First-time ever DNA study: haplogroup N9b marker shows continuity from Jomon to Emishi people of Tohoku

Jomon ancestry in the Tohoku: initial DNA studies.
(Reproduced from the Emishi-ezo webpage URL:

A recent publication in kotsu kokogaku to Emishi, Hayato (2012:100-4) traces the DNA of material taken from ancient to modern remains of skeletal material from the Tohoku region (northestern Honshu). This is the first time such an analysis has been done that the author is aware of. It puts more teeth into the science that has already been accumulating from the skeletal (mainly cranial) studies done.

Studies done previously on the Hokkaido Jomon (2012:100) is consistent with the Tohoku data, and consistently show the DNA marker for the Jomon is the haplogroup N9b. The percentage for this group in the sample taken from the Jomon of the Tohoku (N=20) is sixty percent. The authors point out that this haplogroup N9b shows up relatively high among this population group.

Going forward in time to the Heian through Medieval time periods (2012:103) after the conquest of the Emishi (a group whose core populaion is still assumed to be mainly Jomon) the haplogroup N9b shrinks to 9.1 percent of the remains studied (N=12). Other markers that are widespread among other East Asian people as a whole such as haplogroup D4 expands to 36.4 percent (from 5 percent during the Jomon period), by far the largest haplogroup during this time reflecting the population studies shown elsewhere of the influx of Yayoi immigrants. It must be pointed out that the number in this sample is fairly small.

The Edo sample (seventeenth century) is an anomaly that does not fit into this gradual shift. Though the sample is from Aomori prefecture (N=30) and represent the northern most part of the Tohoku there are no N9b haplogroup markers at all, and the D4 marker at 43.3 percent is higher than what it is in modern Japan a statistical impossibility. The explanation for this is that the human remains come from one location, Hatakenai, and it looks like this one location had a preponderance of Yayoi Japanese who settled here early before the Edo period.

The modern sample that is much larger (N=336) shows the haplogroup N9b at 2.7 percent. This is pretty sizable when considering the centuries of Yayoi Japanese settlement that took place. The D4 group shows at 36.9 percent in the modern population that is only a few tenths of a percentage above the Heian-Medieval sample.

The last DNA sample comes from the Kofun period, germane to this study, but the sample size at three is far too small to be anything but random. However, interestingly two out of the three individual remains show that they were in the N9b haplogroup. This maybe a random finding but nonetheless show what was seen already in other population studies that Jomon people continued to live side by side with the Yayoi kofun population in the Tohoku.

The limitations of this study is very apparent in the small sample sizes, and regional anomalies such as the sample from the Edo period of Aomori that obviously does not reflect the population of the Tohoku as a whole. There is also a possibility that the N9b haplogroup is larger than that reflected in the Heian-Medieval sample and that the D4 group is smaller. However, due to the small size of the sample this is not reflected in the data. The problem is in finding recoverable DNA material which is difficult at best from remains that are hundreds of years old. The one conclusion with near certainty is that the N9b haplogroup reflects the Jomon population, and that traces of the Jomon can be found even in the modern Japanese population in the Tohoku. However, even though the findings from the Heian-Medieval is suggestive, both that sample and the Edo sample needs more data to be useful. The Edo sample needs to include more remains from other regions of the Tohoku. The Heian-Medieval sample though geographically widespread needs more numbers to verify the population markers. The other issue with the study is the lack of analysis of other DNA markers which were found in the Jomon sample, and in the other samples. Though N9b is dominant among the Jomon there were other markers which seemed to be persistent across the different time periods as well but were not part of the analysis.


Adachi, Noboru., “Emishi no iden shi-kei o saguru” (In search of Emishi heredity) in Tagikagwa, Wataru, ed., Kotsu koko gaku to Emishi, Hayato. Tokyo: Doseisha, 2012.

Origin of haplogroup N9b

This paper linked below ties the prehistoric Jomon people of Hokkaido, by highlighting mtDNA haplogroups that originate from southeastern Siberia, but some haplogroups present there today were lacking in them. On top of the inherited Jomon gene pool, this paper shows major lineages tying the Ainu to the Okhotsk people of Siberia.

