DNA analysis of soil from paw prints could help save Sumatra’s tigers

By Katie Hunt, CNN

Dr. Mrinalini Watsa, a researcher at San Diego Zoo Wildlife Alliance in California, scoops up soil from a fresh paw print made by Rakan, a 4-year-old male Sumatran tiger who lives at the San Diego Zoo Safari Park, and secures it in a specimen jar.

Back in her lab, Watsa analyzes the sample using a small electrophoresis device that’s connected to a smartphone. Jackpot. She’s able to detect Rakan’s DNA in the soil.

The proof of concept experiment is part of her work adapting existing genome-sequencing technology so it can be easily used to detect individual tigers in the wild using their DNA. Watsa hopes the application will make it easier to track Rakan’s wild counterparts in Sumatra, Indonesia’s biggest island, and tiger populations across the rest of Asia.

“Now, instead of saying we’ve seen about 40 prints in this 3-kilometer-square (1.8-mile-square) area, actually you can see those 40 prints come down to four tigers and that gives us so much more power in terms of how we go about counting them,” she said in the latest episode of CNN Original Series “This Is Life with Lisa Ling.”

All living organisms, including humans, shed genetic material into the environment when they excrete waste, bleed, or shed skin or fur.

Conservation scientists are increasingly making use of this environmental DNA — whether it’s in soil, water, snow or even air — to gather information about particular species or ecosystems. It can alert scientists to the effects of the climate crisis or the existence of harmful pathogens, and help them track animal populations.

In her experiments to date, Watsa has been able to detect Sumatran tiger DNA in soil and determine the sex of the animal. Watsa wants to refine her approach so she can identify individual tigers before testing it in the field.

Success story?

Tiger numbers have increased 40% in seven years, from 3,200 in 2015 to 4,500 in 2022, according to the latest estimates released in July by the International Union for Conservation of Nature.

This promising population growth has been hailed as a conservation success story, but Watsa and other tiger experts say it’s not mission accomplished. Tigers still hold endangered status on the IUCN Red List of Endangered Species and are a fraction of the 100,000-strong population that roamed Asia at the beginning of the 20th century.

Plus, the headline figures mask a more nuanced picture.

Tiger populations are growing in some places in India and Nepal, but the big cats are clawing out a much more fragile existence in Southeast Asia. Tigers have been extinct in Vietnam, Cambodia and Laos since 2000 and are teetering on the brink in Malaysia. In Sumatra, where Watsa’s work is focused, it’s thought that fewer than 800 tigers remain, with only two protected areas containing more than 25 breeding female tigers.

What’s more, it’s not clear to what degree the detected increase in numbers is down to intensified and improved tracking techniques or actual population increases. Tiger counts are rarely based on direct sightings; instead, population numbers are inferred from tracks or pugmarks, or how often tigers are detected by hidden cameras.

“It’s a cautious optimism. Tiger numbers are better known than they’ve ever been. More than a rebound, I’d say it’s a much more accurate estimate,” said Abishek Harihar, the deputy director of the tiger program at big cat conservation group Panthera.

“A lot of so called increases are more to do with better estimation methods,” he added.

For example, Harihar said that India, which accounts for about 64% of the world’s wild tiger population, conducts a survey every four years — but the area surveyed has increased over the past 12 years, making it hard to truly understand population trends.

Population monitoring in India is typically done using camera traps, Harihar added. He believes DNA techniques could help scientists better understand how some tigers disperse between different areas, which can be hard to pick up with cameras.

“It’s good to understand where the different tigers come from and then we can secure these dispersal routes,” he added. “DNA techniques will also be useful where camera trapping is difficult,” he added, such as the remote, mountainous regions in Southeast Asia.

Watsa belives the techniques she is pioneering will overcome some of the weaknesses of camera-based monitoring.

“The camera is only looking at a very small radius around it, so an animal could walk just outside of that and it would be missed entirely. This means they have a massive margin of error,” she said.

In developing techniques that are more cost effective and easy to use, Watsa is aiming for more accurate tiger population numbers.

Tiger trade

Watsa also has hopes her portable DNA analysis techniques could be used for forensic investigation. The biggest threat to tigers today is poaching and trade in their body parts, which are prized for traditional medicine in places like China.

Tigers only occupy 45% of the 2.1 million square kilometers (1.3 million square miles) of remaining tiger habitat that still exists in South Asia and East Asia, an indication of the magnitude of poaching, Harihar said.

Analysis of DNA samples from confiscated skins, bones and animals could help identify tiger populations most at risk from poaching and track down people and organizations involved in the illegal tiger trade, Watsa said.

Between 2000 and June 2022, there were 2,205 confiscations of tigers and their body parts across 50 different countries, according to Traffic, a group that monitors the illegal wildlife trade. Of these, one-third involved whole tigers, with 665 found alive and 654 found dead.

In the United States, the popular 2020 Netflix documentary “Tiger King” publicized the exploitation of tigers for entertainment. The Big Cat Public Safety Act, a piece of legislation that would set limits on private ownership of tigers and help prevent big cats from entering the illegal animal trade, was passed by the House of Representatives in late July.

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Correction: An earlier version of this story misstated the name of Dr. Mrinalini Watsa’s institutional affiliation and the location where Rakan the tiger lives. Sign up for CNN’s Wonder Theory science newsletter. Explore the universe with news on fascinating discoveries, scientific advancements and more.