Who Are You?

Three distinct ancestral lineages are inscribed in the modern Japanese genome.

In 2021, an international research team led by Kanazawa University published a paper proposing a revision to the standard account of Japanese origins. The conventional dual-structure model held that the population arose from the intermingling of Jōmon people and Yayoi immigrants; in its place the team proposed a tripartite-structure model, in which a further wave of migrants arrived during the Kofun period (3rd–7th century CE).

In 2024, the RIKEN research institute analyzed the complete genomes of 3,256 individuals and refined the model further. Three ancestral components—Okinawan (K1), Tōhoku or northeastern (K2), and Kansai or western (K3)—mix in intricate patterns across modern Japanese populations.

Japan is home to 80,507 Shinto shrines, roughly 1.5 times the number of convenience stores in the country.

Their distribution is uneven, and the pattern is legible. Shrines of the Hachiman lineage are the most numerous at about 7,800, followed by Shinmei at about 5,300 and Suwa at about 5,000. These concentrations trace the migration routes of ancient peoples and the spread of the faiths they carried.

A himorogi (神籬; historically himoroki) is a temporary precinct or installation for the worship of kami, the deities of Shinto. It has often been described as a ritual form that predates widespread permanent shrine buildings, though archaeologists dispute whether its ancient form can be equated directly with today’s arrangement centered on the sakaki evergreen. HIMOROGI takes the word as a metaphor for a place where different evidence and interpretations meet (see Chapter 2, “Himorogi—Ancient Word, Modern Form”).

Tadanobu Tsunoda reported that different listeners process the song of bell crickets in different parts of the brain.

Tadanobu Tsunoda of Tokyo Medical and Dental University spent thirty years from the 1970s on the relationship between language and the brain. His conclusion was unexpected. Japanese speakers process natural sounds—the chirping of insects, the whisper of wind, the murmur of a stream—in the left hemisphere, the seat of language. Speakers of English, French, Chinese, and most other languages process those same sounds in the right hemisphere, the domain of non-verbal noise.

The account turns on the vowel-dominant structure of Japanese, one of the world’s rare “vowel languages.” The five vowels—a, i, u, e, o—form the skeleton of the language, and a single vowel can carry meaning on its own (“i” for stomach, “e” for picture, “o” for tail, “ka” for mosquito). A brain raised in that linguistic environment detects vowel-like frequency patterns even in natural sounds and routes them to the language center as meaningful.

For a Japanese speaker, then, the song of insects is not noise but something spoken to the listener. This difference at the level of neural circuitry may be the biological foundation of the worldview called yaoyorozu no kami—the myriad deities, a recognition of spirit in every element of nature. Language does not simply reflect a culture. Language builds the brain, and the brain decides how the world sounds.

There are reports that non-native speakers who live in Japan for long periods and immerse themselves in the language begin to show the same tendency. Language rewires the brain through environment rather than genetics. The result is a second brain, one built by the Japanese language itself.

The Jōmon period is often cited for its unusually long span with little archaeological evidence of organized warfare.

The Jōmon period ran from roughly 16,000 years ago to about 300 BCE, and for more than ten thousand years the people of the archipelago lived without organized warfare. The archaeological record bears this out. Among tens of thousands of excavated artifacts, not one weapon designed to kill people has been found: no swords, no shields, no fortification walls, no defensive moats. Stone arrowheads and bone tools for hunting are present, but no implement purpose-built for harming people has turned up.

Mesopotamia moved to organized warfare within a few thousand years of adopting agriculture. The Yellow River and Indus Valley civilizations followed the same course. Why the Jōmon alone sustained so long a span without war is the question archaeologists have tried to answer.

They point to the “circular settlement” as one factor. Jōmon villages were arranged in rings, with a central plaza or burial ground at the core. No king’s palace dominated the center; every dwelling stood at equal distance around an empty heart, an architecture of community without domination. About 95% of excavated dogu (clay figurines) are found deliberately broken, and archaeologists read the practice as transferring illness or injury into the figurine, which was then shattered as a prayer for healing. Violence was not directed at others but sealed inside vessels of earth. This was the ritual technology of the Jōmon.

