DNA barcodes: Creative new uses span health, fraud, smuggling, history, more

The scientific ability to quickly and accurately identify species through DNA “barcoding” is being embraced and applied by a growing legion of global authorities — from medical and agricultural researchers to police and customs authorities to palaeontologists and others.

Some 350 experts from 50 nations gathering in Mexico for their 3rd global meeting will outline the latest creative applications of DNA barcoding, including projects to sequence ancient plant and animal remains extracted from northern permafrost cores.

Using new techniques to identify species from degraded DNA, the results could reveal how life on Earth responded to global climate change in ages past.

Meanwhile, by analyzing the DNA of gut contents, scientists have started unravelling secrets of what eats what in the animal world.

The International Barcode of Life Project, headquartered in Guelph, Canada, where barcoding was pioneered, will present new research showing that eight bat species feed on over 300 types of insect — one of the largest food webs ever revealed. This extension of DNA barcoding to unravel complex dynamics in the wild is an exciting new research field with important conservation implications.

“DNA barcoding is opening a new window into the relations between hunter and prey in the wild and how diets may be changing due to climate change,” says Scott Miller, Acting Under Secretary for Science at the Smithsonian Institution and Chair of the Consortium for the Barcode of Life (CBOL).

CBOL is co-host of the Mexico City meeting Nov. 7-13 at the Mexican Academy of Sciences with the Instituto Biologia, Universidad Nacional Autonoma de Mexico (UNAM).

Like gut contents, soils contain a mix of species hard to identify using traditional science tools.

“Tiny soil organisms eat each other, roots, and all sorts of plant and animal debris,” says Dr. Miller. “Knowing what eats what is important to many studies, including investigations into how much carbon dioxide and other greenhouse gases are being released from soils into the atmosphere.”

Barcode experts continue to exercise previously demonstrated powers of their relatively young science in myriad ways — amassing information relevant to better agriculture, human health and environmental well-being while uncovering, for example, new instances of consumer fraud and helping to prosecute smugglers of wild bushmeat and other products made from endangered species.

The technology identifies and distinguishes known and unknown species quickly, cheaply, easily and accurately based on a snippet of genetic code.

In animals, the DNA “barcode” is a short region of a gene in the mitochondrion, a structure present outside the nucleus in cells of all multi-cellular animals. In 2003, scientists agreed on a 645 base pair region of the COI gene that mutates quickly enough to distinguish closely-related species but slowly enough that individuals within a species have similar barcodes.

In Mexico, scientists will seal a global agreement on the elusive challenge of how to do likewise reliably with plants, a historic breakthrough that may open the door to global crackdowns on illegal timber trading and better regulation of herbal medicines, among other potential uses.

“Biodiversity scientists are using DNA technology to unravel mysteries, much like detectives use it to solve crimes. It is having a profound impact on our understanding of organisms in nature and how they interact with the environment,” says CBOL Executive Secretary David Schindel.

Barcoding and law enforcement

The sale of wild African bushmeat, including antelope, buffalo, zebra, warthog and wild pig, is an industry estimated to have netted $15 billion worldwide last year. It is also increasing the likelihood of extinction of many rare and endangered species. When smoked or sundried, only DNA barcoding can differentiate bushmeat from domestic animal meat like beef, goat or pork. Dr. George Amato of the American Museum of Natural History in New York has been building the DNA barcode library of endangered species and law enforcement agencies are increasingly asking for his help.

Researchers say the courts of Uganda and Kenya traditionally extend benefit of doubt to the accused, thus barcoding technology could profoundly impact bushmeat prosecutions. They recommend educating magistrates, prosecutors and police on barcoding in wildlife law enforcement, along with development of a bushmeat barcoding manual.

At the Mexico conference, the US Food and Drug Administration, which is responsible for ensuring the safety and accurate labeling of America’s food supply, will describe the particular challenges posed by seafood due to the number of species marketed, the high percentage of imported seafood, and the fact that seafood often is processed “to a point where traditional morphologic species determination is not possible.”

Fraudulent labeling of fish has led to puffer fish poisoning cases in the US.

“New methods that allow accurate and rapid species identifications are critical for both food borne illness investigations and for the prevention of deceptive practices, such as those where species are intentionally mislabeled to circumvent import restrictions or for resale as species of higher value,” according to the FDA.

The FDA is working with experts at various institutions to build a vouchered library of seafood species standards, which will include barcodes.

Another presentation will describe the arrest of a Brazilian man caught smuggling 58 eggs in 2003, who alleged they were quails but airport police suspected they were parrots.

The embryos never hatched and, with no other way to tell, DNA barcoding showed three of the eggs were blue and gold macaws (a vulnerable species, according to IUCN), 51 blue-bellied or yellow-faced Amazon parrots (both near threatened species) and four yellow crowned (listed as a species of least concern).

