Some people still carry the genes of an unknown hominin that our ancient ancestors once intermingled with. 

The family tree of hominins is a real muddle. It’s widely known that Homo sapiens, Neanderthals, and Denisovans all widely interbred with each other on multiple historic occasions. The legacy of that canoodling still lives on today, with up to 3 percent of DNA in modern Europeans and East Asians coming from Neanderthals. Up to 4 percent of DNA in modern Oceania people also comes from Denisovans after the intermingling between Denisovans and early modern humans in Asia. 

However, a new study suggests there’s perhaps another mysterious character that’s found its way into this tangled web of interbreeding. Scientists have discovered that a significant amount of Denisovan genome likely came from an unknown and more distant relative. Furthermore, this DNA may have also been passed down from Denisovans to humans who are alive today.

Reported in the journal PLOS Genetics, researchers at Cornell University sifted through the genomes of two Neanderthals, a Denisovan, and two African humans using a newly developed algorithm.

They found that around 3 percent of the Neanderthal genome came from ancient humans through interbreeding that occurred between 200,000 and 300,000 years ago. Furthermore, they found 1 percent of the Denisovan genome was introduced through breeding with an “unsequenced, but highly diverged, archaic hominin ancestor”. Up to 15 percent of these "super archaic" regions were also subsequently passed from Denisovans to modern humans. 

But the question remains: who was this mystery ancestor? Well, the researchers speculate that it could be Homo erectus, an extinct species of archaic humans that roamed the planet for 2 million years until around 110,000 years ago. This species was most likely one of the first human ancestors to leave Africa, spreading as far as southeast Asia and western Europe. 

However, pointing to H. erectus as the mystery ancestor is only an educated guess at the moment. Researchers have not sequenced the genome of this ancient hominin, so it’s not possible to prove this link with certainty yet. 

"What I think is exciting about this work is that it demonstrates what you can learn about deep human history by jointly reconstructing the full evolutionary history of a collection of sequences from both modern humans and archaic hominins," co-author Adam Siepel from the Cold Spring Harbor Laboratory said in a statement.

"This new algorithm... is able to reach back further in time than any other computational method I've seen. It seems to be especially powerful for detecting ancient introgression."