Interbreeding between archaic and modern humans

Based on Wikipedia: Interbreeding between archaic and modern humans

If you're reading this, you're probably part Neanderthal. Not as an insult—as a scientific fact. Somewhere between one and four percent of your genome, assuming you have any ancestry outside sub-Saharan Africa, came from a species that supposedly went extinct forty thousand years ago. They didn't entirely die out. They live on, in you.

This discovery upended decades of scientific consensus. For most of the twentieth century, paleoanthropologists fought bitterly over a fundamental question: when modern humans spread across the globe, did they completely replace every other human species, or did they interbreed with them? The replacement camp won, mostly. The orthodox view became known as the "Out of Africa" model—modern humans evolved in Africa, migrated outward, and replaced archaic populations like Neanderthals without significant genetic mixing.

Then came the genomes.

The DNA Revolution

On May 7, 2010, everything changed. Scientists published the first draft sequence of the Neanderthal genome, extracted from bones found in Vindija Cave, Croatia. The results were unambiguous: Neanderthals shared more genetic variants with people of European and Asian descent than with people of sub-Saharan African descent. The simplest explanation? Interbreeding. Our ancestors didn't just coexist with Neanderthals—they had children with them.

The initial estimates suggested that Eurasians carry between one and four percent Neanderthal DNA. Subsequent studies refined this figure. Some researchers found as little as 1.5 percent, others as much as 7.3 percent. The current consensus lands around 1.8 to 2.6 percent for people outside Africa and Oceania.

But here's where it gets interesting. If you add up all the Neanderthal DNA fragments scattered across different human populations, the total is far larger than what any individual carries. Studies have found that roughly half of the entire Neanderthal genome survives in modern humans—it's just distributed across different people. One person might carry Neanderthal variants for certain immune genes, another for skin pigmentation, a third for hair texture. Collectively, we're carrying an enormous archive of Neanderthal genetics.

In 2023, researchers discovered that gene flow went both directions. Around 250,000 years ago—long before the main interbreeding events—modern humans contributed DNA to Neanderthals. About six percent of a Neanderthal specimen from the Altai Mountains in Siberia came from our ancestors. The species had been exchanging genetic material for hundreds of thousands of years.

Not Just Neanderthals

Neanderthals weren't our only ancient partners. Enter the Denisovans.

We know almost nothing about what Denisovans looked like. The entire species was discovered from a single finger bone and a handful of teeth found in Denisova Cave in southern Siberia. But we have their DNA, and it tells a remarkable story.

People in Oceania—Aboriginal Australians and Melanesians—carry between four and six percent Denisovan DNA. That's even more than the Neanderthal contribution to Eurasians. Smaller amounts appear in Southeast Asian and American populations. The Denisovans, whoever they were, left a significant genetic legacy.

The geography is puzzling. Denisova Cave sits in the Altai Mountains of Siberia, thousands of miles from Australia and Papua New Guinea. Yet Siberians today show minimal Denisovan ancestry. The most likely explanation is that Denisovans were spread across a vast swath of Asia, and the interbreeding happened in Southeast Asia as modern humans made their way toward Australia. The Siberian Denisovans were just the ones whose bones happened to survive in a cave with ideal preservation conditions.

The African Puzzle

For years, scientists assumed that sub-Saharan Africans had no Neanderthal ancestry. The logic seemed straightforward: Neanderthals lived in Europe and western Asia, and modern humans only encountered them after leaving Africa. Therefore, people whose ancestors never left Africa should have no Neanderthal DNA.

This assumption was wrong.

A 2020 study by Chen and colleagues found that African populations do carry Neanderthal DNA—about 0.3 percent of their genome. The explanation involves a phenomenon called back-migration. After modern humans interbred with Neanderthals in Eurasia, some of their descendants migrated back into Africa, bringing Neanderthal genes with them. This appears to have happened around 20,000 years ago, when a population that had already diverged from ancestral Europeans returned to the continent.

Some geneticists remain skeptical. David Reich, one of the leading figures in ancient DNA research, has called the signal of back-migration "really weak." But the finding has important methodological implications. Because scientists previously assumed Africans had no Neanderthal ancestry, they used African genomes as a baseline for comparison. This led to systematic underestimation of Neanderthal ancestry in everyone else.

The picture becomes even more complex in North Africa. Populations there show Neanderthal ancestry levels comparable to Europeans and sometimes higher. Tunisian Berbers, for instance, show even more Neanderthal genetic signal than many Eurasian populations. This isn't simply due to recent migration from Europe or the Middle East—the pattern suggests that North African populations may have had their own ancient encounters with Neanderthals or closely related groups.

