The Japanese, an Endangered Species Carrying Archaic Humans｜Neanderthals and Denisovans

Within our bodies, traces of those who should long since have vanished are still breathing.

About 40,000 years ago, the Neanderthals disappeared abruptly from the lands of Eurasia. Shrouded in mystery, they are usually described as “another humanity” that Homo sapiens interbred with and drove out. Yet they did not simply perish. Deep in our cells, within the genome that serves as the blueprint of life, they have left an unmistakable mark, and through it they live on.

Remarkably, the genomes of modern Japanese people contain roughly 2 to 3 percent Neanderthal DNA. Interbreeding with Neanderthals is itself evidence that modern humans, after leaving Africa, mixed with the archaic humans who already lived in the lands they entered, and everyone of non-African descent carries roughly 1 to 4 percent of that inheritance. Carrying archaic genes, in other words, is nothing rare by global standards.

The genomes of East Asians like us, however, are distinctive in striking ways. First, East Asians have been found to carry 20 to 40 percent more Neanderthal genes than Europeans. Second, they have inherited the blood not only of the Neanderthals but also of another extinct archaic human, the Denisovans.

In 2024, a study made a quiet but profound impact. When RIKEN and other Japanese institutions analyzed the whole genomes of 3,256 Japanese people, they found that the genomes of modern Japanese contain no fewer than 44 regions of DNA derived from archaic humans. According to RIKEN’s report, 11 of these regions come from Neanderthals, with contributions from Denisovans and others layered on top.

The legacies of several extinct humans are woven together like a mosaic, and they still survive at high frequency. Here lies the rare singularity of the Japanese genetic background, and in fact no other people in the world are quite like this. In a sense, the Japanese may be an endangered species, one that still carries in its genome several archaic humans older than Homo sapiens and lives on.

What is intriguing is that this ancient genomic inheritance is no mere memory of the past. It is deeply bound up with the bodies we live in now, and with illness itself.

For example, a genetic variant around SLC16A11 inherited from Neanderthals is known to raise the risk of type 2 diabetes and abnormal lipid metabolism by about 25 percent, and the genetic burden East Asians bear from it is roughly 21.5 times that of Europeans. NKX6-1, which comes from Denisovans, is also involved in insulin secretion and acts as a diabetes risk particular to the Japanese.

In the same way, the TLR gene cluster from Neanderthals is the legacy of an immune system sharpened long ago to fend off unknown pathogens, but in a modern world with far fewer pathogens, it has become a source of overreactions such as atopic dermatitis and allergies. The further genetic analysis advances, the more the mystery of our very existence as “Japanese” rises up from the depths.

What interests me most personally is the link to depression, which is common among Japanese people. In 2016, a large American study that matched the electronic health records of about 28,000 people with their genomes showed that specific DNA sequences inherited from Neanderthals were significantly associated with the risk of depression in people today. The research is still in progress, but Neanderthal gene variants are thought to account for perhaps 1 to 2 percent of an individual’s risk of developing depression.

What we must not misread is that the Neanderthals did not carry some “defective gene that causes depression.” The truth was the opposite. To begin with, the variants most strongly correlated with depression risk cluster near the genes of the body clock, the genes that govern circadian rhythm.

For modern humans who left Africa and stepped into high-latitude Eurasia, where daylight swings violently with the seasons, it was a wisdom on which survival depended to take on the sleep and waking rhythms of the Neanderthals, who were already adapted to that environment. To pass through the darkness of brutal winters and bring the body into step with the cycle of light was a brilliant shortcut that evolution had laid ready.

Today, however, with nature laid waste, with artificial lighting and blue light all around us, and with night work and irregular lives become the norm, this ancient rhythm falls into a serious mismatch. A body clock optimized for a primeval environment loses its way in the light of cities that never sleep, twenty-four hours a day. That this gives rise to sleep disorders and opens the door to depression is a fact.

The immune system carries the same structure. Some of the genes inherited from Neanderthals heightened inflammatory responses to unknown pathogens and sped up blood clotting to prevent bleeding. Yet this robust immunity, which saved lives in ancient times, turns into excessive inflammation in a modern world where hygiene has gone too far. And now the chronic, low-grade inflammation that smolders quietly in the brain is regarded as a leading candidate among the causes of depression.

This is the clearest evidence that the power that once protected ancient bodies is, across the gulf of time, eating away at the minds of people today. Japan’s reputation as the world’s most gambling-addicted nation, the land of pachinko, shares the same root, as do the effects on mood disorders that work through changes in the structure of the brain. The more “old genes” people carry, the worse the modern environment suits them. Indeed, modernity itself could be translated as a structure produced by the forces of Homo sapiens in an effort to sweep the old powers off the face of the earth once and for all, and the further genetic research advances, the more squarely we will find ourselves facing a vast contradiction.

Our melancholy, then, may be neither personal weakness nor a disorder of brain chemistry, but the echo of a deep rift between bodies adapted to a primeval environment and the modern civilization that raced ahead and left those bodies behind.

At the same time, “the Japanese” themselves have a complex genomic structure built on three ancestral populations. Beneath that foundation, the legacies of the Neanderthals and Denisovans, older than Homo sapiens, are folded in layer upon layer, drawing a map of disease susceptibility unlike any other in the world. The “evolutionary shortcuts” that humans once seized in order to survive in new lands now smolder within us, after drastic changes in the way we live, as the embers of modern diseases such as depression, type 2 diabetes, and allergies.

Are the Japanese, heirs to the legacies of several extinct archaic humans, destined to go extinct wherever the modern age is heading? Or will they become the one light that shows what lies “beyond” the world of Homo sapiens, the conqueror that has gone too far, made everything excessive, and finally reached a dead end?

How closely can we listen to the ancient voices still sleeping within us? And what are those who were supposed to have perished trying to tell us? Our bodies, as we make our way through the second half of the twenty-first century, are already asking that question from the depths of life itself.