In 2003, researchers published a paper in PLoS Biology that came to a conclusion often reached by biologists studying unique, island-bound species: Borneo's pygmy elephants - forest-dwelling pachyderms of diminutive stature and timid demeanor - are genetically distinct from other Asian elephant subspecies, and they've evolved for millennia separated from their cousins in Thailand, Burma, and elsewhere. But then the researchers changed their minds.
Since that paper, they've fleshed out an alternate scenario that's decidedly more exotic. Specifically, wildlife biologist Junaidi Payne, based at the World Wide Fund for Nature-Malaysia, and colleagues now suspect that the elephants are remnants of a population believed to be extinct for more than 200 years.
Their theory goes like this: The sultan of Java gifted a few hundred elephants native to the island of Java (now part of Indonesia) to the sultan of Sulu more than 600 years ago. The sultan of Sulu kept the Javan elephants on Jolo island, the capital of Sulu, which is an archipelago that is now part of the Philippines. The elephants were presumed extinct on Java by the end of the 18th century, but the small population sent to Sulu ended up in Borneo, and the six- to seven-foot-tall animals persist there today.
"It's a very appealing theory," says Michael Stuewe, a World Wildlife Federation biologist who studies Borneo's elephants and coauthored the 2003 paper. "If it turns out that [the Javan elephant] really made it in one little corner of Borneo, it would be a remarkable discovery."
The conclusion from the 2003 paper was based on mitochondrial DNA data, which suggested that Borneo's elephants had evolved on the island since the Pleistocene. But there were some nagging issues. "That  paper made the non sequitur conclusion that the Borneo elephants are different from the other elephants of Southeast Asia, and are therefore native to Borneo," admits Payne. "They're clearly different, but that doesn't automatically mean they're native." Moreover, Borneo is essentially devoid of elephant fossils.
Approximately one year ago, Gathorne Gathorne-Hardy, the Earl of Cranbrook, rediscovered a Borneo elephant tooth that Bornean villagers found in a cave and sent to him in the 1970s. "It had been sitting at the bottom of my inbox," says Gathorne-Hardy, who is the honorary curator of mammals at the Sarawak museum. He sent the tooth to researchers at the British Museum of Natural History, who radio-dated it and found that it was not "of any great antiquity." The tooth, one of the very few elephant remains found in Borneo, couldn't have been from the Pleistocene.
Then, Gathorne-Hardy discovered a 1908 account by a Syrian-born American living in the Philippines that, according to Payne, says the ruler of Java sent the Sultan of Sulu a small number of elephants in 1395. Gathorne-Hardy then found other historical accounts from British explorers that placed elephants on Jolo. He shared his findings with Payne.
Benoit Goossens, a Cardiff University conservation geneticist, says that mitochondrial DNA he's collected from Borneo's elephants supports the newest theory. For example, the population appears to contain only one mtDNA haplotype, suggesting that it came from a single female. "If they were there since the Pleistocene, we would expect more matrilineages."