Barcoding science represents “a significant contribution towards the implementation of the Convention on Biological Diversity,” says CBD Executive Secretary Ahmed Djoglaf. The CBD is a United Nations agreement among 190 countries to stem and reverse the loss of biodiversity.

“I encourage the Consortium for the Barcode of Life to further facilitate the building of systems for the identification and monitoring of endangered species, harmful species such as invasive alien species, and economically and environmentally important species.”

Global barcoding projects to be described at the conference include some of its many health-related applications.

For example, FDA officials will report on a study showing that DNA barcoding reliably distinguished the seedpods of an herb, Star Anise (known scientifically as Illicium verum, used in teas, herbal remedies and cooking) from otherwise identical seedpods of a sister species, Illicium anisatin, considered a health risk due to neurotoxic compounds.

Barcoding projects designed to help contain diseases include:

  • The mosquitos of India, some species of which spread malaria, filariasis, Dengue and Chikungunya fevers, Japanese encephalitis and other diseases affecting millions in India;
  • Black flies of Brazil, Venezuela, Peru, Ecuador and Bolivia, some of which spread river blindness disease. The 70 species barcoded to date represent about 20% of those known to science plus three previously unrecognized species;
  • Freshwater snails of Cameroon’s crater lakes, some suspected of transmiting parasites to humans and livestock;
  • Poplar trees fungus, to identify, evaluate and monitor the distribution and spread of fungal pathogens and generate data useful for disease management decisions; and
  • Parasites of Mexico, including eight new species that attack the lungs of reptiles and an invasive American bullfrog parasite now harming populations of native leopard frogs in the Yucatán Peninsula and Costa Rica. Others being barcoded in Mexico are nematode parasites that attack vertebrate animals ? one of the most lethal agents of diseases affecting crops, humans and livestock.

Scientists worry that changes in climate and the geographic distribution of species can expose new susceptible hosts and spread emerging diseases. One researcher calls the emerging infectious disease crisis today “the tip of an iceberg,” adding that barcoding can help identify and locate potential disease vector species and anticipate the spread of illnesses.

New barcode factories in Mexico, elsewhere

“This work in Mexico and elsewhere is enormously important,” says co-host Patricia Escalante, chair of the Zoology Department, Institute of Biology, UNAM. “Barcoding is a tool to identify species faster, more cheaply, and more precisely than traditional methods.”

Under the auspices of CONACYT, its National Council on Science and Technology Mexico has established a national barcode network (MexBOL) involving 60 researchers from 15 institutions and new “barcode factories” have been created at institutions in the north, center and south of the country: CIBNOR (Centro de Investigaciones Biológicas del Noroeste), IBUNAM (Instituto de Biología, UNAM), and ECOSUR (El Colegio de la Frontera Sur).

The world’s largest barcode factory is in the Biodiversity Institute of Ontario at the University of Guelph in Canada, where DNA barcoding was first proposed and developed. Similar facilities are being created at the French Museum National d’Histoire Naturelle, as well as in the Netherlands and Poland.

The MexBOL network will produce barcodes in all important taxonomic groups including national campaigns, such as barcoding all trees (ArBOL), fungi, bees, aquatic insects, crayfishes, fishes, birds, mammals and more.

“We need an accurate inventory of global biodiversity to recognize parasites of medical, economic or ecological importance,” says Dr. Escalante. This work will help develop biological control measures, monitor and control of human diseases and potential zoonoses, manage agricultural and aquaculture pathogens, and detect the presence of invasive species.”

In a race to document Earth’s diminishing biodiversity, other groundbreaking barcoding projects include:

