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Portable DNA analysis tool identifies species on site to help combat wildlife crime

  • Distinguishing legally from illegally traded wildlife products using the size, shape and origin of the sample often fails when samples are of young individuals or wildlife parts, such as a teeth, bones, skins, seeds or powders.
  • Rangers, police and port-of-entry officials can now use a portable DNA analysis tool to rapidly identify the species of plant and animal samples found on suspected smugglers.
  • The developers hope the new LifeScanner Lab-In-A-Box system will help officials catch smugglers and better understand transit routes for trafficked wildlife and plant products.

Each year, trafficking in wildlife parts earns international crime syndicates some $8 billion to $10 billion. The illegal timber trade brings in another estimated $7 billion, and illegal fishing $10 billion to $23 billion. The legal trade of these items is worth even more.

Effective enforcement is contingent on police, customs and other officials being able to distinguish animal and plant products that can be traded legally from those that can’t. However, the typical traits that authorities look out for — size, shape, location and behavior —are often insufficient to tell species apart, especially if the samples are young individuals or animal parts, products, and processed samples, such as teeth, bones, skins, tusks, seeds or powders.

Elephant herd in Tanzania. DNA analysis can identify ivory from African elephants, which is shipped illegally to Asia and difficult to distinguish from legally traded Asian elephant ivory. Photo credit: Sue Palminteri

Scientists and trade authorities have increasingly turned to the DNA of traded products to identify the associated species. They typically collect and send a sample of the plant, animal or its product to a laboratory for genetic analysis. Over the last decade, scientists have developed DNA barcoding, a technique that scans a short sequence from a standard part of the organism’s DNA and compares it to a database of sequences to see where it matches. Similar to how a supermarket scanner recognizes products using the black stripes of the Universal Product Code (UPC), DNA barcoding can associate a sample with a particular species for which samples already occur in the reference database.

This technology is cutting-edge but can still take several days to return an answer, which is unfeasible for a real-world setting. Researchers have sought a way for frontline officials to rapidly analyze the DNA of plant or animal parts on-site, using portable equipment, and get a reliable result that can help tackle wildlife and timber trafficking.

Barcoding for Life

The international Barcode of Life (iBOL) initiative has developed a new portable DNA barcoding tool for port-of-entry officials that can identify the species of wildlife samples. The new LifeScanner Lab-In-A-Box portable DNA barcoding kit, presented this past month at the 7th International iBOL conference at Kruger National Park in South Africa, makes rapid species identification possible on site, within a few hours.

Participants at the 7th International iBOL conference in South Africa get hands-on with the LifeScanner Lab-In-A-Box portable DNA analysis tool to rapidly identify the animal and plant species. Photo credit: University of Johannesburg

The iBOL initiative, based at the University of Guelph in Canada, has built and manages a DNA barcode reference library to enable species identification through DNA-based analysis. Launched in 2010, iBOL coordinates scientists in 25 countries that develop both the sequence library and the technology used to identify organisms rapidly and inexpensively through DNA barcoding.

Scientists identify an animal species from a sample of its DNA using a specific gene, known as cytochrome c oxidase 1, or CO1, that they can match against the same gene in a DNA sequence from a known species.

“The [CO1] region is selected as the barcode region because it has the closest concordance to the clusters we call species,” said the Smithsonian Institution’s David Schindel, director of the Consortium for the Barcode of Life (CBOL), which provides outreach for iBOL. “The discontinuity between species corresponds to the discontinuity between DNA sequences.”

CO1 can be compared across individuals within one species as well as across different species. Either comparison requires both an uncontaminated DNA sample from the animal in question and at least one known reference sample against which the gene can be compared.

A reference library for DNA

Officials using the new Lab-In-A-Box system will need access to such reference samples to be able to confirm whether the sample at hand has been illegally obtained or traded. DNA barcoding relies on reference databases, or libraries, for the reference samples that underpin the analysis.

The LifeScanner Lab-In-A-Box, a portable DNA barcoding laboratory, is a new tool to help rangers, police, customs agents and other officials quickly determine whether wildlife samples are endangered, invasive or legally traded. Photo credit: Rob O’Flanagan, University of Guelph

The Lab-In-A-Box connects with the freely available Barcode of Life Data System (BOLD) online data storage and analysis platform. Developed at the Centre for Biodiversity Genomics in Canada, the BOLD database enables users to assemble, manage and analyze DNA barcode data together with information on species form and distribution.

