Counting tigers, hidden DNA
The first time I saw a tiger in the wild it was Christmas morning of 1998. I was perched precariously on the back of an elephant, a mode of temporary transportation utilized by the Indian Forest Department to bring observers closer to reclusive tigers in Central India. The male tiger lay basking in the sun a mere 8 feet from me, seemingly indifferent to the presence of the two human-toting elephants that lingered by him, their trunks waving as cameras whirred and clicked.
Fortunately for me, the memory of this encounter has never faded because, despite countless drives through Indian national parks in the years since, I have never seen another tiger in the wild.
Twenty years later, that just might be about to change.
As the Institute for Conservation Research’s newest Bud Heller Fellow, I am embarking on an investigation into the conservation genomics of Sumatran tigers (Panthera tigris sumatrae), the smallest of the six living tiger subspecies found only on the island of Sumatra in Indonesia.
An iconic animal, the tiger symbolizes strength and mystery to many cultures, and is the national animal of no less than four countries. Nevertheless, its populations have plummeted over the last century from a hundred thousand individuals to less than 4,000 tigers left in the wild. On Sumatra, it is expected that not more than 800 tigers remain, with only 2 protected areas with over 25 breeding females each.
But how certain are we of these numbers? How, in fact, do we count tigers?
It might be a little surprising that we still do not have a counting strategy that all scientists and assessors can agree on. This is because, despite being the largest carnivores in their habitats and topping out at as much as 680 pounds, tigers are remarkably elusive and difficult to spot.
Thus, tiger counts are rarely based on direct observations of the animals themselves, but instead are predicted from tiger signs, such as the number of pugmarks observed or how often tigers are detected by hidden cameras.
These estimations tend to be contentious, difficult to apply in a standardized way, and prone to a certain amount of error. Furthermore, counting tigers is a politically charged endeavor, with national reputations and a minimum of US$47 million hanging in the balance - a strong incentive to either shrink numbers to demonstrate a need for further funding or to bloat numbers to demonstrate progress and funds well spent.
My job this year is straightforward (but not simple): Find an accurate and practical way to count wild tigers. I propose to do so using a combination of traditional monitoring methods (for eg. motion-detecting camera-trap grids) and more novel approaches.
In particular, I want to adapt novel genome sequencing technologies to detect individual tigers in the wild using their DNA.
Every living thing on our planet has a genome, which you can think of as containing a DNA fingerprint unique to each organism. Some regions of an animal’s genome are very similar to others within its species, while other regions are distinguishable between individuals.
But most wonderfully (for likeminded conservationists), all of us are constantly shedding DNA as we move through life. In the case of a tiger, these trace amounts are deposited in the soil in which it walks, in the hair it sheds seasonally, in the pungent scent-marks it leaves to mark its territory, in the scat it produces, on the carcasses of prey items it consumes, and even in the water it drinks.
At the same time, the forces of nature - wind, sun, and rain - are continually degrading these tiger DNA traces from the moment they are deposited. Additionally, all the other living things in a forest are similarly shedding DNA continually, making environmental DNA, or eDNA, a simply delightful organic mystery soup left to the likes of me to decode.
But if we collect environmental samples soon after deposition, and isolate tiger DNA from them, I believe we could use this information to create a database of wild Sumatran tiger DNA profiles. Better still, I think we can do this without a single tiger tissue leaving the island of Sumatra.
The first human genome was sequenced for an astounding US$2.7 billion over ~23 years. In 2020, sequencing service providers have developed technologies that bring that cost down to <US$200 per genome. So too has it gone with sequencer size and the complexity of laboratory work. You can now sequence DNA on a portable sequencer that is powered off a laptop, and people have done so in space, under water and pretty much everywhere in between.
Last year, I was able to identify ~500 species in Peru in a single sequencing session, an experience I hope to put to good use in my new position with San Diego Zoo Global.
Our ultimate goal and purpose at the Institute for Conservation Research has always centered on developing practical applications for the conservation of endangered species in the wild. During my Fellowship, I hope to achieve this goal to help assess tiger populations.
After all, you cannot protect an animal you cannot even count.