Genome Sequencing of 5 New Neanderthals Adds to the Human Family Tree

At-home DNA testing is supposed to give people insight into their human ancestry, but it’s had the unexpected effect of showing how much of our DNA isn’t human. Now we know that Europeans and Asians have approximately 2 percent Neanderthal DNA, and that proportion may well increase, now that scientists have sequenced the genomes of five new Neanderthal specimens that lived between 39,000 and 47,000 years ago.

These late Neanderthals, evolutionary geneticists explain in a paper released Wednesday in Nature, are more closely related to the Neanderthals whose DNA lives in some humans today than older Neanderthals whose genomes have been previously sequenced. Since 2010, whole-genome sequences have been generated from four Neanderthals specimens. This study adds five new Neanderthal genomes from a much later time period and a wider geographic range.

“It is the case that having the genomes of these younger Neanderthals increases the amount of Neanderthal DNA that can be identified in present-day people,” explains senior author and Max Planck Institute professor Janet Kelso, Ph.D., to Inverse. Kelso says that with new genomes scientists can identify 10 to 20 percent more Neanderthal DNA in people living today than was possible when they were just relying on the Altai Neanderthal genome, the first Neanderthal genome sequenced.

Scientists are now well aware that Neanderthals and modern humans mated, but they don’t know as much about the genetic diversity of Neanderthals and how they interacted with each other and with early modern humans. Their investigations have been limited by a dearth of Neanderthal specimens and difficulties extracting endogenous DNA from ancient bones, which have made it difficult to sequence Neanderthal genomes. However, Kelso and her team, using new methods for removing contaminated DNA from microbes, generated the genomes of five Neanderthals sourced from Belgium, France, Croatia, and Russia using their powdered bones and teeth.

Analysis of the genomes revealed that these Neanderthals, even though they lived at the same time as early modern humans, did not have any human in their own DNA. This indicates that gene flow between these populations may have been unidirectional — from Neanderthals into modern humans, but not the other way around.

Unfortunately, Kelso explains, this conclusion doesn’t allow them to determine whether the gene flow was from male or female Neanderthals — so the mystery of the dynamics of these ancient hookups still remains.

Nevertheless, these genomes, representing some the latest-surviving Neanderthals in Europe, allowed the scientists to begin reconstructing Neanderthal population dynamics: Genetic similarity between the Neanderthals is correlated with their geographical location, and when compared to the genomes of people living today, it appears that the late Neanderthals were more similar to the Neanderthals that mated with the ancestors of modern-day Europeans and Asians than older Neanderthals found in Siberia.

It also seems like a population turnover happened among Neanderthals toward the end of their run, with groups moving through Eurasia and replacing each other.

“We were fortunate to have two Neanderthals from the same cave in the Caucus mountains,” says Kelso. “One of the two Neanderthals lived tens of thousands of years earlier in time than the other.”

Kelso and her team found that the younger Neanderthal was more genetically similar to other younger Neanderthals in other parts of Europe than the older Neanderthal that was found in the same cave. This implies that older populations of Neanderthals were, at some point, replaced by different populations. This likely happened close to — and close here is relative— the time Neanderthals became extinct, and our ancestors replaced them as the only hominins on Earth.