Closest link to our universal mitochondrial ancestor found

HE DIED later than Socrates and Aristotle, but a man who fished along the coast of southern Africa is the closest genetic match for our common female ancestor yet found.

If you trace back the DNA in the maternally inherited mitochondria within our cells, all humans have a theoretical common ancestor. This woman, known as "mitochondrial Eve", lived between 100,000 and 200,000 years ago in southern Africa. She was not the first human, but every other female lineage eventually had no female offspring, failing to pass on their mitochondrial DNA. As a result, all humans today can trace their mitochondrial DNA back to her.

Within her DNA, and that of her peers, existed almost all the genetic variation we see in contemporary humans. Since Eve's time, different populations of humans have drifted apart genetically, forming the distinct ethnic groups we see today.

Now a skeleton from around 315 BC, not long after the death of Alexander the Great, has been identified as a member of a previously unknown branch on the human family tree. It is the earliest group to diverge from all other modern humans ever identified (). The man was 50 years old when he died, and is the first ancient human from sub-Saharan Africa - the cradle of humanity - to have had its DNA sequenced.

"He belongs to the earliest diverged lineage - the oldest we know of," says Vanessa Hayes of the Garvan Institute in Sydney, Australia, who led the work. She says his ancestors diverged from other humans roughly 150,000 years ago.

How disease sneaked into genomes

There's a lot of information hidden in our genomes, if only we can figure out how to find it. Vanessa Hayes's work on early humans (see main story) may look like anthropology, but she is actually in the field of medical genomics. Her desire to understand the origins of humanity is largely about understanding human disease.

Working at the Garvan Institute in Sydney, Australia, she wants to combine this work with more sequencing of ancient and contemporary genomes, to find the basis of genetic diseases and disease susceptibility. To identify these, we need to go back to the origin, she says.

Ancient genomes can provide a baseline to help us understand modern diseases, Hayes says. It is difficult to hunt for the emergence of disease susceptibility genes in modern genomes alone, because recent travelling and mixing of different genetic lineages obscures this information.

"Prostate cancer is strikingly more common in African Americans [than white Americans]," says David Thomas, a cancer geneticist also at the Garvan Institute. "And the genetic basis of that is really not clear."

He says that by building a detailed evolutionary tree, we can start to find the point in our history at which such variations arose.

"Sampling an early branch is an insight into how populations evolve and have different susceptibility to diseases in our community," says Thomas.

"This is a very exciting paper," says geneticist David Reich at Harvard University. "It is the first old ancient DNA ever to be convincingly extracted from an African context."

The man was found at St Helena Bay in South Africa in 2010 by archaeologist Andrew Smith at the University of Cape Town, and examined by anthropologist Alan Morris at the same university.

Morris discovered that the man was a marine forager. A bony growth in his ear canal - known as "surfers' ear" - revealed he spent a lot of his time in the cold waters of the South Atlantic Ocean, gathering food.

A fisher's life

The "surfers' ear" ailment of mitochondrial Eve's closest known relative (see main story) suggests he spent a lot of time in the water. This adds to evidence of the importance of the marine environment in the success of modern human, says Rebecca Cann of the University of Hawaii at Manoa.

"Archaeologists have argued that exploitation of the marine environment was an essential achievement in the incremental advance of modern human populations," she says. "These resources were important and allowed for exponential population expansion. They are predictable, defendable, nutritious."

"If you are going to move out of a known area, you follow a coastline or a river: You can always work your way back and, you have the refrigerator there at your feet," Cann adds.

But Hans-Peter Uerpmann, an archaeologist at the University of Tübingen in Germany doesn't think this necessarily means that fishing was particularly important in our prehistory.

"Humans are able to adapt to different niches and they did so all the time as a result of changes of environmental conditions," he says. "There is no obvious - or even obligatory - reason to believe that humans went through an 'aquatic phase' during their evolution."

The man was 1.5 metres tall and was buried in a grave with a large number of shells. That is unusual for African hunter-gatherers, who are not known to bury their dead, says Hayes.

By examining the similarities and differences between the man's mitochondrial genome and those of living Africans, Hayes confirmed that the man's group split from Eve's descendants earlier than the two oldest previously known groups, which have been found among living members of the click-speaking southern African peoples known as the Khoisan.

Old genes

"It is, so far, the oldest identified lineage," says Rebecca Cann of the University of Hawaii at Manoa, a geneticist who helped develop the work that led to the idea of mitochondrial Eve.

Although he lived more than 100,000 years after mitochondrial Eve, he provides the closest insight yet into the genetic make-up of the link between all living humans. The DNA he carries is genetically "older" than ours, says Hayes.

Because mitochondrial DNA is inherited only from the mother, geneticists use it to trace how much it has changed over the years and identify branches in human evolution and our spread around the globe. It was part of what convinced scientists that anatomically modern humans originated in Africa.

Even though the specimen is only 2330 years old, other human lineages that were around at this time had diverged more from mitochondrial Eve. Genomes from remains in Europe - even if chronologically much older - have been changed by several large selection events - genetic bottlenecks that wipe out huge amounts of genetic diversity and create new lineages.

The age of the remains suggests that the fisherman lived in the region that is now South Africa before any of the known human migrations back into that area, in particular before the crucial arrival of herding groups from further north some 500 years later.

"We know very little about the more than 100,000 years of history within the continent, despite it being the cradle of mankind," says Wolfgang Haak, a palaeobiologist from the University of Adelaide in Australia.

Haak says this man's mitochondrial genome, especially if we find more like it, will help scientists develop a map of how early modern humans moved around Africa. And sequencing his nuclear genome - the genetic information inherited from both parents - and that of other ancient specimens could give a more complex picture of the way groups mixed with one another.

Hayes is particularly keen to see how the genomes of the earliest African agriculturalists differ from those of hunter-gatherers. "The most significant thing that changed the face of the planet is conversion from hunter-gatherer to farmer," she says. "Where did we start, and how did that change our genome?" She says this genome can provide a reference to which the genomes of herders in the region can be compared.

Hayes is now producing a better map of where early humans moved, using genomes she has sequenced from living people in Africa belonging to early human lineages. Step-by-step, Hayes says, she is homing in on the root of humanity.

This article appeared in print under the headline "Eve's closest relative found"