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American Researchers Validate Use of DNA Barcodes in Bushmeat Species

NEW YORK (GenomeWeb News) – In a paper appearing online in Conservation Genetics, American researchers demonstrated that DNA barcoding can distinguish between dozens of wild animal species that are hunted — often illegally — in Africa or South America.

Researchers from the American Museum of Natural History, the University of Colorado, and Barnard College tested a barcode — based on part of a mitochondrial gene — on hundreds of tissue and blood samples from 25 frequently hunted mammals and reptiles. They found that in most cases the barcode could identify and differentiate between species, even turning up cryptic species within some animal groups.

"We wanted to, with this study, demonstrate that even with closely related species, the differences in their barcodes are sufficient that you wouldn't confuse their sequences," senior author George Amato told GenomeWeb Daily News.

Amato, who is director of the American Museum of Natural History's Sackler Institute for Comparative Genomics, also chairs the Consortium of the Barcode of Life committee on conservation.

In the past, wildlife has been harvested primarily at a subsistence level to meet local food needs, Amato explained. But the bushmeat trade has surged in recent years, with wild animal products from Africa, South America, and elsewhere turning up all over the world. Researchers estimate that wildlife-related products are worth somewhere between $5 billion and $15 billion annually, with illegal products contributing as much as $5 billion to $8 billion.

And enforcing wildlife laws, such as those imposed by the Convention on the International Trade of Endangered Species or the US Endangered Species Act, relies on the ability to accurately detect and track animal products — no easy task, since many products are processed, obscuring visible species traits.

Amato and his team decided to test whether they could distinguish between a range of bushmeat species using DNA barcodes. To do this, they tested 204 samples from 25 mammal and reptile species that are hunted for bushmeat, including old world monkeys, alligators, and crocodiles.

Their samples included everything from tissue and blood samples collected in the Republic of Congo to samples collected from live crocodiles in Congo and Gabon to American museum samples and items confiscated by the US Fish and Wildlife Service.

When they generated barcodes using 645 bases of a mitochondrial gene called cytochrome c oxidase subunit 1, or COX1, the researchers found that, for the most part, there was relatively little variation in barcode sequences within each species.

On the other hand, there were enough differences between species to distinguish one from the next: on average, the researchers found nearly 9.8 percent sequence divergence between different species.

"We have shown that the method effectively and unambiguously identifies a large number of species," lead author Mitchell Eaton, who did the research as a graduate student at the University of Colorado, said in a statement.

The barcode could also pick up cryptic species, previously grouped to together. For instance, the team not only confirmed a previously identified genetic split between dwarf crocodiles from Congo and Gabon, but also detected unexpected genetic diversity within a group of forest antelope called a duiker.

Even so, challenges remain. For instance, while the researchers found it relatively straightforward to generate barcode sequence from blood and tissue, obtaining useful sequence from leather was more difficult, due to processing and DNA degradation. Although they could get some useable DNA, Amato explained, these sequences tended to be shorter.

To overcome such problems, the researchers are currently working on a method for generating "mini-barcodes" between 120 and 130 base pairs long, Amato said. By stitching these together, they hope to reconstruct barcodes that are as informative as those from less processed samples.

The researchers are interested in sampling species from other parts of Africa and South America, Amato added. They are also involved in other barcoding research with implications for conservation, including studies of sharks, fresh water turtles, and tortoises, tuna, and parrots.

"We're continuing to expand this," Amato said.

The team plans to submit barcode data from the current study to the Barcode of Life Data System, an online repository of species barcodes that's freely available to other members of the research community.