DNA Sequencing to Save Endangered Species

Since the 1980’s, DNA evidence has been used in the criminal justice system to help convict violent offenders and, just as importantly, exonerate innocent individuals. An approach often used is DNA profiling, a technique where investigators compare the base pair order of DNA found at the crime scene to a suspect’s DNA. Now, another type of genetic analysis – DNA barcoding – is being used to combat illegal wildlife trading.

Illegal wildlife trade is estimated to be right behind drugs and weapons in terms of size and profits, with experts estimating a yearly wildlife black market of $70 billion. Wildlife is sold as exotic pets, trophies and souvenirs, luxury items, religious items, and alternative medicines. High profits and low risks attract transnational criminal syndicates to this business. Because illegal wildlife trading funds and strengthens these criminal networks (networks that are also involved in human, drug, and weapon trafficking) it is considered a threat to global and national security. Wildlife trafficking can also have a long term negative effect on local communities. Finally, there is the very real environmental impact.

Animals and plants that are illegally traded are put under enormous stress. Sadly, endangered species are often targeted because their rarity increases their market value. The decrease/disappearance of these species can affect the health of the entire ecosystem. Accessing these animals provide an additional layer of ecological damage. In 2010, 179 nations came together to form the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES) to combat illegal wildlife trade.

A major challenge in enforcing CITES and other wildlife trade laws is that poachers will often disguise their product. For example bones, horns, and medical plants are often ground into powders before transport. This is where DNA barcoding proves a valuable tool. DNA barcoding uses a combination of genetic, taxonomic, and computational analysis to rapidly identify the species of a confiscated sample. Briefly, DNA is extracted from the confiscated sample and then sequenced at one or more pre-established genetic locations. These sequences are then searched against a database of sequences from voucher specimens. A match between the sample and several voucher specimens allows the sample to be classified down to genus or species.

An example is the 2003 case against Joao Migel Folgosa. Mr. Folgosa was apprehended at the Recife Internal Airport of Brazil when police discovered him hiding 58 eggs under his shirt. Based on egg morphology – and Mr. Folgosa history as an exotic pet trafficker – officials suspected that the eggs were parrot. However, they were unable to specify the species. Because Brazil has 21 endangered parrot species but 83 species overall only limited charges could be brought against him. The case was further weakened by Mr. Folgosa claim that the eggs were from quails.

Twelve years later Dr. Miyaki and colleagues picked up this cold case. They retrieved tissue samples from the 58 eggs/embryos and isolated DNA from each. Then, using a combination of primers, they amplified and sequenced the DNA at two locations in the mitochondrial genome. Finally, they compared their results to publically available records in BOLD (Barcode of Life Data System) and Genbank. Through this process they were able to positively identify 57 of the eggs. All 57 were parrot eggs. More specifically fifty belonged to Alipiopsitta Xanthops (a IUCN vulnerable species), three belonged to Ara ararauna, and four were either Amazona aestiaval or Amazona ochrocephala.

This research illustrates how DNA barcoding could be used to prosecute criminal traffickers. However, the connected case also emphasizes an obstacle that still need to be overcome, making the DNA technology affordable and available to law enforcement in many countries. Many hope that new developments in nanopore sequencing will enable this. Equally important to the use of DNA barcoding in criminal investigations is developing a robust database. This database must (a) have all possible taxa are represented, (b) be readily accessible and searchable, and (c) be able to withstand the scrutiny of a legal investigation. Two organizations working towards these two goals are the Wildlife Crime Tech Challenge and the Barcode of Wildlife Project.

To explore DNA barcoding with your students check out kit #338 – Exploring Plant Diversity with DNA Barcoding.