DNA Diversity Studies Trace Ancient Human Migrations

David Reich is fascinated with the stories of our past. By analyzing DNA from a vast swath of human populations, he and his colleagues have discovered surprising twists in human history, including evidence suggesting that more than one group of early humans settled the Americas many thousands of years ago. A geneticist at Harvard Medical School, Reich received funding from the Simons Foundation to explore genetic diversity in humans. He recently spoke to us from his office in Cambridge, Massachusetts. The following is an edited version of the conversation. 

What drives your research in human genetic diversity?

The human world is extremely diverse, with different cultures, different languages, different regions of the world, different ways of life. Yet we’re all linked by common ancestry. It’s very interesting to understand how all this diversity arose.

How do scientists study human diversity?

Scientists have traditionally studied diversity based on the languages people speak, seeing which are most closely related to each other. That’s called historical linguistics. Researchers have also relied on the very important field of archaeology, which digs into old layers where people left their marks and tries to identify material that might be indicative of past cultures.

Genetics is a third plank. It’s a new science of the human past that’s enabled by DNA. Every time we collect data from a population that nobody’s collected from before, we find a surprise because it’s such uncharted territory.

What have studies of genetic variation revealed about human history?

Svante Pääbo’s laboratory at the Max Planck Institute for Evolutionary Anthropology miraculously and successfully obtained genome-scale data from an approximately 40,000-year-old set of Neandertal remains. His team was able to compare DNA from Neandertals with the DNA of present-day people. The comparison revealed that during the migration of modern humans out of Africa, which happened 50,000 years ago, those people encountered Neandertals and interbred with them. All non-Africans today descend from that interbreeding. That was a big surprise.

Another huge surprise came from a bone found in Siberia that was around 50,000 years old. It turned out to belong to yet another population, not Neandertal or modern human, but from the same time period. It was a sister group to Neandertals now called Denisovans. Their discovery was not even previously suggested by skeletal remains or analysis of archaeological specimens.

From what kind of populations did you analyze DNA?

This is the Simons Genome Diversity Project, which offers access to complete genome sequences from 300 people representing 142 diverse populations around the world. It includes hunter-gatherers in central and southern Africa, as well as from New Guinea and islands in Southeast Asia. It also includes some Native American populations, quite a number of Siberian indigenous populations, and hunter-gatherers of northern Scandinavia and other parts of Europe. Analyzing these populations is important for understanding human history and the true nature of the present-day structure of populations.

Using genetic data, you and other researchers recently reported that some South Americans had traces of Australo-Melanesian ancestry. What does the finding say about the peopling of the Americas 20,000 years ago?

This is an amazing finding. We looked at Native Americans from today, people from Amazonian populations, and found that some of them share a small amount of DNA with native Australians and Melanesians. This implies that Native American populations do not descend from just one source; instead there were at least two populations that migrated to the Americas very early on. One of those populations was a previously unknown lineage of present-day Amazonians.

Where do you see this field of genetics and human diversity heading in the next five to 10 years?

The field is moving toward ancient DNA. In the data we have from past people, we can already see that the structure of human populations even 10,000 years ago was very different from what it is today. It was just as diverse, but very different. Creating catalogs of past people will be a very powerful way to understand how present people got to where they are today.

If you can piece together the stories of our deep past from modern DNA, what does looking at ancient DNA add to that story?

Ancient DNA is a powerful tool. It allows you to cheat and go back in time to look at the genetics of populations from the distant past. You can compare past populations in different regions and look at the genetic variation to see how it may have influenced modern populations. It gives us an opportunity to see how populations transformed over time.

There have been reports of epigenetics studies that have been done on ancient DNA. How valuable could this data be for understanding human history?

This is an exciting idea. You could look at chemical changes to the microstructure of DNA, not the code itself. These changes probably modified the activation of certain genes in the past. You could learn a lot about the modifications and how they compare with changes seen in the microstructure of today’s DNA. These changes are influenced by such factors as diet and stress — essentially your environment. At this point, however, we are very far away from gaining strong insights into how past epigenetic changes may have been linked to people’s environments and lifestyles.

The stories of human history revealed by genetic data are largely about migrations of populations. There’s a lot of migration going on today. How will that shape humans’ genomes going forward?

We’re in a period, not just now, but in the last 100 years or so of mass movements and mixing of peoples. This happened in the distant past, and it is now happening again. There’s mixing of Scottish and Irish and Italian and Jewish and African-American. Distinctions are breaking down. This is greatly affecting our genetics. New populations are forming, even in this country. In the future, our populations and our genetics will look completely different.