Crocking the Genetic Code

Nature

Conservationists trying to save the critically endangered Siamese crocodile (Crocodylus siamensis) face a unique challenge.

Only about 1,000 of these relatively small, heavily poached crocodiles remain in the wild, where their populations are scattered between several Southeast Asian countries. Cambodia, the country with the most Siamese crocodiles, only has about 250 adults, all of which live in small, isolated populations of 50 or fewer individuals. Recent research has shown that very few of these groups are actively reproducing.

Even as the wild population disappears, hundreds of thousands of Siamese crocodiles—perhaps more than a million—can be found on farms in Southeast Asia, where their soft skin is harvested as a valuable commodity. Tapping into this plentiful supply of captive animals could, in theory, help to save the wild crocodiles from completely disappearing.

There’s just one problem, and it’s a doozy. For years now, the captive crocs have been considered useless for conservation purposes because they’re all thought to be hybrids of Siamese, saltwater and even Cuban crocodiles.

According to anecdotal knowledge of the industry, the two non-native species were imported and bred with Siamese crocodiles in order to increase their size and growth rates. That was great for commercial interests, but not much good for the species as a whole. Taking any of those hybrids out of captivity and introducing their genes into wild populations “would alter the fate and identity of the species permanently,” says Frank Rheindt, an evolutionary biologist and assistant professor with National University of Singapore.

Here’s the thing, though: What if that common wisdom about the scope of this hybridization isn’t completely correct?

For several years now, researchers have been investigating whether farmed Siamese crocodiles really are all hybrids. One of the first signs that this might not be the case turned up in 2009, when tests conducted on 69 crocodiles at a wildlife rescue center did not find any evidence of hybridization in 35 of the animals, suggesting that they were possibly pure Siamese crocodiles.

Ten years later, a new paper by Rheindt and his colleagues, published in the journal Molecular Ecology, takes this further. The researchers used novel genomic approach (a much more advanced series of tests than were used a decade back) and examined 60 Siamese crocodiles, including some wild-caught individuals that have been on a farm for many years and another group from breeding centers and other farms. The researchers sequenced thousands of genome-wide markers and found evidence of genetic “introgression” (hybridization) from other species, but not to the degree expected. Only six of the individuals tested contained hybrid genetics from saltwater crocodiles, while another two carried unidentified “ghost” genes that the researchers suspect may have come from Cuban crocs.

The results were so good that 12 of the animals tested in the study were released to the wild. Four more pure Siamese crocodiles were selected for captive-breeding efforts.

This is obviously a small study, but it has broad implications. For one thing, it suggests that there may be more purebred Siamese crocodiles on farms than previously believed—perhaps many more.

“I was highly surprised that we found such a limited volume of genetic introgression,” says Rheindt. “It’s heartening to see that estimates of the surviving pool of pure Siamese crocodiles have risen from the hundreds to the tens of thousands as a result of our study.”

Rheindt says they are now talking with their partners about screening crocodile genetics on a larger series of farms in Cambodia. They’ve also been approached to conduct similar studies on another Siamese crocodile population in Indonesia.

There’s actually a tight deadline to start this work, because the same research contains another startling revelation: The remaining wild Cambodian crocs now have such low genetic diversity that they risk possible extinction in just five generations if their situation doesn’t change.

“Five generations is not a lot,” says study coauthor Balaji Chattopadhyay, a population geneticist and research fellow at the National University of Singapore. “When we see such a drastic drop in genetic diversity, it’s not good for any population.” Species with impaired genetic diversity often have problems breeding, become more susceptible to disease and lose the ability to adapt to changing environmental conditions—all threats the Siamese crocodiles could now face over the next few decades.

For Cambodia’s crocodiles, he says, “It’s like an impending doom situation.”

Finding additional healthy, pure specimens on farms and releasing them into breeding wild populations would start to reverse the genetic loss and “slow the train of extinction,” Chattopadhyay says.

How many more crocodiles would need to swim free in Cambodia for that to happen? “For a slowly reproducing and large species such as the Siamese crocodile, ideally we would want to see a Cambodia-wide population in the high hundreds or more to see this species move out of the immediate danger zone of extinction,” Rheindt says. He believes there’s enough remaining habitat left in the country to sustain those higher numbers.

Of course, other threats still exist, including ongoing poaching. Ensuring that relocated crocs aren’t later recaptured for sale to farms would be critical to the success of any reintroductions. Rheindt admits that the “great value of each crocodile individual and the financial incentives for capture” hampers many of the ongoing conservation efforts for the species.

If the techniques from this study end up revealing more pure Siamese crocodiles, it could be the next step in a long road toward the species’ recovery. Chattopadhyay says the government, farms and conservation groups would need to establish policies on the use of farm animals for reintroductions. After that there would need to be field studies to find the best release sites, and then ongoing monitoring to make sure the relocated animals start breeding in the wild.

“They should be monitored for a few generations at least,” he says. “This is a long-term effort.”

While further decisions about the Siamese crocodile are in the works, the researchers hope the new genomic toolkit they developed for this study will be of use for a wide variety of additional species.

“We wanted to propose a methodology that can be adopted by any conservation effort,” Chattopadhyay says. “We believe this kind of genetic component can help a lot for any conservation management effort where you’re looking into reintroduction from captivity.”

In fact, Rheindt reports, they already have work in the pipeline to study the genetics of heavily trafficked species such as pangolins, frogs and birds.

“Here in Southeast Asia, the scale of the environmental crisis is daunting,” Rheindt says. New tools like this might not stop illegal wildlife trade from happening in the first place, but they could help to heal some of the damage it has caused—starting with the Siamese crocodile.

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