Mitochondrial DNA analysis of Hokkaido Jomon skeletons: Remnants of archaic maternal lineages at the southwestern edge of former Beringia (Noboru Adachi et al. AJPA DOI: 10.1002/ajpa.21561)

Abstract: To clarify the colonizing process of East/Northeast Asia as well as the peopling of the Americas, identifying the genetic characteristics of Paleolithic Siberians is indispensable…. In the present study, we analyzed ancient DNA recovered from Jomon skeletons excavated from the northernmost island of Japan, Hokkaido, which was connected with southern Siberia in the Paleolithic period. Both the control and coding regions of their mitochondrial DNA (mtDNA) were analyzed in detail, and we confidently assigned 54 mtDNAs to relevant haplogroups. Haplogroups N9b, D4h2, G1b, and M7a were observed in these individuals, with N9b being the predominant one. The fact that all these haplogroups, except M7a, were observed with relatively high frequencies in the southeastern Siberians, but were absent in southeastern Asian populations, implies that most of the Hokkaido Jomon people were direct descendants of Paleolithic Siberians. The coalescence time of N9b (ca. 22,000 years) was before or during the last glacial maximum, implying that the initial trigger for the Jomon migration in Hokkaido was increased glaciations during this period.

[The study also notes that Hokkaido Jomons lack specific haplogroups that are prevailing in present-day native Siberians, implying that diffusion of those haplogroups in Siberia might have been after the beginning of the Jomon era, about 15,000 years before present…thus showing the antiquity of the Jomon genes]

Another study by Shinoda of mtDNA across the different tine periods, and also across regions, shows that Jomon Tohoku and Jomon Hokkaido were the most alike in sharing the N9b and M7a Jomon markers, while showing the least diverse set of genes, but that from Epi-Jomon and Satsumon periods onwards, Hokkaido populations gained the G and Y genes from Northeast Siberia and the Amur region, while Tohoku lacked Yayoi components, gaining new genetic components from adjacent Kanto regions…only from the Edo Period onwards which suggests, those new genetic components were gained after pacification of the area by the Yamato regime and at a very late stage. Nevertheless, the Tohoku still remains most representative and closest to ancient Jomon peoples todate. The study, unfortunately is limited only to mtDNA, Y-DNA might likely be more informative on new arrivals from the continent if any.

Who then were the Emishi?

In “Rethinking Japanese History” Amino Yoshiko writes:

“From the perspective of the ruling class of the Ritsuryo state (centered as it was in Yamato), all of northern Honshu and the northern part of Niigata — then known as Koshi– was an area known as Emishi. It was inhabited by a people the Ritsuryo rulers considered different….

About the same time [as when the Satsumon culture transformed the Jomon culture in northern Japan extending as far as the northernmost sections of the Honshu], it appears that a branch of the Amur River-based Tungus people, either the Joshun or the Gilyak, had settled in eastern Hokkaido, bringing with them the Okhutsk culture. This culture was completely different from previous societies in the Japanese archipelago. Its people were so skilled at sailing and ocean hunting (of whales and so on) that they have been called the Northeast Asian Vikings. The bear worship of the Ainu, who came later, is said to have been  influenced by this culture. In any case, the Satsumon people were active traders, frequently traveling across Northeast Asia. Through their movements, northern culture influenced the peoples living in northern Honshu and on the Kanto Plain.

For example, recent excavations have uncovered the remains of a large-scale foundry in southern Tohoku [it was always assumed that casting technology moved from west to east] … when the Tohoku foundry remains are compared to those found in the west, the Tohoku are found to be much bigger. Traces of ironworks have also been discovered in northern Tohoku. In addition, the “inner ear” pots of the Northeast Asian hunting peoples can be found in Tohoku, Kanto, and the central Alps region. Ritsuryo aristocrats and officials who were stationed in the Kanto area are also engaged in trade with the Emishi people. From about the eighth or ninth century on, the frequency with which they bought horses from the Emishi became a problem for the central government. This means that horses were being raised in large numbers in the Tohoku region, with a culture of horse breeding and training already well-developed. There is a strong possibility that this culture came from the north.”

The Emishi are known to have lived in northeastern Japan, in the area of Tohoku around the river Kitakami (which suggests “god of the Khita(n)), and called the land of Hokkaido, kita-no-kuni (as it is still referred to today) which means country of the Khita. From the circumstantial evidence, it is also possible that the horse-riding nomadic Khitan tribes may actually have been present (they would have contributed haplogroup C3 Y-DNA material to the genepool of the northern Japan.

The Emishi at least based upon circumstantial evidence, referred to their northern neighbours as the Kita, a reference to their awareness of the fiercesome presence of proto-Khitan tribes, and there are many Kita surnamed people still in Japan, a possibly forgotten heritage from the north. Who were the Khitan / Kita people?

