A new genomic-geospatial analysis approach could help in the global crackdown on pangolin poaching, which is part of an annual trade in illegal wildlife valued at $20 billion, according to INTERPOL.
A pangolin looks like a curious combination of an armadillo, a pinecone, and a baby dinosaur. Pangolins range in size from 10 to 60 pounds and sometimes shuffle upright on their hind feet, although they usually move on all fours. Hundreds of scales made of keratin cover their bodies and keep them safe from all predators—except humans.
The demand for pangolin meat and scales, which are used in traditional medicine across East Asia, has driven Asian pangolin populations to near extinction over the past decade. At the same time, poaching of African pangolins has placed all other species of pangolins in danger, and made Africa’s white-bellied pangolin (Phataginus tricuspis) the most trafficked mammal in the world.
Pinpointing Poaching
Determining where pangolins are being poached has been challenging. Pangolin scales end up in East Asia, where demand is highest, but the animals range widely across sub-Saharan Africa. Typical analysis techniques are not at a scale that law enforcement can use to map poaching hot spots to prioritize efforts, according to Jen Tinsman, a forensic scientist at the US Fish and Wildlife Service’s National Fish and Wildlife Forensics Laboratory and a researcher at the University of California, Los Angeles (UCLA) Center for Tropical Research.
Tinsman and a group of her colleagues at UCLA and elsewhere have gathered genetic data from trafficked pangolin scales to build a new kind of map. This map can identify poaching hot spots within tens of kilometers. The researchers outlined their results in a paper, Genomic analyses reveal poaching hotspots and illegal trade in pangolins from Africa to Asia, that was published in the December 2023 issue of Science.
“We’re getting really fine-scale resolution with where pangolins are coming from in central Africa,” said Tinsman, who began studying the white-bellied pangolin at the institute even before the surge in poaching. The animals, hard to study in their habitats, are difficult to tag due to their size and behavior and don’t do well in captivity.
“We have a really good sense of how many tigers are left in the wild, how many elephants are left in the wild, how many rhinos are left in the wild, other big charismatic things that we see in the trade, but we don’t know how many pangolins are left. It will be so sad if a species like that goes extinct before we can even study them in the wild,” she said.
Tracing an international supply chain depends on a network of partners from across the globe. The project was born out of efforts to track and map pangolin poaching by the Congo Basin Institute, a joint initiative of UCLA and the International Institute of Tropical Agriculture. More than a dozen research organizations and government agencies, including the International Union for Conservation of Nature and the US Fish and Wildlife Service as well as universities in countries, such as China, Gabon, Nigeria, Cameroon, and the Czech Republic, were involved in the project. The idea to map the origins of seized pangolin scales was inspired partially by work done estimating trafficked elephant ivory.
Follow the Birds
The project also depends on a set of techniques first developed for tracking breeding populations of migratory birds. This genomic approach was developed by the UCLA’s Center for Tropical Research Bird Genoscape Project. DNA from a single collected feather is sequenced to identify base pairs unique to each bird. Birds with unique combinations of base pairs tend to be found together and strongly indicate geographically separate populations of species. This allows them to be mapped, creating a genoscape. This genscope shows where migratory birds spend the winter. This is vital to conservation efforts. As of the end of 2023, 15 of the 100 geoscapes planned by the Bird Genoscape Project have been completed.
Like birds, pangolins also migrate—just not on their own. Previous genetic research on pangolin scales looked at mitochondrial DNA. Plot that on a map, Tinsman said, “and you can get, ‘Oh, they’re in West Africa’—so anywhere from Senegal to Ivory Coast maybe.”
Instead, Tinsman and her colleagues (including more than 20 African scientists who are authors on the Science paper) analyzed the animal’s whole genome and built the first range-wide set of genome sequences for pangolins. Shifting from genetics to genomics, “you can just get so much more data, so much finer resolution,” said Tinsman. A lower error level combined with enough samples can provide a good sense of not only where pangolins are being poached, but also where they come from.
To connect confiscated scales to their origins on the map, the team needed to gather samples from white-bellied pangolins near their habitats before they were trafficked. Although some pangolin parts would come from recent tissue specimens from natural history collections, the easiest way to gather samples was to go to local bushmeat markets where hunted pangolins were brought for sale.