The concept of the “Four Great Civilizations” rests on a Western framework that measures civilization by agriculture, writing, metallurgy, and urbanization. Whether ten thousand years of peace counts as primitive by that measure is a fair question. The Jōmon period puts pressure on the definition of civilization itself.

From August 15, 1945, the day of defeat, the psychological architecture of people in Japan was deliberately and systematically restructured.

The War Guilt Information Program (WGIP), implemented by GHQ (General Headquarters of the Supreme Commander for the Allied Powers), was an information campaign designed to instill a sense of war guilt in the population. The Shinto Directive dismantled State Shinto, the Imperial Rescript on Education was abolished, moral education courses were withdrawn, and martial arts were banned. All of it was carried out in the name of eradicating militarism, and all of it uprooted spiritual traditions built up on the archipelago over thousands of years.

A further fact emerged in the 2000s, when declassified U.S. State Department documents confirmed that Matsutaro Shoriki, president of the Yomiuri Shimbun newspaper, had served as a CIA asset. His codenames were “PODAM” and “POJACKPOT-1.” Shoriki led the construction of Japan’s postwar television broadcasting network, which means that the media infrastructure carrying information to the public after the war was in part designed as an extension of occupation policy.

The question worth asking is not whether this amounts to conspiracy. The documented facts—the existence of WGIP, the implementation of the Shinto Directive, Shoriki’s CIA ties—are matters of public record. What matters is the effect they had on a national sense of self. The swing runs from a prewar excess of self-affirmation (“Japan is a divine nation”) to a postwar excess of self-negation (“Japan is a perpetrator”), and the amplitude of that swing is itself the scar tissue of psychological re-engineering.

To this day, many people in Japan feel a faint unease in speaking of their own cultural roots. It is the fear of being labeled “right-wing,” a ghost program still running eighty years after the war.

The fragments can now be set side by side.

The genome holds the memories of three ancestral lineages. Eighty thousand shrines blanket the archipelago, and their distribution mirrors the map of genes. Japanese, a vowel language, has sculpted a brain that hears nature as speech. The Jōmon sustained ten thousand years of peace in circular societies with no seat of power. And after the war, all of these memories were systematically sealed away.

These are not scattered facts; they converge on a single question: “Who are the Japanese?” For the geneticist the answer lies in sequences of DNA, for the linguist in the architecture of vowels, for the archaeologist in the fragments of clay figurines, for the historian in the documents of occupation policy. It is one question lit from different angles.

HIMOROGI examines Japanese origins from six perspectives: the findings science draws from the genome, the old memories shrines preserve, the deep psychology urban legends reflect, the universality that surfaces in connections with the world, and the cosmos, where consciousness meets matter.

HIMOROGI does not dismiss urban legends as “lies.” The question “Why do people want to believe this?” is itself a light on the spiritual history of the archipelago. Facts that science can verify and stories that resist verification yet keep their hold are set out here side by side, with the same respect.

The chapters that follow take those questions one at a time.

One more perspective belongs here, before the chapters begin.

Of the world’s 196 countries, only Japan carries the character for “sun” in its name: hi izuru tokoro, the land where the sun rises. That self-definition was at once a geographical fact and a civilizational claim. At the eastern edge of the world, where sunlight first arrives, people crossed the seas and made landfall. What were they seeking when they came?

The Jōmon arrived from the south, the Yayoi from the continent, and the Kofun-period immigrants from lands further off still. Wave upon wave overlapped and intermingled until they formed the single collective now called “Japanese.” The record their genes carry reaches back tens of thousands of years.

HIMOROGI takes its name from a word for a temporary ritual precinct or installation, one that appears in ancient texts and continues in present-day practice. Its material form need not have remained unchanged across time. HIMOROGI adopts that space between the documented and the unsettled as an editorial metaphor: a place where different forms of evidence and interpretation can meet without being collapsed into one answer.

Who are you? The answer is scattered across your DNA, your mother tongue, the shrines you visit, and the legends still unread. Gathering those fragments begins now.