Fossils are the most reliable way we can piece together the history of humans, but some clues have been inside us all along. The human genome can tell us where we’ve come from, and it’s hiding more than a few surprises. Now researchers from the University of Adelaide have found evidence of two unknown, archaic human species in modern DNA.

Although we won the race to many corners of the world, modern humans weren’t necessarily the first hominins to leave Africa. It’s long been known that more archaic species like Homo heidelbergensis beat us into Asia and Europe, where they eventually split into sub-species like Neanderthals and Denisovans.

By the time Homo sapiens made it into these regions, other species already called it home. What happened next was only natural – humans bred with these other species.

“Each of us carry within ourselves the genetic traces of these past mixing events,” says Dr João Teixeira, first author of the study. “These archaic groups were widespread and genetically diverse, and they survive in each of us. Their story is an integral part of how we came to be.

“For example, all present-day populations show about two percent of Neanderthal ancestry which means that Neanderthal mixing with the ancestors of modern humans occurred soon after they left Africa, probably around 50,000 to 55,000 years ago somewhere in the Middle East.”

The team identified the islands of Southeast Asia as a particular hotbed of this interbreeding, with modern humans cozying up to at least three different archaic species. One of them is the Denisovans, which have previously been identified in the genomes of people of Asian, Melanesian and indigenous Australian descent. But the other two remain unidentified.

The researchers reconstructed migration routes and examined fossil vegetation records, and suggested the likely locations of these two mixing events. The first appears to have occurred around southern Asia, between modern humans and an unknown group the team is calling Extinct Hominin 1.

The second seems to have occurred around East Asia, the Philippines, and Indonesia, with a group dubbed Extinct Hominin 2.

“We knew the story out of Africa wasn’t a simple one, but it seems to be far more complex than we have contemplated,” says Teixeira. “The Island Southeast Asia region was clearly occupied by several archaic human groups, probably living in relative isolation from each other for hundreds of thousands of years before the ancestors of modern humans arrived. The timing also makes it look like the arrival of modern humans was followed quickly by the demise of the archaic human groups in each area.”

This isn’t the first time clues to unknown human species have turned up in our own DNA. A recent study found evidence of a “ghost” species in human saliva samples, DNA from an as-yet-unknown relative was found in the “dark hearts” of our chromosomes, and genetic studies on an Alaskan fossil revealed a previously-unknown population of Native Americans.