Scientists in Nigeria, Gabon, and Cameroon—armed with GPS receivers to geotag their samples—went to local markets. To avoid buying meat, which would support the poaching economy, they ask sellers to give them tongues. “Normally, they don’t care if you ask for the tongue,” said Tinsman. “They want to eat the meat and then sell the scales.”
The team ultimately procured a total of 551 samples of blood, muscle, and scales from across the pangolins’ habitat, from Senegal and West Africa to Zambia and central East Africa. (Some samples had been gathered during a years-long disease surveillance project that ended years before the pandemic.) From these samples, 111 high-quality genome sequences were extracted. By analyzing 96 individual changes to the genome, five distinct population groups strongly associated with distinct geographic areas—from Sierra Leone to the Democratic Republic of the Congo—were identified.
Next, Tinsman and her colleagues began developing a process to quickly and cheaply sequence a pile of hundreds of scales confiscated at ports and markets and donated by the Hong Kong government. Ultimately the researchers analyzed 643 samples of scales, each tagged with a date between 2012 and 2018, a period when pangolin trafficking reached a new peak.
Mapping Shifts in Poaching
Previously, the official seizures database simply indicated Nigerian origins for pangolins that transited through Nigeria. Of all seized animals, 95 percent of seized animals have no recorded source other than Nigeria.
However, the DNA painted a far more detailed—even opposite—picture. When traced to their true source, only 4.2 percent of pangolins that were shipped from Nigeria originated there. While Nigeria is a key hub, most confiscated scales came from two major hot spots: along Cameroon’s southern border with Equatorial Guinea and Gabon, and from western Cameroon, near the border with Nigeria.
When mapped over time, the scales reveal a decade-long shift. In 2012 and 2013, most shipments were from West African pangolins, but over time, researchers documented a shift in intensity and geography as poaching expanded into central Africa to Cameroon, Gabon, and Equatorial Guinea. A remarkably large number of pangolins originated in the border areas between those countries, a multinational area where enforcement is difficult. “It’s shocking that so many pangolins are coming out of such a small geographic area,” said Tinsman.
The DNA contains no clear explanation for the shift, but Tinsman and her colleagues speculate that the trend could reflect a few factors: increased enforcement; declining pangolin populations in West Africa, or traffickers taking advantage of new, more convenient trade routes—or some combination of all three.
They also noted the full scale of the pangolin industry was grossly underestimated. Many shipments are never detected and are estimated to range from 400,000 to 2.7 million African pangolins per year.
The testing process to determine the origin of scales that Tinsman and her team built was also crucial. Eventually the team could analyze scales for $8 per sample and get results delivered in under a week. The project’s goal was to make a quick and simple assay.
Researchers hope maps will help anti-trafficking authorities focus their attention on traffickers. More generally, maps could help capture the public’s attention by instantly illustrating the impact that demand has on faraway—and increasingly connected—ecosystems. “You need a map to understand the whole story,” Tinsman said.
Pangolin Supply Chain
Consider the typical pangolin supply chain. Hunters in countries in central Africa sell an animal to a middleman for around $10, “which is a lot of money for them, but nothing for the middleman,” Tinsman said. Locals will eat or sell the meat, but the scales are dried and gathered into overseas shipments at ports, mostly in Nigeria. They arrive in a port in Southeast Asia, like Hong Kong, Singapore, Malaysia, or Vietnam, before being distributed to markets across the region. To see how scales from poached pangolins move across central Africa, get amassed and shipped, and move to end consumers in Southeast Asia, you need a map.
Tinsman pointed to the construction of the Kribi Deepwater Port in Cameroon, which opened in 2018, as a development that increased poached pangolin traffic. Port construction led to building roads into the forest for timber—and, incidentially, wildlife harvesting. “And it’s really easy to just pop a dead pangolin on a truck with some timber and send it to the port as well and make some money that way,” said Tinman. “So all of this increasing economic activity that’s really good for Cameroon is actually really bad for Cameroon’s biodiversity.”
Tinsman sympathizes with colleagues who jump through all the permitting hoops to legally obtain samples and send them to the West. “I feel very personally attached to pangolins, but it’s got to be a whole other level to work on them, to spend months trying to track one down to get a radio collar on it, and then to have them just completely bulldoze their habitat. That’s got to be hard.”
