Who Has Opposable Thumbs and a Prehensile Tail? This Tree Rat That Few Have Ever Seen

After sequencing the DNA of the world’s only Emmons’s tree rat specimen, museum scientists have returned to the Bornean forest to learn more about the mysterious rodent

For many, the mere mention of rats conjures up images of rodents scurrying around on the ground, darting across city sidewalks and subway tracks at night. But learning about some of the world’s more elusive rats requires a look upward.

A trek through Danum Valley on the island of Borneo in Southeast Asia means navigating through twisted and mossy vines, with a dense canopy close to the trail in some places and trees hundreds of feet tall in others. The tropical forest is full of highly protected biodiversity, and its rich vegetation conceals a mysterious tree-dwelling rodent.

“It’s the perfect place to have a little nest if you are an arboreal rat,” said research zoologist Melissa Hawkins, the curator of mammals at the National Museum of Natural History.

Earlier this year, Hawkins and her team completed the first-ever DNA sequencing of the Emmons’s tree rat (Pithecheirops otion), one of Borneo’s rarest species that is documented by only three photographed sightings and one preserved specimen housed in the museum’s collection. The team’s genetic analysis helped them confirm the rat’s placement in its family tree, but that’s just the starting point. They are now collecting environmental samples in Borneo to uncover more about the species.

“Most people want to go to Borneo to study orangutans, but I like to go for these weird little rats that nobody knows anything about,” Hawkins said.

With a prehensile tail and opposable thumbs for gripping, climbing and balancing, the Emmons’s tree rat isn’t like your typical city rat. When Louise Emmons, a longtime researcher at the museum, first captured the rat in 1991, it wrapped its tail around a tree branch, demonstrating its ease among the trees. Emmons described it not only as a new species, but as the sole member of an entirely new genus, Pithecheirops. Emmons hypothesized that the new rodent was most closely related to other Southeast Asian tree rats in the genus Pithecheir.

By sequencing the specimen’s DNA, Hawkins and her team confirmed that Emmons was correct about the species’s phylogenetic placement [its evolutionary relationship to other organisms]. Because the specimen is the only representative of the species in existence, Hawkins was extra careful when taking samples from it to analyze. She took four samples from the rat: a skin sample, a bone sample from the foot, a piece of intestine to attempt to analyze its diet and a bit of muscle and cartilage left on its skull that scientists affectionately refer to as “crusties”.

Each sample gave her a different window through which to study the rat. “I always say a single specimen is actually an ecosystem, and you can use it to zoom into different scales and ask a lot of questions,” she said. 

Thanks to the extensive collections at the museum, she was also able to take samples from specimens in the Emmons’s tree rat’s sister genus, Pithecheir, to compare the DNA of the two groups. But besides the rat’s genetics and clear arboreal nature, little else is known about it — such as its conservation status, preferred habitat and geographical range.

"We don’t see what we don’t look for and we can’t conserve things we don’t know about.”
— Melissa Hawkins, Curator of Mammals at NMNH

To learn more, Hawkins and her team returned to Borneo this past April and placed environmental filters in the forest consisting of pieces of household filter paper stretched across plastic embroidery loops. Despite their rudimentary appearance, the filters could be a powerful tool to study lesser-known species by capturing bits of DNA floating in the air.

Hawkins is testing out the filters to see if they work well in the rainforest environment. When she takes the filters back to the laboratory for analysis, she’ll search them for evidence of Emmons’s tree rat DNA — something she wouldn’t be able to do if she hadn’t already confirmed the rat’s DNA sequence.

Hawkins also hopes to improve the environmental DNA sampling technique so that it can be used to study how other understudied mammals in Southeast Asia move through habitats, ultimately advancing conservation efforts.

“We don’t see what we don’t look for,” she said, “and we can’t conserve things we don’t know about.”

Ashley D'Souza | Read More

Ashley D’Souza is a science writing intern at the Smithsonian’s National Museum of Natural History, where they cover natural history research and collections news for the museum’s blog, Smithsonian Voices. Ashley is currently completing their master’s degree in science writing at MIT, where they write about any and all things wildlife. They also run the blog and YouTube channel, Confessions of a Bird Freak. In their free time, Ashley can be found wandering through the woods with their camera and binoculars and talking to trees and birds. See more of Ashley’s work at https://ashleydsouza.contently.com/ and https://confessionsofabirdfreak.com/.