DNA forensics to tackle illegal wildlife trade with MinION technology

THE QUESTION

Can the MinION DNA/RNA sequencer technology support conservation authorities in tackling illegal wildlife trade?

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LOCATION: Colombia
SECTOR: Climate & Environment
TECH: Biotech
TIMELINE: September 2022 - Present
PIONEERS: Chabelly Medina, Luis Calzadilla
PARTNER: The Alexander von Humboldt Biological Resources Research Institute

The Challenge

In the climate change context, biodiverse-rich countries, such as Brazil, Colombia, Ecuador, Mexico and Peru play an increasingly important role in biodiversity loss prevention. The Latin American region holds ~40% of the world’s biodiversity, making it appealing for illegal wildlife trade (IWT), and Latin America is home to 25% of the 14,000 species at high risk of extinction. 

Preventing biodiversity loss through fighting IWT activities can strengthen the response of biological communities to fight climate change. One of the roots of this problem is that there is scant scientific evidence on IWT for authorities to act upon. In many cases, confiscated specimens or products remain without a valid taxonomic identity that constrains law enforcement. In other cases, unreliable taxonomic identification prevents specimen relocation to the wild.

The Idea

This initiative aims to use the MinION technology to generate genetic information from IWT specimens and their derived products. This information could then be used by conservation authorities to prevent and tackle IWT, as well as inform the relocation of specimens. In conjunction with utilizing the MinION technology, the project proposes to run a hands-on training addressed to environmental authorities and researchers in Latin America to simulate a field portable laboratory, where DNA sequencing can be run from samples in the field. If successful, it will enable environmental authorities to target this angle of environmental criminal activities with greater accuracy and quicker timeframes.

During the pre-pilot phase, the team sought to answer three questions:

1. Does the MinION technology identify and establish differences between animal species?

2. What stakeholders (research, authorities, policy makers) present in Cali, Colombia, could benefit from the use of MinION technology to tackle IWT?

3. Based on the results from Cali, (i) what is needed to build and maintain a sufficiently comprehensive database?; and (ii) is MinION a cost-effective and replicable methodology for other regions of Colombia?

The Humboldt Institute conducted a workshop in Palmira, Colombia, at the International Center for Tropical Agriculture to test whether the MinION technology could provide the data to identify animal species, and to host a round-table discussion with environmental and conservation stakeholders to gauge their interest in a solution and potential avenues for cross-collaboration employing the MinION. 

The workshop allowed stakeholders to have a realistic outlook on the illegal wildlife trade in Valle del Cauca region, establish a list of the most affected species, test the performance of the MinION technology to generate DNA data to identify species, and provide lessons to engage on a second phase. Stakeholders raised the need to identify species in an accurate way, and that genetic information is a major aid to this task. They also expressed there is an urgent need to identify the geographic origin of the species that are confiscated. While molecular approaches and sequencing technologies remain expensive, participants saw forming strategic partnerships between institutions as a way forward: some of them would have the samples, others the know-how of the technologies, and others the biological expertise of the species. They jointly identified this as a means to unlock resources and be an effective taskforce to inform wildlife management and tackle IWT. At the end of the workshop, attendees shared a priority wishlist of species they would like to focus on should the initiative become a full pilot.

Organisations present at the workshop:

• Departamento Administrativo de Gestión del Medio Ambiente (DAGMA)

• Corporación Autónoma Regional del Valle del Cauca (CVC)

• Fundación Biodess

• Laboratorio de Identificación Genética Forense de la Policía Nacional (DIJIN)

• Universidad del Valle

• Universidad EAFIT

• Universidad del Rosario

• Fundación Cardioinfantil

• Fundación Zoológico de Cali

• Ministerio de Ciencia

• Tecnología e Innovación (Minciencias)

• Wildlife Conservation Society (WCS)

• Alliance of Bioversity International and CIAT

• British Embassy of Colombia

• Instituto Alexander von Humboldt (IAvH).

Key Metrics

• Five species were uploaded in BOLD (Barcode of Life Data System) for the first time;

• Authorities shared a priority list of 9 species to devote future efforts to 

• Authorities and key stakeholders estimate that, given an ideal budget, it would take 5 years at a nationwide level of effort to build a complete and a solid database based on genomic information of illegally traded animals.

What we learned

The MinION technology can identify and differentiate species;

• Authorities see an urgent need to build a database with real-time data on rescued wildlife. 

• A database would help environmental authorities to focus activities and indicate research priorities e.i. distribution models, population dynamics that could be executed by universities.

• Preliminary estimates suggest conducting the same experiment using Sanger technology would have increased the cost significantly, thereby indicating potential savings when using MinION technology;

• The MinION technology should be acquired just before being used for sequencing. This is due to special temperature storage requirements - sealed at 2-8°C up to four weeks. In addition, this means it is key to maintain the cold chain throughout the acquisition process (imports, customs, delivery).

• Authorities believe a collective effort in sourcing technical expertise, equipment and information storage is the only way to ensure a cost-effective strategy using MinION technology to identify, document and build a database to inform authorities on their conservation  efforts and policies.

What happened next?

The learnings from the Discovery Phase have informed the team to narrow-down the scope and focus on carrying out a population stock count on the priority wishlist of species identified at the workshop. Tackling IWT would be a positive externality from the improved data collection and processing procedures in conservation efforts.

The learnings have formed a broader and deeper understanding with the team that permitted them to form a strong case for further funding that has been awarded from the Frontier Tech Hub for the next phase of the work, a Pilot, which is currently underway! To find out more you can watch a short video here:

This pilot is ongoing and key learnings are forthcoming. Stay tuned!

Read more:

Read about the pilot’s findings during the discovery phase in the discovery report here