Tracking Rare Tigers With DNA From Poop

Bengal tigers can be elusive. They're classified as an endangered species, they're mostly nocturnal, and if they had their way, they wouldn't see many humans, either. Native to Southeast Asia, there are only an estimated 1,850 left in the wild. That makes counting them somewhat difficult—but researchers in Nepal have developed a system that they think will make it easier to figure out how many tigers live there. It works for other species as well.
Kashish Das Shrestha
http://sustainablenepal.org/technology-and-the-tiger-dna-study-of-wildlife-in-nepal
Sustainable Nepal
May 3, 2013
A new project uses poop to gather genetic information on rare tigers.
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Sergey Uryadnikov/Shutterstock

National exclusive on the emerging DNA study of wildlife in Nepal. A part of this report has been published in Republica national daily’s weekend edition, The Week, today as Part-One of a two-part series. 

Update: Washington DC based journalist Kate Sheppard of Mother Jones magazine was in Nepal recently. We visited the office of Center for Molecular Dynamics- Nepal together. Her report on the Nepal Tiger Genome Project has also been published. You can read that here

A Tiger mural on the streets of Kathmandu, where the Nepal Tiger Genome Project  is headquartered. All Photos: Kashish Das Shrestha

A Tiger mural on the streets of Kathmandu, where the Nepal Tiger Genome Project is headquartered. All Photos: Kashish Das Shrestha, unless otherwise mentioned.

In 1962, When the Noble Prize in Physiology or Medicine was given for discovering the structure of DNA, the BBC started its report with the following words: “In Stockholm today, five men are receiving Noble prizes. The highest honors that international science has to offer; for work that will eventually lead to the healing of sickness, and the preservation of human life.” James Watson, with Francis Crick, discovered the “structure of life” in 1953. 60years later, DNA has gone well beyond that realm and become an important tool in understanding and conserving the world’s wildlife and ecologies. Here, 2013 will mark Nepal’s completion of its first genome project, the Nepal Tiger Genome Project  (NTGP) conducted in a state-of-the-art laboratory in Kathmandu.

“We collected a lot more shit than planned,” Dibesh Karmacharya, who developed NTGP and is the International Director of Center for Molecular Dynamics-Nepal (CMDN), said light-heartedly of the project that identifies tigers and its habitat based on the DNA information retrieved from tiger feces. After 216 days of collecting 1200 samples of scat (the term used for feces of carnivores) from four national parks by multiple teams, the two-year project funded by USAID-Nepal comes to a close in June. But the crucial chapter of genetic study of wildlife in Nepal is only beginning.

“USAID set up the NTGP as a two year project to build capacity in Nepal to do cutting edge genetic research to inform wildlife conservation,” Bronwyn Llewellyn, Environment Officer, USAID Nepal, explained. “We considered this important because Nepal has a long history of traditional conservation and is ready to bring their efforts to the next level through advanced technology such as genetics.”

Tiger Scat Samples collected for the USAID funded Nepal Tiger Genome Project.

Tiger Scat Samples collected for the USAID funded Nepal Tiger Genome Project.

Nepal Tiger Genome Project 

Nepal is by no means the first country to use DNA to study wildlife. India began its first DNA based enumerations of Tigers in 2007, and the San Diago Zoo Global’s Genome 10K Project is aiming to “assemble a genetic zoo” with a “collection of DNA sequences of 100,000 species” by 2015.

Nepal, however, does not allow any biological samples to be taken out of the country. And this is what makes the current genetics studies in Nepal groundbreaking: simply the fact that these studies can finally be done here in Nepal itself, at the CMDN, established in 2007 as a non-profit making Non-Government Organization. In their 2011 preliminary study of Snow Leopards for WWF, CMDN worked to identify species and gender based on samples originally collected in late 2000s by WWF’s field biologists for a dietary survey.

With the Tiger Genome Project, initiated in collaboration with the Ministry of Forest and Soil Conservation and the Department of National Parks and Wildlife Conservation, and funded by USAID Nepal, CMDN is able to add the final crucial element: fingerprinting of the species identified. In this case, creating a unique ID for individual species that have been identified as a male or female tiger.

 “We are only creating a database of 700 samples, which is what the resources of the project allows us to do,” Dibesh explains. The DNA extraction takes three days, species identification then takes about a week, gender identification takes about three to four days, and finally another three days for “fingerprinting” the sample, i.e. creating a unique ID of that particular Tiger. The team is currently establishing 10 DNA markers on each sample.

