Modern humans interbred with Neanderthals before they disappeared, and most people of non-African ancestry still carry roughly 1 to 4 percent Neanderthal DNA today — meaning part of the human population we once thought we simply replaced never actually vanished

A man who died in a Romanian cave about 40,000 years ago carried more Neanderthal DNA than any other human ever sequenced, ancient or modern. His jawbone turned up in Peștera cu Oase, and when geneticists analysed it the result was startling: between six and nine per cent of his genome came from Neanderthals. Because those segments were still long and unbroken in his chromosomes, researchers reporting in Nature could work out that he’d had a Neanderthal ancestor only four to six generations back.

He was simply closer to the event than anyone alive today.

What the first Neanderthal genome settled

For most of the twentieth century the textbook story was replacement. Modern humans left Africa, Neanderthals died out, end of chapter. Anatomists had spent decades staring at skull shapes and reaching opposite conclusions from the same fossils. That held until 2010, when a draft sequence of the Neanderthal genome, assembled by Richard Green, Svante Pääbo and a large team from bones found in Vindija Cave in Croatia, showed that Neanderthals shared more genetic variants with living Eurasians than with living sub-Saharan Africans. Their estimate put the Neanderthal contribution to non-African genomes at one to four per cent.

Sixteen years of better data have tightened that figure rather than overturned it. Most current estimates sit closer to one or two per cent, with East Asians carrying about a fifth more than Europeans.

The meeting had a duration

How long did the two species actually overlap before Neanderthals disappeared? Two papers published on the same day in December 2024 finally gave a precise answer. A study in Science, led by Leonardo Iasi and Manjusha Chintalapati, compared 58 ancient Eurasian genomes against 275 present-day ones and dated the average moment of mixing to about 47,000 years ago, with gene flow continuing for some 7,000 years. A companion analysis, published in Nature, examined 45,000-year-old remains from Ranis in Germany and Zlatý kůň in Czechia and traced the archaic stretches in those genomes to a single admixture event between 45,000 and 49,000 years ago, shared by every non-African sequenced so far.

Seven thousand years is a long time to call an encounter. It is longer than everything that has happened since the first cities of Mesopotamia.

The parts that did not make it

“These deserts may have formed very rapidly after the gene flow,” Leonardo Iasi, one of the authors on the Nature paper, told UC Berkeley. He was describing what he and his colleagues call Neanderthal deserts, long stretches of the modern genome where archaic DNA is completely absent. Ancient human genomes from roughly 40,000 years ago already show no ancestry in those deserts, which is what led him to that conclusion. Read plainly, it means certain Neanderthal variants were harmful enough in a modern human body to be scrubbed out within a few thousand years.

The Oase man makes a similar point from the other end.

For all his recent Neanderthal ancestry, his population left little genetic trace in later Europeans.

What the surviving fragments do

Picture Neanderthal DNA as a jigsaw dropped and scattered across a crowd. No single person holds more than a sliver, but the crowd between them is still carrying a fifth of the picture. That is roughly what Benjamin Vernot and Joshua Akey found, writing in Science in 2014, when they sifted the genomes of 379 Europeans and 286 East Asians and recovered Neanderthal sequence covering roughly twenty per cent of that species’ entire genome.

There is a second archaic contributor in the mix too. Priya Moorjani of UC Berkeley, a senior author on the 2024 Science paper, is now studying people of East Asian descent, who carry both a larger Neanderthal share and up to 0.1 per cent of their genome from the Denisovans, a population known mainly from a handful of bone fragments and an enormous quantity of statistics.

Some of the surviving Neanderthal DNA is doing useful work. The variants that reached high frequency cluster around immune function, skin pigmentation and metabolism, which fits a group that had spent a few hundred thousand years adapting to Europe’s winters and its pathogens before anyone else showed up.

Some of it is a liability. In a paper published in Nature in 2020, Hugo Zeberg and Svante Pääbo showed that the strongest genetic risk factor then identified for severe COVID-19 was a stretch of roughly 50,000 bases on chromosome three, inherited from Neanderthals and carried by about half the population of South Asia and around sixteen per cent of Europeans. One paper, one chunk of chromosome, and the biology behind it is still being argued over. The provenance, though, is not really in dispute.

What to call an ending like that

Extinction normally means a line stopping. Neanderthals did stop existing as a distinct population, around 40,000 years ago, and no amount of genetics changes that. What the genetic evidence changes is the shape of the ending. A population that dies out and a population that gets absorbed look much the same in the fossil record and nothing alike in the genome.

That leaves an odd little fact sitting in the middle of human prehistory. The last Neanderthals were not necessarily childless. Some of them had children, those children had children, and the arithmetic has been running quietly ever since, through a few hundred million bedrooms, down to whoever happens to be reading this.