Exploring the Cradle of Humanity Reveals Genetic Traces of Extinct Human Species

Here's my column for this week. It also appeared in Monday's Philadelphia Inquirer:

Once DNA evidence made clear that all humanity came from Africa, researchers have been scouring that vast continent in search of a fuller story of our origins. Where in Africa was the cradle of humanity? And how are modern people related to the common ancestor that all humanity shares?

Two groups have recently added surprising new details to the picture by using DNA collected from modern hunter-gatherers - the Pygmies of Cameroon, the Sandawe and Hadza of Tanzania and Khoe-San of southern Africa.

Those studies suggest a new narrative of our human roots. The old story of a single superior group bursting through Africa and beyond is being replaced by a more complicated one that traces our roots to a fractured collection of ethnic groups who periodically interbred across the lines.

“There is a story of multiplicity of populations which is not well understood today,” said anthropologist Jean-Jacques Hublin of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. “There is no sort of magic moment where somebody became like Robert Redford and afterward it was done.”

The evidence of early ethnic divisions was bolstered by a new DNA study of the Khoe-San, published last week in Science. That paper backed earlier studies showing that these light-skinned African hunter-gatherers make up the oldest known ethnic group, branching off from the human family tree in Africa about 100,000 years ago. It’s a split that occurred long before the ancestors of today’s Europeans, Asians, Australians and other non-Africans left the mother continent.

Another striking find came from a University of Pennsylvania-led study released a few weeks ago showing that modern Pygmies, Hadza and Sandawe all shared some unusual, foreign-looking stretches of DNA.

The researchers concluded that ancestors of all these groups interbred with members of a much more distant branch of the family tree – some sort of “archaic” human similar to the Neanderthals. There are no fossil remnants of this mystery group, however.

The intermixing evidence was a surprise, said Penn geneticist Sarah Tishkoff, who led this study along with colleague Joseph Lachance. They were looking for signs of recent human evolution – genetic changes that adapted these very different groups to their unique environments. “Africa is the place of greatest linguistic, cultural and genetic diversity,” she said. “If you want to understand...when, where and how modern humans evolved, you should be looking in Africa.”

By sequencing the entire genomes of a small sample from each group, the Penn-led study found genetic differences that influence smell, taste, immunity, production of fats in breast milks, and even a genetic variant in Pygmies that might account for their short stature. Average height for a Pygmy man is 4’11”.

“Lots of regions of the genome appear to be still under selection and evolving,” Tishkoff said.
Some archaeologists are impressed with the new DNA work. “That is a really interesting paper,” said Arizona State University archaeologist Curtis Marean, referring to the Penn team’s paper, which first appeared in the journal Cell.

The evidence for mixing between “modern” and “archaic” humans follows other studies showing that ancestors of modern Europeans and Asians intermixed with Neanderthals, and ancestors of Pacific Islanders mingled with another archaic group called the Denisovans.

The idea that early Africans also mixed with archaic humans is “not that surprising given what we’ve seen with the Neanderthal genome,” said Arizona State’s Marean. “It shows that…when the modern human lineage arose, it’s not alone on the African continent.”

Whoever propelled these far-off bits of DNA into the modern African population haven’t left behind any distinct fossils – at least none yet found – but there is some fossil evidence that very ancient groups of proto-humans survived in Africa until surprisingly recently, Marean said.
The most surprising is a skull found in Nigeria that looks like a proto-human called Homo heidelbergensis. That group flourished 500,000 years ago and may have been ancestors of Neanderthals. But carbon dating shows this individual lived just 16,000 to 11,000 years ago.
Not that ancient Africans necessarily intermixed with members of this group, said Marean. “But this is evidence that really ancient lineages were hanging around.”

Other clues to our species’ past come from reconstructing past climates in Africa, he said. Between 195,000 and 125,000 years ago, Africa was dry and pockets of people were separated by vast stretches of desert. During that period, the continent appears deserted, said Marean. Then, 120,000 years ago the continent became wetter again and disparate populations grew and started coming together. “Then things got really complicated.”

One of the first things that happened next, he said, was that the Khoe-San broke off, he said. The latest analysis shows surprisingly deep divisions then formed among the Khoe-San, with northern and southern groups separating in Africa around 45,000 years ago. “What we’re seeing is the modern tendency to form groups.”

The evidence for intermixing also reflects a persistent human behavior pattern, he said. When invaders entering someone else’s territory, they attempt to kill the men and children and take the women.

Max Planck’s Hublin said that while the DNA may clearly show this intermixing happened in Africa, he’s not convinced the other group was “archaic” – a term he finds misleading. If we had fossils showing what members of this group looked like, he said, we might classify them as a branch of early modern humans that happened to die out.

When lay people hear the term “modern”, he said, they think of people who looked and acted like us, but scientists sometimes use the term “modern humans” to describe our lineage. But 200,000 years ago, our “modern human” ancestors didn’t look or act like people today. “The whole notion of archaic humans is ambiguous and misleading.”

Hublin said our history probably included many intermixing groups, some of which would look and act more like today’s humans than others. “That’s evolution,” he said.



"Genomic Variation in Seven Khoe-San Groups Reveals Adaptation and Complex African History," by C.M. Schlebusch et al. Science, 2012.

Contact Faye Flam at 215-854-4977 215-854-4977 or fflam@phillynews.com, or follow on Twitter @fayeflam. Read her blog at philly.com/evolution.
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