University of Alberta: U of A anthropologist uncovers oldest human DNA ever found in Africa

A University of Alberta anthropologist has uncovered the oldest human DNA yet found in Africa, shedding new light on a period of ancient human history about which little is known.

Banting post-doctoral fellow and bioarcheologist Elizabeth Sawchuk found skeletal remains of a middle-aged woman on her first dig in Africa 12 years ago as a master’s student under U of A anthropologist Pamela Willoughby.

However, it’s only recently that technological breakthroughs have allowed for genetic analysis of the woman’s ancient DNA, said Sawchuk, whose findings were published last month in Nature.

“It was challenging to study this individual because the remains are so fragmentary — and about 18,000 to 20,000 years old,” Sawchuk said.

“This person was very small and the bones had turned almost to dust, in part because of an Iron Age smelting furnace that was later built very close to her grave. It was very difficult to reconstruct aspects of their life from her skeleton,” she said, adding that she hesitated to estimate the individual’s sex until the DNA revealed it.

Archeological detective work reveals a rare find
Though the bones were too poorly preserved to radiocarbon date, Sawchuk’s team determined when this individual lived by dating ostrich eggshell beads in the grave. That analysis was led by her fellow graduate student in the Department of Anthropology and dig companion Jennifer Miller, who continues to study the beads and published further results in Nature late last year.

The oldest ancient human DNA yet discovered is 430,000 years old, found in Spain’s Atapuerca mountains. Finding ancient human DNA in Africa, the birthplace of humanity, is difficult because climate conditions cause it to degrade so quickly.

Co-led by Sawchuk, the 44 authors of the study sampled 31 ancient individuals whose remains were between 5,000 and 18,000 years old. After sending the samples to Harvard University for analysis, the team successfully extracted genome-wide data for six individuals from five sites in Tanzania, Zambia and Malawi.

“That called for popping champagne,” said Sawchuk, since DNA of that age is such a rare find in the tropics.

The age of the DNA allowed the team to focus on ancient foragers — people who lived by hunting, gathering and fishing. By comparing the new individuals with previously published data from 28 other ancient individuals and with sequences from present-day groups in Africa, the researchers identified patterns that existed before sweeping changes that came with the spread of herding and farming, the rise of cities and trade routes, and slavery and colonialism that changed the African genetic landscape within the past 5,000 years.

Illuminating a “black box” of human history
The discovery begins to illuminate a period of human history in Africa between 80,000 and 20,000 years ago — “a kind of black box” around the transition from the Middle to Later Stone Age — that archeologists don’t know much about, said Sawchuk.

“People started behaving in ways that seem a lot more modern — for example, using new and more refined stone and bone tools and creating different types of art. From Jennifer Miller’s work, we see an explosion of ostrich-eggshell beads hinting at the development of early long-distance social networks.”

This was also a time of major environmental change during the Ice Ages, suggesting people may have had to get creative, said Sawchuk, interacting in different ways and establishing connections between regions.

“We found evidence for extensive moving and mixing between people during this time. Despite being separated by thousands of kilometres and years, all the individuals in this study could be modelled as a variable mix of central African ancestry, eastern African ancestry and southern African ancestry,” noted Sawchuk, adding that the only explanation is if people were travelling and having children with people far from where they were born. What’s more, this was happening around the same time archeologists see evidence for the development of long-distance trade.

Sawchuk was surprised that the woman she recovered from Mlambalasi, the most ancient individual in the study, yielded DNA at all.

“Her bones were compressed into a fine layer of dust, so it was incredibly difficult to recover her in the first place,” said Sawchuk, adding that she was nonetheless able to glean a few details about the ancient woman’s life from fragments that did survive.

“She was carefully laid to rest and did not have any obvious signs of trauma or disease on her skeleton, apart from dental disease including several cavities. That’s interesting, because it’s unusual to see cavities in ancient hunter-gatherers and raises questions about her diet.”

Another surprising finding was a small bone fragment of a child buried with the woman: “We don’t know if it was her child, because we weren’t sure we could recover any DNA from such a small fragment,” said Sawchuk, who was also involved in developing ethical guidelines for such research, published separately in Nature last year.

Studying the DNA of ancient foragers, including the woman from Mlambalasi, highlights the need for more archeological research in Central Africa — an understudied part of the continent, Sawchuk said.

“It’s becoming apparent that more research is needed to understand our species history between our initial origins and recent past — a really big piece of the human story.”

Most gratifying for Sawchuk is seeing how scientific advances have already changed the way the past is studied.

“I recovered this individual in 2010, the same year the first fully sequenced ancient human genome was published. If you had told me then that I would one day be studying her DNA, I probably wouldn’t have believed you.

“I recovered and analyzed this individual as a master’s student, studied her teeth as a PhD student, and her DNA as a post-doc. It’s like she and I have been walking together for a dozen years.”

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