“The Mongols held on to their stronghold in today’s Guangxi-Yunnan areas much longer after they lost China. Recent DNA tests conducted against the remains of the Khitan tombs, however, pointed to the possibility that those Mongolians in today’s Yunnan-Guangxi areas were more Khitan than Mongolian, and in fact those people had historically claimed that they were the descendants of Khitans who were dispatched to southern China by the Mongols in the 14th century. (The DNA tests, interestingly, also linked the Dawo’er or Dagur people in today’s Manchuria as the closest kin of the ancient Khitans.)

The New History Of Tang Dynasty mentioned that the Khitans were descendants of the Kebi’neng Xianbei. (Alternatively, The Old History Of Five Dynasties said that the Khitans were an alternative race of the Huns.) In the section Sixteen Nations, we mentioned that the Yuwen Xianbei, after fleeing to the north of Song-mo (pine desert in the Jehol mountains, i.e., today’s sandy river basin along the Laha-he River or the origin of the Western Liao River), later split into two tribal groups of Kuzhen-xi and the Khitans. In February 344, Murong Huang defeated Yuwen Gui at Changli, driving the Yuwen Xianbei remnants to north of the desert. So to say that the Tanshikui Xianbei engendered the Yuwen clan, and the Yuwen clan, after a defeat, fled to the north where they were to become the ancestors of the Khitans. Historian Lv Simian had a thorough dissertation on the Xianbei or Tungunsic people, including the tracing of the Khitans and Kuzhen-xi [i.e., Xi] people. The New History Of Tang Dynasty said that by the time of Tuoba’s Northern Wei Dynasty (AD 386-534), the ancestors of the Khitans adopted the name ‘Khitan’ for themselves. The Khitans lived around the Liao River in today’s Manchuria. To the east of the Khitans will be Koguryo, to the west the Xi Nomads, to the north Mohe (Malgal) and Shiwei Tribes, and to the south Yingzhou Prefecture of Tuoba Wei Dynasty.”

The Emishi on the other hand, may have been a Saka-descended tribe, or have had a significant northern Altaic genetic component.

The Emishi or Ebisu (蝦夷) constituted a group of people who lived in northeastern Honshū in the Tōhoku region which was referred to as michi no oku, outside of the control of the Yamato polity. The original kanji (毛人) means ‘Hairy Men’, and is seen in Chinese accounts as a term to describe those outside of the ‘civilized’ lands (i.e. beyond Chinese control).
However, the term Emishi appears to have been applied to various Japanese families as well, depending on their relationship with the court. Many famous families of later periods, including the Fujiwara family appear to have originated as local Emishi leaders.

By the Nara period, most of the Emishi people were located in the provinces of Dewa and Michinoku (aka Mutsu); by this time, the kanji 毛人 fell out of use, and were replaced with 蝦夷 as the most common characters to refer to the Emishi.

Some Emishi tribes resisted the rule of the Japanese Emperors during the late Nara and early Heian periods (7th–10th centuries CE).

Because Emishi clans are found among the Mainstream Yamato Japanese, many scholars are of the view that they were natives of northern Honshū and were descendants of those who developed the Jōmon culture. Soga no Emishi was also called an Emishi, the sirname written with the kanji character meaning of hairy people. “Soga” itself is a cognate term for “Saka” people.

The many titles used in conjunction with Emishi are Turkic/Altaic sounding, such as Emi (Emir or Amir are Turkic congnates), as are Ate-be/ji, Isawa (Isa means price or lord) together with Kimi(Turkic word for prince or lord). The simple catacomb burials (yokoana) suggest a Northern Altaic provenance and Caucasian influences.

Historically, the Emishi appear to be represented by different tribes, some of whom became allies of the Japanese (fushu, ifu) and others of whom remained hostile (iteki). The Emishi in northeastern Honshū relied on their horses in warfare. They developed a unique style of warfare where horse archery and hit-and-run tactics proved very effective against the slower contemporary Japanese imperial army that mostly relied on heavy infantry. Their livelihood was based on hunting and gathering as well as on the cultivation of grains such as millet and barley. Recently, it has been thought that they practiced rice cultivation in areas where rice could be easily grown. The first major attempts to subjugate the Emishi in the 8th century were largely unsuccessful. The imperial armies, which were modeled after the mainland Chinese armies, were no match for the guerrilla tactics of the Emishi.