Through NTGP, CMDN has also developed a customized software in which each sample’s details are carefully cataloged, accessible instantly by scanning a barcode.

A memer of the CMDN scans a barcode at their lab. This reveals that particular tiger's data on a customized software developed for the Nepal Tiger Genome Project.

A member of the CMDN scans a barcode at their lab. This reveals that particular tiger’s data on a customized software developed for the Nepal Tiger Genome Project.

Indeed, the NTGP offers a long-term capacity for Nepal even after the project ends. The DNA Sequencer, which the USAID funded project of little over $268,000 helped pay for, enables this local service provider to do what could not be done in Nepal before. That is to say, a technology brought in for tigers will serve many in days to come, and already is. CMDN is now also now working with several international researchers, mostly University researchers, who are not able to take their samples out of Nepal.

“We are extremely proud of what CMDN has accomplished in this time frame.  By setting up a lab with this capability, USAID has opened the door for more research as well,” Bronwyn added. “Other donors and projects are now coming to CMDN to work on everything from Rhinos to Snow Leopards. Nepal is becoming known as a leader in the region on genetics research, and we are confident that this ability is going to continue to grow.

Stanford University’s Study

Last week, at an environment-reporting workshop organized by the USAID-funded Hariyo Ban program, Secretary for the Ministry of Forest and Soil Conservation spoke about Nepal’s potential as an international research site. [Disclosure: I was moderating the workshop]

The current emphasis on studying climate change and considering Nepal’s unique topography and ecology, the country is a hub for global research, the Secretary explained.

One such researcher is Professor Elizabeth Hadly of Stanford University, and her team. Prof. Hadly is currently researching the impact of climate change on the Himalayan Pikas.

“We could not have done the work without the collaboration of Dibesh and his team,” Prof. Hadly said over email.

Describing her team’s research, Prof. Hadly said, “ Pikas are unusual mammals closely related to rabbits and hares, but very special because of their occurrence only at high latitudes and high elevations.  They cannot tolerate heat.  And the climate in high elevation tropical areas such as Nepal and northern India is changing at a faster rate than other areas of the world.  Our research team, –[includes Katie Solari (my grad student), Uma Ramakrishnan (my collaborator in India) Nishma Dal (Uma's grad student)] is working on pikas in the Himalayas of Nepal and India for the main reason that they are very speciose there and because the species span a variety of elevations.”

The genetics connection? “Not only have pikas never been studied genetically in Nepal, we aren’t really sure exactly how many species are present in your country!” she added.

The team has also found “pikas do appear to be changing their ranges.  Some of the locals we talked to remarked on the absence of pikas where they used to be common.”

And an exciting development: the study by Uma Ramakrishnan and Nishma Dal have revealed “that there is at least one species in the Himalayas that has never been identified before.”

Illegal Wildlife Trade

Nepal has emerged as a major transit hub for smuggling of all kinds of goods, of which illegal wildlife trade is becoming significant. During last week alone a group of men were caught with a rhino horn in Bardibas Mahottari, an Indian citizen from Utter Pradesh was caught in Kathmandu with leopard hide, two men were also caught with leopard skin in Kathmandu, while police arrested a group smuggling red sandal wood beads in “false compartments” inside fuel tanks of two cars. The product was being moved from India to China, and passing through Kathmandu when found.

Tiger skin confiscated by the Nepal Police. Photo: WWF Nepal/Diwakar Chapagain

Tiger skin confiscated by the Nepal Police. Photo: WWF Nepal/Diwakar Chapagain

“Smugglers don’t care what they are smuggling, they just want to smuggle,” the Director General of the Department of National Parks and Wildlife Conservation had explained at the Earth Matters media workshop last week. “They will trade in wildlife parts, and human smuggling at the same time. And they use technology far advanced than the ones we use, they are better equipped.”

As poachers and smugglers become increasingly sophisticated in their trade, genetics works such as the Tiger Genome Project becomes ever more important.

“One of the exciting potentials of genetics work is in the field of law enforcement. With the dreadful rise in poaching world wide, law enforcement officers need every tool possible to capture and convict wildlife trade criminals. Already we have seen cases of ivory seizures made in Thailand tracked back to the elephant’s home in Africa due to an elephant genetics project,” Bronwyn said. “The NTGP has the potential to do the same for Nepal’s tigers as well. The government of Nepal is testing out this theory now, working with CMDN to use genetics in the case of recent seizures.  We’re a ways from being able to use this data in court, but this is an important first step.”

