UCLA genomic research uses statistics – rather than ancient DNA – to look back more than 600,000 years

From Matthew Chin |

UCLA computational biologists have discovered that four populations in West Africa can trace about 8% of their genetic ancestry to an archaic hominin, an extinct relative of humans that branched off from the hominid evolutionary tree more than 600,000 years ago — about 100,000 years earlier than Neanderthals did. The study is published in Science Advances.

Over the past decade, advances in computing, statistical analysis, molecular biology and genetics have revealed a richer picture of humans and their interactions with ancient relatives, such as Neanderthals. But research on the genetic ancestry of African populations has lagged behind discoveries about people with ancestral roots in Europe.

The researchers, from the UCLA Samueli School of Engineering, analyzed modern DNA obtained from an international repository of genomic data. In the past, researchers would have needed to compare the modern DNA to so-called “reference DNA” from ancient fossils to draw such conclusions. But the improved statistical techniques available today enabled them to look backward in time hundreds of thousands of years without fossil DNA.

“This opens a new path in understanding the complexity of human evolutionary history in Africa, where the picture hasn’t been as clear,” said Sriram Sankararaman, the study’s principal investigator, a UCLA assistant professor with appointments in computer science, human genetics and computational medicine.

The archaic hominin identified in the UCLA research is a close evolutionary relative of humans.

“There is not a lot known about these archaic hominins, which makes finding out how this ‘ghost population’ fits into human evolutionary history challenging. But our findings are very exciting,” said Sankararaman, who also is a member of UCLA’s Bioinformatics Interdepartmental Program.

Previous genomic studies have presented evidence that modern populations in Africa have complex genetic lineages, in which humans and close evolutionary relatives intermixed as recently as just a few thousand years ago. But this study may provide the strongest evidence yet that this intermixture took place.

The UCLA research reveals much more of that story for the four modern groups of people, the Yoruba of Nigeria, the Mende of Sierra Leone, the Esan of Nigeria and the Gambian in Western Divisions of Gambia.

“We don’t need reference DNA from fossils of the archaic hominin to confirm that, somewhere deep in our ancestry, humans intermixed with them,” Sankararaman said. “We can now see that such events took place by looking at our DNA itself.”

Segments of Neanderthal DNA extracted from fossils have been found in most modern populations outside of Africa. DNA has also been extracted and analyzed from the more recently discovered Denisovans, another extinct group of archaic humans, whose DNA is found in people living today in South Asia and Oceania.

Archaeological evidence shows that modern and archaic humans coexisted in Africa, and some fossils have features that suggest mixing between the two populations. However, usable DNA has not yet been extracted from archaic human fossils that have been found in that region — which is why the researchers’ ability to draw conclusions about evolution without reference DNA information could go such a long way toward solving previously unanswered questions.

Although the researchers found evidence of the archaic population’s DNA in modern humans, the findings are not clear enough to determine whether these two distinct populations intermixed just once or several times over hundreds of thousands of years.

Sankararaman and Arun Durvasula, a UCLA graduate student studying human genetics, used two new statistical methods that look for patterns in the genome that could reveal the presence of DNA from a distantly related unknown archaic population. They looked at genomic data of 405 people from the 1000 Genomes Project, an international public repository of genomic data from around the world. The results of both analyses were consistent.

The research was supported by the National Science Foundation, the National Institutes of Health, the Alfred P. Sloan Foundation and the Okawa Foundation.