How ancient DNA is transforming our view of the past

From BBC - April 10, 2018

Prof David Reich of Harvard Medical School is one of the leading lights in the field of ancient DNA. His team's work has cast a new perspective on human history, reconstructing the epic migrations and genetic exchanges that shaped the people of different regions worldwide. Here he explains how this revolution in our understanding unfolded.

If it seems as if there has been an avalanche of recent headlines revealing insights into the travails of our ancient ancestors, you'd be right.

From the fate of the people who built Stonehenge to the surprising physical appearance of Cheddar Man, a 10,000-year-old Briton, the deluge of information has been overwhelming.

But this step change in the understanding of our past has been building for years now. It's been driven by new techniques and technological advancements in the study of ancient DNA - genetic information retrieved from the skeletal remains of our long-dead kin.

At the forefront of this revolution is David Reich of Harvard Medical School in Boston Massachusetts. I met Prof Reich recently at the BBC while he was in the UK to talk about his book Who We Are and How We Got Here, which draws together the most recent scientific results in this field of study.

The Harvard professor, who is 43, was recently highlighted by the journal Nature as one of 10 people who mattered in all of science for his role in transforming the field of ancient DNA from "niche pursuit to industrial process".

Reich was raised in Washington DC, by parents who were distinguished in their own fields. His mother Tova is a novelist and his father Walter is a professor of psychiatry who also served as the first director of the United States Holocaust Memorial Museum.

"In my family, there was a premium and a strong belief placed on creativity - doing something new and interesting and edgy. Science was seen as the highest thing someone could do," he says. "I had lots of interests, but the things I was most interested in were history and science."

Reich says that he "fell in love" with human evolutionary history at the beginning of his PhD in biochemistry, but then moved away from the subject towards medical genetics. He explained: "The technology at the time really was not very good for learning a lot about human history."

Throughout the 1990s and early 2000s, studies of ancient DNA from our own species were highly contentious because of observations that skeletal remains were easily contaminated by the DNA of living people.

As such, there were always nagging doubts about whether a genetic sequence belonged to the long-dead individual being studied or to an archaeologist involved in excavating the remains, a museum curator who had handled them, or a visitor to the lab where they were being analysed.

However, crucial progress in overcoming these obstacles began in the late 90s with the effort to sequence DNA from Neanderthals, which was led by Professor Svante Pbo at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany.

Pbo's group developed a set of protocols to prevent contamination slipping through, including having the same samples sequenced in two laboratories by different teams.

But the field experienced a revolution with the emergence of so-called next-generation sequencing technology. When an organism dies, the DNA in its cells begins to break down - over time it splits into smaller and smaller chunks, as well as accumulating other forms of damage.

It also gets contaminated with vast amounts of microbial DNA from the wider environment. The new sequencing machines could be used to isolate the human genetic material from bacterial DNA and then stitch together the tiny fragments into a readable sequence.

In 2006, Reich and his close scientific collaborator Nick Paterson were invited by Svante Pbo to join the Neanderthal genome effort. Pbo had been particularly impressed by a Nature paper they had authored on the complex separation of the human and chimpanzee evolutionary lineages, and thought the techniques they had used would be relevant to the question of whether Neanderthals and modern humans had interbred.

"I was working on the last 10,000 years of human history, reconstructing it on the basis of present-day people, especially in India it was obvious the ancient DNA techniques that worked in Neanderthals were going to work even better in more recent humans," Reich explains.

"I talked to Svante and he said: 'This is very important but it's not my focus. I am focused like a laser beam on archaic humans and early modern humans.'"

Reich took a radical decision to completely re-tool his laboratory at Harvard - which had been focused on medical genetics - along the lines of Pbo's lab in Leipzig.

"There was a scientist in my laboratory, Nadin Rohland, who had worked in Leipzig (with Svante Pbo) who knew how to do everything they helped us to establish this laboratory. It was a big bet that this was a good thing to do."

The bet paid off in a major way. Reich used his next-generation sequencing tech to power through genome after genome. To date, the lab has retrieved DNA from more than 900 ancient individuals.

The results are helping assemble new narratives for the peopling of our world. In some cases, the results have forced archaeologists and historians to re-visit some long-held ideas, sparking no small amount of debate and controversy.

Reich's team has helped unravel the tangled web of migration and interbreeding that set down the present-day genetic landscape of Europe. Archaeologists had long suspected that the spread of farming out of the Near East and across Europe was a formative event in the continent's prehistory.

Reich's work helped confirm that this meeting of rather distantly related Near East farmers and indigenous hunter-gatherers had been crucial to the mix of ancestry that characterises Europeans, but his team added a third population to the mix.

In a paper published in the journal Genetics in 2012, Reich and his colleagues had spotted that Northern and Central Europeans appeared to have received genetic input from a population related to Native Americans.


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