Study shows how DNA from ancient ancestors was passed down to modern humans

According to a new study of ancient genomes, different branches of the human family tree could have interbred numerous times, and certain human beings carry DNA from an unfamiliar and ancient ancestor.

Melissa Hubisz and Amy Williams from Cornell University and Adam Siepel from the Cold Spring Harbor Laboratory have reported these discoveries in a study published in the PLOS Genetics journal on August 6^th, 2020.

About 50,000 years ago, a set of humans shifted from Africa and interbred with Neanderthals based in Eurasia. However, that is not the only period that prehistoric human ancestors and their relatives exchanged their DNAs.

The genomic sequence from Neanderthals and the Denisovans—a less familiar prehistoric group—has provided several new insights into such interbreeding events and also into the migration of prehistoric human populations.

In the latest study, the team created a new algorithm for studying genomes that can detect DNA segments that evolved from other kinds of species, even if that specific gene flow took place several thousands of years ago and emerged from an unfamiliar source.

The researchers applied their algorithm to examine genomes that evolved from two Neanderthals, two African humans, and a Denisovan. They came across proof that 3% of the Neanderthal genome originated from prehistoric humans, and predicted that the interbreeding took place around 200,000 to 300,000 years ago.

Moreover, 1% of the Denisovan genome could have evolved from a more distant and unfamiliar relative, probably Homo erectus, and around 15% of those “super-archaic” areas might have been passed down to the current generation of humans living today.

These latest discoveries support the earlier reported cases of gene flow that occurred between prehistoric humans and their relatives, and also indicate new cases of interbreeding. Considering the number of these interbreeding events, the team believes that genetic exchange probably occurred whenever a pair of groups overlapped in space and time.

The researchers’ new algorithm resolves the complex issue of detecting insignificant remains of gene flow that took place hundreds of thousands of years before, when just a few prehistoric genomes were available. The new algorithm may also prove handy for analyzing gene flow in other kinds of species in which interbreeding took place, for example, in dogs and wolves.

What I think is exciting about this work is that it demonstrates what you can learn about deep human history by jointly reconstructing the full evolutionary history of a collection of sequences from both modern humans and archaic hominins. This new algorithm that Melissa has developed, ARGweaver-D, is able to reach back further in time than any other computational method I’ve seen. It seems to be especially powerful for detecting ancient introgression.”

Adam Siepel, Study Author, Cold Spring Harbor Laboratory