Indeed, this year the Police and CIB have reached out to CMDN to check the DNA of several confiscated illegal wildlife parts.

Dr. Ghana Shyam Gurung, Conservation Director, WWF Nepal, understands its importance too. “The first thing we will be able to do is check, for example, the tiger parts came from a tiger in Nepal’s parks or not,” he said. “After we run that check, we can tell our partners in India that perhaps it is one of theirs. Or if turns out to be Nepal’s, then we will know exactly where the tiger was based and that will help us figure out what went wrong there in terms of conservation.”

Samples collected for analysis through the Hariyo Ban project, also funded by the USAID.

Samples collected for analysis through Hariyo Ban project, also funded by the USAID.

Shaping Policy

“Conservation relies on genetic work for all sorts of reasons, perhaps the most important, that it allows us to understand just how connected, or disconnected, surviving (or extinct, using ancient DNA) populations are,” Prof. Hadly explained.

Genetics study has many immediate and long-term impacts on conservation policies. For one thing, understanding the genetic diversity of a certain species population in an area is crucial to understanding that group’s survival viability. The larger the genetic pool, the better the chance of their survival. For example, if a group of tigers in western Nepal appear to have limited genetic diversity, conservationists can develop ways in which to introduce tigers from other regions to diversify the population’s gene pool and give them a better chance at survival.

“For Snow Leopards, we are also now working on a more in-depth genetic study to understand how far these animals are traveling,” Dr. Gurung said. “In our eastern Himalayas there isn’t a very large area for them to move around in. But if we find they are traveling across to India in the Kanchenjunga range, for example, then we are able to develop trans-boundary conservation strategies.”

Snow Leopard in Upper Mustang, Nepal. Photo: R. Gurung

Snow Leopard in Upper Mustang, Nepal. Photo: R. Gurung

Limited Resources, Shared Resources

WWF’s study on Snow Leopards and the Standford University’s on Pikas has occurred independently. Yet, the two creatures are intricately linked in the wild naturally, and now for the first time Nepals has an opportunity to understand just how closely they are linked with an unprecedented degree of details.

“Pikas form a significant part of the snow leopard diet! That means that the changing climate and its impacts on the little pika may exert an influence on the snow leopard survival.” Prof. Hadly noted. “Species in ecosystems interact, after all.”

Combining the results of these two independent studies would naturally result in a broader understanding of the Himalayan wildlife ecology, at least as shared by the Snow Leopard and Pikas. But could a conversation amongst those conducting genetic research in Nepal help, by design, to produce studies on corresponding species? Now that the significant Tiger Genome Project has been undertaken, what might be some of the best species to study that could enhance the research on tiger, and who might be able to conduct those studies? Considering the fact that resources are limited, could shared investment in research produce directly related studies to help create genomic databases of certain ecosystems? Perhaps bodies such as the National Trust for Nature Conservation could even produce such proposals and find researchers to work on them, as opposed to waiting for researchers to come in and seek permit.

A similar project for the endangered Rhinos, which shares the tiger’s habitat in the Terai Arc Landscape conservation area, is underway too. These four projects alone give the kind of detailed data of Nepal’s Himalayan and Terai ecology that would have been impossible before a lab like CMDN got the DNA Sequencer for the NTGP.

‘World of the Future’

The CMDN team itself is excited about the possibilities that lie ahead. As they wrap up the NTGP, they are already looking at ways in which to add more value to the data they have found and documented, namely by using elements of GIS and Landsat images to get a broader scope of not just the tigers, but the way in which their population and the human population have interacted over a certain period of time, and how they might moving forward. It is the logical step forward that needs to be taken sooner rather than later.

“I am interested in how animals respond to climate change,” Prof. Hadly said of her own research. “I work in the past, using fossils I excavate from the last 20,000 years or so, to the present, using extant animals I live-trap in the wild, in order to understand how animals will react to our world of the future.”

Nepal is considered to be the 14th most climate vulnerable country in the world. In a race against a rapidly changing global climate, heightened domestic deforestation and forest encroachments, illegal mining, and a bustling illicit wildlife parts trade, there has never been a more crucial time for Nepal to prepare for its world of the future.

May 5, 2013