  • Specimen holdings of the world’s natural history museums, many collected in the 18th and 19th centuries, the DNA sequence of which is essential for validating current taxonomic research. The oldest sample sequenced was the original type specimen of a owlet moth, first described in 1788. Researchers will report that mini-barcodes (130 DNA base pairs instead of 645) can accurate identify many fauna species and may be readily obtained from specimens up to 200 years old;
  • The bees of the world, vital pollinators of crops and flowers: some 10% of roughly 20,000 described species have now been barcoded;
  • Grasses of the world, one of the largest families of plants in the world including humanity’s most important grain crops — wheat, rice, and maize, and many of the world’s most problematic invasive species;
  • Mexican cacti, many species of which are threatened and protected species under pressure from poaching for sales to low water landscaping companies and private collectors;
  • The birds of Argentina (a surprisingly large 573 species identified from 2,087 specimens so far) and Bolivia (a project that has turned up evidence of several “cryptic” bird species: indistinguishable except via genetics);
  • Shore flies of Utah’s Great Salt Lake, an important component of the ecosystem, removing an estimated 90 million kg of organic matter from the lake bottom and an important food source for both resident and migratory birds. In summer, its estimated nearly 1 billion flies inhabit each kilometer of lakeshore. Barcoders have added at least six species, difficult to distinguish otherwise, to the list of two previously known;
  • Land snails of South American forests (Megalobulimus), a source of food since ancient times that has acquired new economic importance due to its cosmetic and nutritional properties. DNA barcodes of the species will help promote their sustainable use;
  • Heliothinae moths of Australia, a group of some 365 species, including some of the world’s most injurious crop pests and serious biosecurity threats;
  • Fishes of India (nearly 1,570 marine species and 650 freshwater species), Mexico (roughly 2,200 marine and over 500 freshwater species) and Russia (122 freshwater species barcoded to date);
  • Freshwater fishes of Canada and the United States, a project that has barcoded over 6,000 specimens from some 750 North American species (85% of the known species from this region). The knowledge offers important clues to freshwater fishes conservation efforts and enhances understanding of their biogeography and evolution;
  • Fish parasites of Canada, a project in which barcoders found (among fewer than half the fish species populating a single river) four times as many diplostomoid parasite species than had been previously known among all freshwater fishes in that country;
  • Marine macroalgae of Canada — organisms impossible to identify using other approaches. With about 5,000 barcodes completed, scientists have uncovered more than 100 overlooked (cryptic) species, including six unique to the Churchill region in the low Arctic, along with presumed invasive species and a new family of red algae discovered in one of the most studied areas of Canada;

Barcodes answer important questions

  • Who owns what: Knowing the source of a biological property can strengthen or weaken indigenous knowledge ownership claims prior to further scientific research and development.
  • Are imports safe: Timely, accurate identification of potentially invasive agricultural pests is key to decisions on whether goods are rejected or cleared for entry at national borders.
  • Are imports legal: Efficient monitoring of trade in CITES-listed tree specimens, unavailable at most ports and borders, is vital for their protection.

Getting schoolchildren involved

Two presentations will describe ways in which schoolchildren can engage in barcoding research.

In the UK, the Natural History Museum, London, has partnered with an educational charity to engage 1000 schoolchildren in ‘Project BarkCode,’ barcoding up to 10,000 UK trees starting in 2010. The project will shed light on the effects of sampling density on DNA barcode performance where the overall number of species is both known and low but where frequent hybridization can lead to identification difficulties. Educational objectives include student participation in ‘real science,’ rather than repeating canned experiments with known outcomes.

In Canada, students nationwide collected fish samples from stores and analyszed the resulting DNA data, revealing significant market “mislabelling” of seafood.

The Barcode of Life Initiative is an international movement that began in 2003 with a publication by Dr. Paul Hebert of the University of Guelph in Canada, in which he proposed DNA barcoding as a technique for identifying species with a standard DNA region. Since then, researchers, research organizations, and users have been developing DNA barcoding as a global standard for species identification. Many of the studies that will be presented at the Mexico City Conference were based on DNA sequences that were processed in the “barcode factory” at the Biodiversity Institute of Ontario (BIO) and are stored and analyzed in BOLD, both at the University of Guelph. BIO is the principal contributor to the 700, 000 records representing 65,000 species already stored in the interactive Barcode of Life Data Systems (BOLD) database. In 2005, there were 33,000 records covering 12,700 species in BOLD, which demonstrates the accelerating rate at which data are accumulating.

For more information: (www.barcodinglife.org/views/taxbrowser_root.php).

The University of Guelph is now leading the International Barcode of Life Project (iBOL) which,a global partnership of scientists from 25 nations working to build a barcode reference library of five million specimens representing 500,000 species by 2015. Many of the research projects that will be presented in Mexico City are becoming part of the global iBOL network.

For more information: (www.ibolproject.org)

The Consortium for the Barcode of Life (CBOL) is an international initiative hosted by the Smithsonian Institution in Washington, DC. With 200 member organizations from 50 countries, CBOL is the principal organizer of the Third International Barcode of Life Conference in Mexico and supports development of DNA barcoding by promoting:

  • Global standards for DNA barcode data and the laboratory protocols used to obtain barcode data;
  • Participation of all countries in BOLI, especially biodiversity rich but under-resourced developing countries;
  • Rapid compilation of high-quality DNA barcode records in a public library of DNA sequences;
  • Opportunities to apply barcoding and barcode data to new areas of biological research;
  • Development of new instruments and processes that will make barcoding cheaper, faster, and more portable;
  • Formation of partnerships and networks of researchers and potential users, and
  • The use of DNA barcoding for the benefit of science and society.

For more information: (http://www.barcoding.si.edu)

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