It was the development of horse archery and the adoption of Emishi tactics by the early Japanese warriors that led to the Emishi defeat. The success of the gradual change in battle tactics came at the very end of the 8th century in the 790s under the command of the general Sakanoue no Tamuramaro. They either submitted themselves to imperial authority as fushu and ifu or migrated further north, some to Hokkaidō. By the mid-9th century, most of their land in Honshū was conquered, and they ceased to be independent. However, they continued to be influential in local politics as subjugated, though powerful, Emishi families created semi-autonomous feudal domains in the north. In the two centuries following the conquest, a few of these domains became regional states that came into conflict with the central government.

The record of Emperor Jimmu in the Nihon Shoki mentions the “Emishi” (愛瀰詩) with ateji—whom his armed forces defeated before he was enthroned as the Emperor of Japan. According to Nihon Shoki, Takenouchi no Sukune in the era of Emperor Keikō proposed that they should subjugate Emishi (蝦夷) of Hitakami no Kuni (日高見国) in eastern Japan. The first mention of Emishi from a source outside Japan was in the Chinese book of Song in 478 which referred to them as “hairy people” (毛人). The book refers to “the 55 kingdoms (国) of the hairy people (毛人) of the East. . . .” as a report by King Bu—one of the Five kings of Wa. Most likely by the 7th century CE, the Japanese used this kanji to describe these people, but changed the reading from “kebito” or “mojin” to “Emishi”. Furthermore, during the same century, the kanji character was also changed to 蝦夷, which is composed of the kanji for “shrimp” and for “barbarian”. This is thought to refer to the long whiskers of a shrimp; however, this is not certain. The barbarian aspect clearly described an outsider, living beyond the border of the emerging empire of Japan, which saw itself as a civilizing influence; thus, the empire was able to justify its conquest. This kanji was first seen in the T’ang sources that describe the meeting with the two Emishi that the Japanese envoy brought with him to China (see below). The kanji character may have been adopted from China, but the reading “Ebisu” and “Emishi” were Japanese in origin, and most likely came from either the Japanese “yumishi” which means bowman (their main weapon), or “emushi” which is sword in the Ainu tongue, or an adaptation of the Altaic “Emir/ Amir” Military and chiefly titles. However, the way it sounds is almost phonetically identical to emushi so it has been suggested to have had an Ainoid origin. “Ainoid” distinguishes the people who are related to, or who are ancestors of, the Ainu, who first emerge as “Ezo” in Hokkaido in the Kamakura period, and then become known as Ainu in the modern period.

Battles with Yamato army
The Nihon Shoki’s entry for Emperor Yūryaku, also known as Ohatsuse no Wakatakeru, records an uprising, after the Emperor’s death, of Emishi troops who had been levied to support an expedition to Korea. The compilers clearly felt the defeat of the Emishi was a significant event to be recorded.

In 658, Abe no Hirafu’s naval expedition of 180 ships reaches Aguta (present day Akita) and Watarishima (Hokkaidō). Alliance with Aguta Emishi, Tsugaru Emishi and Watarishima Emishi is formed by Abe who then storms a settlement of Mishihase (Su-shen in the Aston translation of the Nihongi) a people of unknown origin, who are defeated. This is one of the earliest reliable records of the Emishi people extant.

The Satsumon culture

The period of Emishi history from roughly 700-800 CE until 1300 CE is referred to as the “Satsumon period” or “Satsumon culture.” Over the course of the 8th-9th centuries, the Japanese expanded into the north, establishing centers of power, and either pushing the Emishi further north, or assimilating them into their own Japanese communities. Many of these early Japanese centers of control were known as tate (館), a term which remains today in many placenames, e.g. Kakunodate (Akita pref.), Hakodate (Hokkaidô). There were several armed rebellions against Yamato rule, but the area was eventually pacified. Some Emishi who assimilated even developed into samurai clans; the Andô clan of samurai, according to some sources descended from Emishi chiefs, claimed sections of southern Ezo (i.e. the island of Hokkaidô) from the 1430s, if not earlier(Source: Samurai wiki entry “Emishi“).

What the records suggest is that the Yamato Japanese were only able to defeat the Emishi in Tohoku only after conscripting other Emishi groups to fight with them. At present, genetics research shows strong indigenous Jomon components to be present in Tohoku and in the Ainu of Hokkaido still, while the Ainu have also absorbed new genetic components from the Nikvh (aka Gilyaks) as well as from Mongolic-derived populations (possibly the Khitan (or Xianbei) and/ Xiongnu groups.

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