Built to Last: Continuity in Japanese Genetics

A nation endures across the millennia

Ten companies exist on the planet today that were founded before 1000 AD. Seven of those are Japanese, the oldest being Kongō Gumi, a construction firm founded by three craftsmen from Korea who took a commission from Prince Shōtoku in 578 AD. Shōtoku was the great early patron of Japanese Buddhism and was responsible for constructing the Shitennō-ji temple, Japan’s oldest Buddhist house of worship (still in operation, image above). The Kongō clan continued to operate their family firm for centuries, contributing for example to the construction of Osaka Castle in the 1500’s. In the early 2000’s, a scion of this business dynasty, Masakazu Kongō, was still Kongō Gumi’s CEO. But his poor business decisions finally led to its acquisition by a larger firm in 2006. No pressure, Masakazu-san.

The extraordinary longevity of Kongō Gumi (and the fact that it is but one among the majority Japanese contingent in the record books) tells us something significant about the nature of Japanese culture and the value it places on antiquity and continuity (still on the historic if not quite millennial scale, 3,146 of the world’ 5,586 companies older than 200 years are based in Japan). While the Japanese continue to maintain Buddhist temples built 1,400 years ago, conventional wisdom among Uighur Muslims of Turfan ascribes the construction of that city's ancient temples to their Mongol neighbors; the fact that until 1389 AC their rulers were Buddhist and the nation was once devoutly Buddhist have long since passed from common knowledge. A deep attachment to historical memory and tradition is at the root of Japanese identification with their ancestors. No other modern nation has continued to cherish and cultivate its native animist tribal religion as the Japanese have Shinto, fusing its primitive raw spirituality with the more metaphysical Buddhism (in contrast, nearby Korea’s shamanism is culturally marginal and viewed by Koreans with something like embarrassment, even if it is numerically influential).

Japanese reverence for continuity and antiquity was on display in 2020 when Prime Minister Taro Aso declared “No other country but this one has lasted for as long as 2,000 years with one language, one ethnic group and one dynasty.” Of the 125 million residents of the islands of Japan, 98% are ethnic Japanese or Yamato. Japan as a nation-state with Western-style laws and political institutions dates to the late 19th century, long after Yamato identity as a people ruled by their Emperors had been set. To this day, the Japanese view their nation-state as the political manifestation of the Yamato race and its storied cultural traditions, as opposed to the expression of ideals like liberty or justice. This ethnic, rather than idealistic, cast to notions of Japanese nationhood finds outlet in moments like when the first mixed race woman won Miss Japan in 2015; many Japanese objected to her representing them because of her race (her father is a black American). She did not meet her fellow citizens’ definition of Japaneseness, because she was not of 100% pure Yamato blood.

Aso’s contention reflects more than values and aspirations; it typifies the widespread Japanese belief that a single people have inhabited Japan since the Chinese annalists first noted the exotic land of Wa in the islands to their east nearly 2,000 years ago. But for many Japanese, their history began far earlier, with Emperor Jimmu’s founding of the Yamato dynasty in 660 BC. Legend has it that Jimmu and his brothers were lords in the southwestern island of Kyushu, but expanded their domains to the main island of Honshu through war and conquest. The current Emperor of Japan claims descent from Jimmu, tracing his legendary lineage back more than 2,600 years, though the first historically attested emperor is Kimmei, who reigned from 539-571 AD. If the rulers of Greece dated back even to Kimmei’s time, Athens’ emperors today would be descendants of Justinian the Great.

The Chinese first described Wa as a land of fractious principalities at war among themselves, but by the third century AD, the islands came to be ruled by a paramount ruler, the head of the House of Yamato. And so the Japanese self-conception as one people, one nation, with one history, does have attested roots as far back as two millennia. 

But Japan’s story is more interesting than the bland potted history taught in schools, and Aso’s sweeping contention leaves out compelling chapters in the narrative. At the beginning of Japan’s written history, the Yamato shared the islands with other peoples. In the fifth century, the Chinese claimed that there were mojin, or “hairy people,” in Japan. The Yamato called them Emishi, and between the 700’s and 900’s the Japanese imperial state fought a war of conquest against these barbarians of northern Honshu. Though the Yamato defeated the Emishi, they did not exterminate or banish them. Instead, the Emishi were assimilated into the Yamato. Emishi ruling clans were integrated into the nobility, while the Yamato adopted the deadlyEmishi military practice of horse archery, eventually giving rise to the samurai tradition that continued to the 19th century, a millennium later.

The Emishi’s existence belies Aso’s claim about the Japanese nation-state’s continuity as a homogeneous ethnos that occupied the whole of the archipelago. When Japan’s native historical tradition began in the sixth century AD, the Emishi dominated the modern region of Tōhoku, the northern third of Honshu. Legends recorded in the 8th century AD refer to Emperor Jimmu defeating the Emishi in the center of Honshu itself, possibly recalling the more widespread range of these barbarians in the past. And the cultural extirpation of the Emishi was a gradual centuries-long process. The last Emishi tribe that inhabited the northernmost point in Honshu, the Tsugaru peninsula, revolted against their Yamato rulers as late as the 14th century AD.

The Emishi persistence exposes a more complicated ethnogenesis of the modern Yamato than the mainstream narrative; the Japanese cannot have emerged fully formed from the clan of Emperor Jimmu 2,600 years ago. They were an amalgamation of at least two peoples, perhaps more (just as outsiders often classify the native peoples of North America as “American Indians,” while they’ve always considered themselves many distinct and separate nations, so it is possible the Emishi also were significantly culturally divided among themselves, even if not discernibly so genetically). Imperial historical records themselves document the conquest, assimilation and integration of a set of tribes who were avowedly not of the Yamato race on the largest island of Japan centuries after the presumed emergence of a pure and homogeneous race on the archipelago.

But we no longer have to rely on fragmentary mentions in Japanese historical documents and Chinese amateur ethnography to probe the origins of the Japanese. Today, archaeology and genetics allow us to rewind the clock and observe what likely happened thousands of years ago. The scientific excavation of Japanese genetics now yields strong evidence of a synthesis between very distinct threads of human ancestry.