East Versus West

One of the more curious findings in this field is that East Asians carry more Neanderthal DNA than Europeans. Early studies suggested the difference was about 20 percent more in East Asians. More recent analysis has revised this down to about 8 percent, but the gap remains.

Why would this be? Several hypotheses compete for attention.

The first possibility is multiple interbreeding events. Perhaps modern humans mixed with Neanderthals once as they left Africa, and then the ancestors of East Asians encountered Neanderthals again as they moved further east. Each additional mixing event would add more Neanderthal DNA to the gene pool.

The second possibility involves dilution. Maybe Europeans started with the same amount of Neanderthal ancestry, but subsequent migrations into Europe brought in populations with less Neanderthal DNA, diluting the average. The Neolithic farmers who spread agriculture across Europe, for instance, may have had lower Neanderthal ancestry than the hunter-gatherers they partially replaced.

A third hypothesis invokes population size. Smaller populations are less efficient at purging harmful genetic variants through natural selection. If the ancestors of East Asians went through severe population bottlenecks during their migration, they might have retained more Neanderthal DNA simply because selection pressure was weaker.

Computer simulations suggest the third explanation alone can't account for the difference, pointing toward more complex scenarios involving multiple pulses of interbreeding.

Which Neanderthals?

Not all Neanderthals contributed equally to modern human ancestry. Scientists have now sequenced genomes from Neanderthals found across Eurasia—from Spain to Siberia—and they can trace which populations were most closely related to our ancestors' partners.

The Neanderthal DNA in modern humans most closely matches specimens from Vindija Cave in Croatia and Mezmaiskaya Cave in the North Caucasus. It's more distantly related to the Altai Neanderthal from Siberia. This suggests that the interbreeding happened primarily with a western Eurasian Neanderthal population, perhaps somewhere in the Middle East as modern humans first expanded out of Africa.

The timing appears to be between 47,000 and 65,000 years ago. But here's a twist: the modern human DNA found in Neanderthals comes from an earlier period, around 100,000 years ago. This means there was an earlier wave of modern humans leaving Africa—before the main out-of-Africa migration that gave rise to all non-African populations today—and these pioneers interbred with Neanderthals. Their own lineage didn't survive to the present day, but their genes lived on in Neanderthals for tens of thousands of years.

The Missing Maternal Line

There's something strange about the genetic inheritance from Neanderthals. We carry their DNA in our regular chromosomes—the ones we inherit from both parents—but no one alive today has Neanderthal mitochondrial DNA.

Mitochondria are the energy-producing structures inside cells, and they have their own small genome. Unlike nuclear DNA, which comes from both parents, mitochondrial DNA passes only from mother to child. If Neanderthal women had children with modern human men, and those children had children, and so on, we would expect to see Neanderthal mitochondrial DNA in some populations today.

We don't.

Several explanations have been proposed. Perhaps Neanderthal mitochondrial DNA had harmful mutations that caused it to be selected against over time. Perhaps the children of Neanderthal mothers were raised in Neanderthal groups and went extinct alongside the rest of the Neanderthals. Perhaps unions between Neanderthal females and modern human males simply didn't produce fertile offspring.

This last possibility—that hybrid incompatibility was asymmetric, working differently depending on which species was the mother—has some support from biology. Many animal hybrids show exactly this pattern, where crosses work in one direction but not the other.

But there's a complicating finding. The Neanderthal Y chromosome—the male sex chromosome—also doesn't appear in Neanderthals from later time periods. Instead, it was replaced by a modern human Y chromosome that introgressed into Neanderthal populations between 100,000 and 370,000 years ago. The same thing happened with Neanderthal mitochondrial DNA, which was also replaced by a modern human variant.

This suggests that modern human genetic material might have provided advantages that caused it to spread through Neanderthal populations, eventually replacing the original Neanderthal versions entirely. We weren't just absorbing their genes—they were absorbing ours, too.

How Much Interbreeding?

Given that modern humans and Neanderthals overlapped for tens of thousands of years across a vast geographic range, how often did they actually interbreed? The answer appears to be: remarkably rarely.

Mathematical models suggest that the observed levels of Neanderthal ancestry could result from an exchange of just one pair of individuals between the two populations every 77 generations. That's roughly one successful mixed pairing every two thousand years. This wasn't a grand romance between species—it was an occasional, possibly accidental, occurrence.

