We tend to think of Neanderthals as a species that went extinct, but a Princeton geneticist found evidence of three waves of interbreeding over 250,000 years, leading him to argue Neanderthals didn't disappear — they were absorbed into us

We are used to saying that Neanderthals went extinct, around forty thousand years ago, edged out by modern humans. Joshua Akey, a geneticist at Princeton, thinks that is the wrong word. His team’s reading of the DNA finds that Neanderthals and modern humans interbred repeatedly across roughly a quarter of a million years, and he argues that Neanderthals did not so much vanish as get absorbed into us.

The reframing is an argument, and a debatable one. The gene flow underneath it is not.

Three waves, not one

For a long time the story had a single chapter. A brief period of mixing as modern humans spread out of Africa, roughly fifty thousand years ago, left a few per cent of Neanderthal DNA in people outside Africa today, and that was taken to be the whole of it.

Akey and his colleague Liming Li, reporting in Science in 2024, found the contact was older and far more repeated than that. Using a method called IBDmix to compare the genomes of about two thousand living people with those of three Neanderthals and a Denisovan, they identified at least three separate pulses of interbreeding: one roughly 200,000 to 250,000 years ago, another around 120,000 years ago, and the largest about 50,000 to 60,000 years ago. The two groups met and mixed across most of the time they both existed.

Looking the other way

The part that made the difference was a change of direction. Most work looks for Neanderthal DNA inside modern humans. Akey’s team also looked for modern-human DNA inside the Neanderthals, which earlier methods had largely missed.

It was there. The Neanderthal genomes carried an estimated 2.5 to 3.7 per cent modern-human ancestry, the trace of those earlier waves, when groups of Homo sapiens who had left Africa well before the main exodus mixed into Neanderthal populations.

The genes flowed both ways.

Why “absorbed” rather than “extinct”

From there Akey makes his case about the word. Neanderthals were never numerous. As modern human numbers grew, he argues, the smaller population was steadily folded into the larger one, less wiped out than taken in.

His own image is of modern humans as waves on a beach, slowly eroding it until the Neanderthals were demographically overwhelmed and incorporated. “I don’t like to say extinction,” he has said, “because I think Neanderthals were largely absorbed.”

It is worth being precise about what this does and does not claim. Neanderthals as a distinct population did come to an end, roughly forty thousand years ago, and no one has met one since. What Akey is changing is the mechanism and the framing, from a clean replacement in which one group won and the other simply died, to an absorption in which the smaller population was taken up and its genes carried on in living people. It is a reinterpretation of the same facts, and how much weight to put on the word “absorbed” is something on which reasonable researchers still differ.

What it changes

The shift is from a tidy story to a messy one. Instead of two species that brushed past each other once before one of them disappeared, the record now shows populations that met, mixed and merged again and again over a very long time.

Plenty is still unsettled: the exact number and timing of the waves, how much those early out-of-Africa groups contributed, and what the inherited Neanderthal stretches actually do in the human genome. More ancient DNA, and better ways of reading it, will keep sharpening the picture.