing life on earth
The International Barcode of Life (iBOL) was launched at meetings held at Cold Spring Harbor Laboratory in 2003 as a megaproject to identify and categorize all life on earth. Today, iBOL organizes collaborators from more than 150 countries to participate in a variety of “campaigns.” These campaigns census diversity among plant and animal groups (including ants, bees, butterflies, fish, birds, mammals, fungi, and flowering plants) and within ecosystems (including the seas, poles, rain forests, kelp forests, and coral reefs).

In fact, we know very little about the diversity of plants and animals—let alone microbes—living in many unique ecosystems on earth. Less than 2 million of the estimated 5 to 50 million plant and animal species have been identified; more than half of known species are insects. Scientists agree that the yearly rate of extinction has increased from about 1 species per million to 100 to 1,000 per million. This means that thousands of plants and animals are potentially lost each year. Most of these have not yet been identified.

Taxonomy, the science of classifying living things, has grown in importance as we monitor the biological effects of global climate change and attempt to preserve species diversity in the face of accelerating habitat destruction. However, classical taxonomy, which categorizes organisms according to physical features, falls short in this race to catalog biological diversity before it disappears.

Barcodes aid in taxonomy and more
In classical taxonomy, discriminating subtle anatomical differences between closely related species requires the subjective judgment of a highly trained specialist, and few are being produced in colleges today. Specimens must also be carefully collected and handled to preserve their distinguishing attributes. In contrast, DNA barcodes allow nonexperts to objectively identify species—even from small, damaged, or industrially processed specimens. DNA barcodes can be quickly processed from thousands of specimens and unambiguously analyzed by computer programs.

The 10-year Census of Marine Life, completed in 2010, provided the first comprehensive list of more than 190,000 marine species and identified 6,000 potentially new species. There is also a surprising level of biological diversity on land, literally in front of our eyes. For example, Hebert’s group used DNA barcodes to show that a well-known skipper butterfly (Astraptes fulgerator), identified in 1775, is actually 10 distinct species.

The DNA differences correlated with striking differences in the coloration of caterpillars and the food plants they exploit. This sort of cryptic, or hidden, diversity is likely common among insects and other organisms with complicated life cycles. The urban environment is also unexpectedly diverse; DNA barcodes were used to catalog 54 species of bees and 24 species of butterflies in New York City community gardens.

DNA barcodes are also used to detect food fraud and products taken from conserved species. Working with researchers from Rockefeller University and the American Museum of Natural History, students from Trinity High School found that 25% of 60 seafood items purchased in New York City grocery stores and restaurants were mislabeled as more expensive species. One mislabeled fish was the Acadian redfish, an endangered species. Another group identified 3 protected whale species as the source of sushi sold in California and Korea. As of this writing, using DNA barcodes to identify potential biological contraband among products seized by customs is still in its infancy.

Stay tuned
In the next article in this series, I’ll introduce a Carolina kit and computer and community resources that make it possible for you and your students to participate in DNA barcoding.

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