The father of all men is 340,000 years old

Albert Perry carried a secret in his DNA: a Y chromosome so distinctive that it reveals new information about the origin of our species. It shows that the last common male ancestor down the paternal line of our species is over twice as old as we thought.

One possible explanation is that hundreds of thousands of years ago, modern and archaic humans in central Africa interbred, adding to known examples of interbreeding – with Neanderthals in the Middle East, and with the enigmatic Denisovans somewhere in southeast Asia.

Perry, recently deceased, was an African-American who lived in South Carolina. A few years ago, one of his female relatives submitted a sample of his DNA to a company called Family Tree DNA for genealogical analysis.

Geneticists can use such samples to work out how we are related to one another. Hundreds of thousands of people have now had their DNA tested. The data from these tests had shown that all men gained their Y chromosome from a common male ancestor. This genetic "Adam" lived between 60,000 and 140,000 years ago.

All men except Perry, that is. When Family Tree DNA's technicians tried to place Perry on the Y-chromosome family tree, they just couldn't. His Y chromosome was like no other so far analysed.

Deeper roots

Michael Hammer, a geneticist at the University of Arizona in Tucson, heard about Perry's unusual Y chromosome and did some further testing. His team's research revealed something extraordinary: Perry did not descend from the genetic Adam. In fact, his Y chromosome was so distinct that his male lineage probably separated from all others about 338,000 years ago.

"The Y-chromosome tree is much older than we thought," says Chris Tyler-Smith at the Wellcome Trust Sanger Institute in Hinxton, UK, who was not involved in the study. He says further work will be needed to confirm exactly how much older.

"It's a cool discovery," says Jon Wilkins of the Ronin Institute in Montclair, New Jersey. "We geneticists have been looking at Y chromosomes about as long as we've been looking at anything. Changing where the root of the Y-chromosome tree is at this point is extremely surprising."

Digging deeper, Hammer's team examined an African database of nearly 6000 Y chromosomes and found similarities between Perry's and those in samples taken from 11 men, all living in one village in Cameroon. This may indicate where in Africa Perry's ancestors hailed from.

Older than humanity

The first anatomically modern human fossils date back only 195,000 years, so Perry's Y chromosome lineage split from the rest of humanity long before our species appeared.

What are the implications? One possibility is that Perry's Y chromosome may have been inherited from an archaic human population that has since gone extinct. If that's the case, then some time within the last 195,000 years, anatomically modern humans interbred with an ancient African human.

There is some supporting evidence for this scenario. In 2011, researchers examined human fossils from a Nigerian site called Iwo Eleru. The fossils showed a strange mix of ancient and modern features, which also suggested interbreeding between modern and archaic humans. "The Cameroon village with an unusual genetic signature is right on the border with Nigeria, and Iwo Eleru is not too far away," says Hammer.

Chris Stringer at the Natural History Museum, London, was involved in the Iwo Eleru analysis, and says the new Y chromosome result highlights the need for more genetic data from modern-day sub-Saharan Africans. "The oldest known fossil humans in both West Africa at Iwo Eleru and Central Africa at Ishango [in Democratic Republic of the Congo] show unexpectedly archaic features, so it certainly looks like we have a more complex scenario for the evolution of modern humans in Africa."

Journal reference: American Journal of Human Genetics, doi.org/kp4