Koalas are notoriously strange little animals. They’re hyper-specialists, tied to the fragrant eucalyptus groves of Australia, where they somehow make a living off of toxic leaves. They sleep all day; babies eat their mother’s poop; and they succumb to gruesome diseases that don’t seem to affect other animals very badly.

Now, a team of researchers has sequenced the koala genome, finding clues about how the animals survive on eucalyptus leaves, how they sniff out the least toxic leaves, and why they are so susceptible to some diseases like chlamydia.

The number of koalas in most parts of Australia has declined precipitously over the past few decades, as the eucalyptus forests they inhabit have been shaved down to make way for development and devastating diseases spread.

Worldwide search

Rebecca Johnson, a conservation geneticist at the Australian Museum in Sydney and the lead author of the study published today in Nature Genetics, was constantly getting calls from state officials and development companies asking for her advice about how help preserve healthy, genetically diverse koala populations around the country.

What better way to answer these questions than sequencing the animal’s genome? That’s the best information to have “when you’re trying to track and understand genetic diversity in a species,” she says.

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So she rounded up a team of specialists from around the world who slowly assembled the pieces of the genetic puzzle. “It really takes a village to sequence a genome,” Johnson says. “But it’s really not very hard to get people to work on the koala, because they’re very cute.”

Cute, and also very strange. Koalas survive on stringy eucalyptus leaves, which are filled with toxic molecules that render the plant inedible to basically every other living thing. Koalas, though, evolved the ability to flush the toxins out quickly, so they can eat their way through pounds of leaves each day without getting sick.

The leaves contain so few calories, however, that they spend 22 hours of the day resting or sleeping.

Johnson and her team found that the part of the koala genome that codes for detoxifying proteins is about twice as big as in other mammals (or humans). At some point in the deep past, the researchers hypothesize, that section must have accidentally duplicated itself. And once it had doubled, evolutionary pressure could nudge the extra genes in new directions, making the koala’s detox system better and more efficient at clearing out different nasty eucalyptus molecules.

“It’s this coevolving thing,” explains Miriam Shiffman, a researcher now at MIT who studied the way koala’s gut microbiome helps them process eucalyptus. The plants make this “complex cocktail of chemicals” to avoid being eaten, and the koalas evolve better ways to deal with these.

Sniffing toxins

The team also learned something about how koalas pick their food. For years, researchers have watched koalas sniff at leaves and wondered why they chose to eat some but throw others away. They suspected that the koalas were able to somehow sense how toxic or nutritious each leaf was based its smell.

Sure enough, in the parts of the genome that control koalas’ smell organs, they found a lot of extra genes that could help them sniff out subtle scent differences between the different minty, medicinal chemical compounds that give eucalyptus its signature smell.

Koalas are really good at getting rid of poisonous plant molecules, but the system that flushes those out also clears many medicines out of their systems very, very quickly—many times faster than humans. And antibiotics used to treat some diseases mess with their gut microbiome, interfering with their ability to break down eucalyptus leaves, slowly causing them to starve.

This makes it difficult for vets and scientists to treat koalas for diseases like chlamydia, because the medicines scientists would use to treat humans, or even other marsupials, don’t work. Many researchers have spent years trying to develop a vaccine that could prevent koala chlamydia. (Related: As Koalas Suffer From Chlamydia, A New Clue For Treatment)

“All our efforts in the whole koala research community to develop a vaccine... has been limited by the fact that we don’t know enough about their immune system,” says Willa Huston, a microbiologist at the University of Technology Sydney. “Now that we have an understanding of the thousands of genes involved in the immune response, we can use evidence and science to craft a targeted vaccine.”

Koalas also suffer from a retrovirus, similar to HIV, that weakens their immune systems and makes them even more susceptible to diseases like chlamydia or cancer. Sometimes, those retroviruses slip themselves quietly into the genetic code. The researchers found that retroviruses had inserted themselves dozens of times over koalas' evolutionary history, but the sneak-attacks continue today.

At this point, all of the koalas tested in Queensland have some version of the retrovirus. But some of the modern strains are more destructive than the ancient ones. The genome work can help researchers keep track of that strain of the virus, Johnson explains, and give scientists a basis from which to build a better vaccine.

The deep-dive into the genetic code also may help conservationists figure out how to keep some of the fragmented, threatened populations genetically diverse.