Human and Neanderthal Interbreeding Suggests Major Evolutionary Timeline Change

February 22, 2016 | Reece Alvarez

Neanderthal wearing a business suit
Photo credit: Clemens Vasters/Flickr (CC BY 2.0)

According to new research, the convergence of modern day humans and Neanderthals may have occurred earlier in human history than previously thought.

The timeline of human evolution is about to be rewritten if recent findings of an interbreeding event between Neanderthals and modern humans, occurring tens of thousands of years earlier than any other such event previously documented, are correct.

According to researchers at Cold Spring Harbor Laboratory in New York, an international research team used several different methods of DNA analysis and found what they consider to be strong evidence of an interbreeding event that occurred an estimated 100,000 years ago.

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More specifically, the scientists provide the first genetic evidence of a scenario in which early modern humans left the African continent and mixed with now-extinct members of the human family prior to the migration "out of Africa" of the ancestors of present-day non-Africans, less than 65,000 years ago.

"It's been known for several years, following the first sequencing of the Neanderthal genome in 2010, that Neanderthals and humans must have interbred," said professor Adam Siepel, a co-team leader and Cold Spring quantitative biologist. "But the data so far refers to an event dating to around 47,000 to 65,000 years ago, around the time that human populations emigrated from Africa. The event we found appears considerably older than that event."

Professor Siepel explains the possibly historic findings. Photo credit: Cold Spring Harbor Laboratory

The team’s findings were published in the journal Nature and are the result of several kinds of advanced computer modeling algorithms which compare complete genomes of hundreds of contemporary humans with complete and partial genomes of four archaic humans.

"One very interesting thing about our finding is that it shows a signal of breeding in the 'opposite' direction from that already known," Siepel said. "That is, we show human DNA in a Neanderthal genome, rather than Neanderthal DNA in human genomes."

According to the study, modern people who are of European, Eurasian and Asian descent have well-identified Neanderthal-derived segments in their genomes. These fragments are traces of interbreeding that followed the "out of Africa" human migration dating to about 60,000 years ago. They imply that children born of Neanderthal-modern human pairings outside of Africa were raised among the modern humans and ultimately bred with other humans, explaining how bits of Neanderthal DNA remain in human genomes.

Contemporary Africans, however, do not have detectable traces of Neanderthal DNA in their genomes. This indicates that whatever sexual contact occurred between modern humans and Neanderthals occurred among humans who left the African continent.

"Ancestors of present-day African populations likely didn't have the opportunity to interbreed with Neanderthals, who lived largely outside of Africa," said study co-author Ilan Gronau.

Scenario of interbreeding between modern humans and Neanderthals: Neanderthal DNA in present-day humans outside Africa originates from interbreeding that occurred 47,000 -- 65,000 years ago (green arrow). Modern human DNA in Neanderthals is likely a consequence of earlier contact between the two groups roughly 100,000 years ago (red arrow). Photo credit: Ilan Gronau

The team's evidence of "gene flow" from descendants of modern humans into the Neanderthal genome applies to one specific Neanderthal, whose remains were found in a cave in southwestern Siberia in the Altai Mountains, near the Russia-Mongolia border. The modern human ancestor who contributed genes to this particular Neanderthal individual — called the "Altai Neanderthal," and known from a tiny toe bone fragment — must have migrated out of Africa long before the migration that led Africans into Europe and Asia 60,000 years ago, the researchers said.

In contrast, the two Neanderthals from European caves that were sequenced for this study — one from Croatia, another from Spain — both lack DNA derived from ancestors of modern humans. The team also included in their analysis DNA from another now-extinct human relative, a Denisovan individual, whose remains were found in the same cave in the Altai Mountains. Denisovans, like Neanderthals, were members of the human line that eventually became extinct. Both of these archaic human cousins lived in the same cave, although at different times in the past.

The Denisovan analyzed in this study did not have traces of modern human DNA, unlike the Neanderthal found in the same cave. That doesn't mean modern human ancestors never mated with Denisovans or European Neanderthals, but what it does mean, Siepel said, is that "the signal we're seeing in the Altai Neanderthal probably comes from an interbreeding event that occurred after this Neanderthal lineage diverged from its archaic cousins, a little more than 100,000 years ago."

The modern human sequences in the Altai Neanderthal appear to be derived from a group of modern human ancestors from Africa that separated early from other humans, about the same time that present-day African populations diverged from one another around 200,000 years ago. Thus, there must have been a long lag between the time when this group branched off the modern human family tree, roughly 200,000 years ago, and the time they left their genetic mark in the Altai Neanderthal, about 100,000 years ago, before being lost to extinction themselves.

"This is consistent with the scenario of gene flow from a population closely related to modern humans into the Altai Neanderthal,” Siepel said. “After ruling out contamination of DNA samples and other possible sources of error, we are not able to explain these observations in any other way."


Source: Neanderthals mated with modern humans much earlier than previously thought, study finds

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