Scientists can store or search the main BOLD data portal containing several types of DNA-related records, including primers, electropherograms, images and DNA sequences. The reference set of DNA sequences allows a user to identify the species associated with a new, unfamiliar sequence. A user can also see maps of sequence sample origins, organize and view records by taxonomic category, share information, and even publish DNA barcode records. You can upload a sequence of DNA to the database, and it returns a species ID if it has that sequence in the database.

As of Dec. 3, BOLD contained 7,958,596 specimens with records of some sort; nearly 6 million specimens with barcodes, representing almost 275,000 known species. The database includes a public access interface where anyone can search through 1.7 million of the records using multiple search criteria. So, for instance, you could search for all the records available for birds (Aves — it uses scientific names) in Vietnam or for just jaguars in Brazil.

Statistics on the size and distribution of DNA data from the BOLD reference library and database, including nearly 6 million barcodes from over 273,000 species Image credit: International Barcode of Life

DNA analysis on the go

The key features of the new Lab-In-A-Box are its portability and the speed with which it can identify the species of a sample found on a suspected smuggler.

To learn more about this system, Mongabay-Wildtech interviewed its creator, Sujeevan Ratnasingham, informatics director at the University of Guelph’s Centre for Biodiversity Genomics and chief architect of the BOLD database.

Mongabay-Wildtech: What advances in barcoding, portability, or both, were needed to make the Lab-In-A-Box possible?

Sujeevan Ratnasingham: A key advance was the miniaturization of sequences, achieved by Oxford Nanopore. In addition, advances in the analysis of mixtures and the multiplexing of multiple samples on a single sequencing run were critical to developing cost-efficient and effective analysis protocols.

How large is the LifeScanner Lab-In-A-Box? Are there conditions (e.g. no internet access) where it cannot be used? 

All the equipment in the lab fits into a small airplane carry-on case. Internet access is beneficial in some cases, but it is designed to operate without internet access. This is achieved by including a mini-server in the kit with software required to do DNA-based species identification as well as the necessary reference library for some applications (e.g. wildlife crime detection).

How quickly can the Lab-In-A-Box identify a sample to species level? How about to genus level (if no sequence matches to species level)?

The Lab-In-A-Box can identify multiple samples concurrently. In fact, it is intended to be used in this manner. It can be used to analyze a batch of samples in six to 10 hours, depending on the application. For example, if a product being tested is extremely processed, more time would be required to extract and read the DNA. An identification is made to genus level if no species-level match is found.

The U.S. Fish and Wildlife Service wildlife forensics lab analyzes investigative evidence of wildlife crime. DNA analysis is uniquely able to help distinguish among similar confiscated wildlife products. Photo credit: US Fish and Wildlife Service

What current and planned Lab-In-A-Box features will best support port authorities in detecting wildlife crime?

Most of the current features are focused on sensitivity and cost. We want to ensure that we have a reasonably low false-negative [i.e. illegal substances aren’t misidentified as legal] and we want to drive down the price for analysis. With regard to future features, we will be focusing on making the solution easier to use.

What’s on the horizon in applying wildlife barcoding technology?

I believe that these advances in detection technologies, like Lab-In-A-Box, in combination with advanced data analysis, will help law enforcement better understand the supply channels used by criminals, a critical step in targeting the organized crime elements of wildlife crime.

LifeScanner and Lab-In-A-Box aim to address the two challenges of rapid detection and successful prosecution, Ratnasingham said in a statement released by the iBOL conference. “It does this by reducing the cost of adopting DNA analysis infrastructure and by simplifying usage of DNA analysis tools.”

Jaguars are categorized as “Near Threatened” under the International Union for the Conservation of Nature (IUCN) Red List. Increasing demand for bones of jaguars, lions, and other big cats, as a substitute for the now-diminished supply of tiger bones for “traditional” Chinese medicine, means this status may decline in the future.  Photo credit: Sue Palminteri