Such low rates of interbreeding explain why Neanderthal mitochondrial DNA had only about a 7 percent chance of making it into the modern human gene pool at all. The matings were rare enough that entire categories of Neanderthal genetic material simply never got passed along.

The Purge

Here's the uncomfortable truth about our Neanderthal inheritance: natural selection has been systematically removing it for forty thousand years.

Early modern humans in Eurasia carried more Neanderthal DNA than we do today—around four to five percent, compared to our current one to two percent. Over thousands of generations, selection pressure has been chipping away at the Neanderthal contribution, eliminating variants that reduced survival or reproduction.

This process, called purifying selection, has created what geneticists call "deserts"—large regions of the genome where Neanderthal ancestry is almost entirely absent. These deserts are particularly pronounced on the X chromosome, which shows five times less Neanderthal ancestry than the other chromosomes. They also appear in genes expressed in the testes.

The pattern points strongly toward hybrid male infertility. When two closely related but distinct species interbreed, their male offspring are often less fertile than females. This is called Haldane's rule, after the geneticist J.B.S. Haldane who first described it. The X chromosome and testes effects both fit this pattern perfectly.

Male hybrids between modern humans and Neanderthals probably had reduced fertility. Over time, any Neanderthal genes that caused this problem were selected against and eventually disappeared from the human gene pool. What remains is the Neanderthal DNA that didn't cause reproductive problems—or that provided enough benefits to outweigh any costs.

The Gifts

Not all Neanderthal genes were deleterious. Some provided genuine advantages, and these have been actively favored by natural selection.

Consider the immune system. Neanderthals had lived in Europe and western Asia for hundreds of thousands of years, adapting to local pathogens. When modern humans arrived, they inherited some of this hard-won immune knowledge. The Human Leukocyte Antigen system, which helps the body recognize and fight infections, shows heavy enrichment for introgressed Neanderthal variants. These borrowed immune genes may have helped our ancestors survive diseases they had never encountered in Africa.

Skin and hair also show strong signals of adaptive introgression. Neanderthals had evolved to cope with the cold, cloudy environments of Ice Age Europe. Modern humans arriving from sunny Africa needed to adjust. Inheriting Neanderthal variants affecting keratin—the protein that forms skin and hair—may have helped them adapt more quickly than they could through new mutations alone.

The list goes on: genes affecting sugar metabolism, muscle contraction, body fat distribution, enamel thickness in teeth, and even aspects of brain size and function. In each case, Neanderthals provided a shortcut. Rather than waiting for beneficial mutations to arise by chance, modern humans could borrow adaptations that had already been tested over hundreds of thousands of years.

The Denisovans contributed similarly useful variants. The most famous example involves high-altitude adaptation in Tibet. Tibetans carry a variant of the EPAS1 gene that allows them to thrive at elevations where most humans suffer from altitude sickness. This variant came from Denisovans. Somehow, those mysterious hominins—or at least some population of them—had adapted to high altitude, and Tibetans inherited that adaptation through ancient interbreeding.

What It All Means

The discovery of archaic admixture hasn't just filled in details about human prehistory. It has fundamentally changed how we understand what a species is and how species interact.

For decades, biologists defined species partly by their inability to interbreed successfully with other species. Neanderthals and modern humans were classified as separate species—Homo neanderthalensis and Homo sapiens—under the assumption that any interbreeding would have been rare and unproductive.

We now know that these "separate species" exchanged genes regularly enough to leave a permanent mark on billions of people alive today. The children of those unions were fertile enough to pass along their mixed heritage for thousands of generations. Whatever barrier existed between the species, it wasn't absolute.

This has implications beyond human evolution. If two species as distinct as modern humans and Neanderthals—separated by hundreds of thousands of years of independent evolution—could interbreed successfully, similar processes probably occurred throughout evolutionary history. The tree of life may be less like a tree and more like a tangled web, with branches regularly exchanging genetic material.

There's also something humbling about carrying Neanderthal DNA. We like to think of ourselves as the pinnacle of evolution, the species that outcompeted all others. But our success wasn't entirely our own. We borrowed from the peoples we replaced—took their genes, their adaptations, their solutions to problems we hadn't yet encountered. The Neanderthals live on, not as a separate species, but as part of us.

Their extinction was not quite as complete as we once believed. And we are not quite as purely "modern human" as we once assumed. The boundaries between us and them were always blurrier than the fossil record suggested. Now, written in the genomes of billions of people, we have proof that those boundaries were crossed again and again, leaving a legacy that persists to this day.