Nobody Wants Another Pandemic
The demand for African pangolins is a relatively recent phenomenon, largely fueled by the growth of a Chinese middle class in search of traditional medicines. Growing economic ties between China and Africa have likely accelerated the trade. There is no evidence that pangolin scales have anything more than a placebo effect.
Regulations haven’t helped much. In 2016, after years of diplomatic wrangling, pangolins were finally listed in Appendix I of the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES), which extends to them the highest level of protection under an international agreement to regulate the wildlife trade. And yet, despite the ban, approximately 600,000 pangolins were illegally traded between 2016 and 2019 alone.
“We didn’t really see the intended effect, which would be a reduction in the trade of pangolin,” Tinsman said. “It really ramped up to 2019, which was sort of the peak year.”
The locations where pangolins were being killed shifted over the course of two decades from Asia to Africa. According to Tinman, this was an abrupt change in the ecosystem and “we have so little data to project what we think is going to happen. It’s concerning.”
Tinsman emphasized that wildlife trafficking doesn’t just hurt critical animals and the surrounding ecosystem—it also feeds a rise in violence, political instability, and multinational criminal organizations. Trafficking animals is the fourth-most lucrative kind of trafficking, after smuggling humans, guns, and drugs.
“It is these major international criminal syndicates that are involved in this because they already know how to ship stuff illegally,” she said. “It’s not just about the pangolins. These organizations are driving political instability and violence in habitat countries for pangolins.”
Battling wildlife trafficking could also reduce the risk of zoonotic diseases. Pangolins in seized shipments have been found to carry novel severe acute respiratory syndrome (SARS)–related coronaviruses. In the ongoing search for the origins of COVID-19, many analysts implicated a poached pangolin.
“Nobody wants another pandemic,” Tinsman said, “and even if it wasn’t pangolins this time, it could be the next.”
A Global Movement
Given the difficulties of studying pangolins in the wild, genomic-geospatial analysis is giving conservationists a new weapon, and at a moment of urgency. Researchers are digging up more clues in trafficked pangolins. A team of researchers who studied pangolin scales confiscated in Hong Kong in 2012 and 2013 and in Yunnan, China, in 2015 and 2019, found that some samples came from a line of Asian pangolins that belong to a previously unrecognized ninth pangolin species that doesn’t map to any known genetic population using mitochondrial DNA.
A paper on this research was authored by researchers at Kadoorie Farm and Botanic Garden in Hong Kong, another partner in the mapping project. “But we don’t know where the mystery pangolins occur in the wild,” said Tinsman. She hopes that further research and new techniques, such as environmental DNA (eDNA), will offer more answers to these questions.
She looks forward to getting the genomic assays into the hands of the people closest to the pangolins. The biggest problem is figuring out how to get the technology and adequate supplies of chemical reagents to central Africa where pangolins are being harvested. That would save precious time and resources because currently, samples are sent to California for genotyping. However, because pangolins are protected by CITES, Tinsman and her team had to apply for a permit to receive those shipments. The process took 17 months. Export permits were also needed from each country, as well as research permits in Cameroon.
She is encouraged that the technique provides a high level of resolution that will enable mapping in near real time where poaching is happening. “If somebody in Cameroon confiscates a scale, if they were able to do this in their own lab and they send it, it would take less than a week,” said Tinsman.
In 2022, a team from UCLA went to Cameroon to lead what Tinsman hopes will be the first of many local workshops bringing together scientists, conservationists, and people from government and nongovernment organizations to share their findings and demonstrate the limitations and promises of this geospatial-genomics approach.
One of the project’s most encouraging outcomes is that researchers and conservationists are part of a growing global community of pangolin lovers and experts, which includes networks such as the volunteer-run International Union for Conservation of Nature (IUCN) Pangolin Specialist Group. Tinsman sees the glimmers of a budding global movement to conserve pangolins that is long overdue for respect and recognition.
Not Penguins (But Them Too)
“Half the time when I tell people I work on pangolins, they think I’ve said penguins because nobody’s heard of them,” Tinsman said. “And then when I explain them, they’re like, ‘Are you sure you don’t want to work on penguins? Because pangolins are so weird.'”
The new research, she hopes, will help keep them and all their weirdness on the map. “The genomics are cool,” Tinsman said, “but what’s really exciting about this is the momentum that pangolins have. People are finally starting to pay attention.”
