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The Jōmon (縄文) were a prehistoric hunter-gatherer culture that inhabited the Japanese archipelago approximately between 14,000 BC and 300 BC. Both genetically and culturally, the Jōmon are among the earliest known ancestors of the modern Japanese people.

Etymology

Jōmon (縄文, Jōmon), sometimes written as Jomon (American English: /ˈdʒoʊˌmɑːn/ JOH-mahn, British English: /ˈdʒəʊmɒn/ JOH-mon),^[1] is a Japanese word directly translated as "cord-marked" or "cord pattern". The term was coined by American zoologist, archaeologist, and orientalist Edward S. Morse in his book Shell Mounds of Omori (1879), describing his excavation of the Ōmori Shell Mound near Tokyo and subsequent discovery of sherds of cord-marked pottery at the site in 1877. Morse translated "straw-rope pattern" from English to Japanese as Jōmon, which he would use to refer to the people living during this period of Japanese history.^[2]^[3]^[4] Other names for Jōmon pottery had been used in the first few decades after the discovery such as "Ainu school pottery" and "Shell mound pottery" before the term Jōmon became the standard term used by the archeological community.^[4] Indeed, it was not until 1937 that the Japanese historian Yamanouchi Sugao used the pottery-derived term to refer to Japan's Paleolithic inhabitants.^[5]

Jōmon is a compound word composed of two kanji: 縄 and 文, the pronunciation and semantic value each being derived from their respective Go-on reading.

縄 (jō) – meaning "rope" or "cord", specifically "a flexible, heavy cord of tightly intertwined hemp or other fibers." This kanji derives etymologically from Old Japanese, from the Proto-Japonic napa, related to the verb 綯う (nau, "to plait or twist together into twine or line").^[6]^[7]^[8]
文 (mon) – meaning "pattern" or "design", as seen in words such as moyō (模様) or mon'yō (文様).^[9]

The word can thus be used as a common noun meaning "cord pattern", or as a shorter proper noun referring specifically to the Jōmon period. These kanji appear in various related terms, creating a lexical field centered around the Jōmon culture, which includes:

縄文時代 (Jōmon jidai, "Jōmon period")
縄文式土器 (Jōmon-shiki doki, "Jōmon ware")
縄文人 (Jōmon-jin, "Jōmon people")
縄文土器 (Jōmon doki, "Jōmon pottery")^[10]

History of Jōmon archaeology

Early descriptions and depictions

The study of the Jōmon people and their material culture has evolved significantly since the Edo period. One of the earliest recorded depictions of Jōmon artifacts dates back to Edo-period antiquarians, who began to catalogue and produce sketches of unusual pottery fragments brought to them from shell middens. The eighteenth century traveler Sugae Masumi mentioned Jōmon-era remains in his writings, including his book Sumika no Yama (c. 1800), referencing the shell mounds and prehistoric pottery discovered throughout his travels.^[11] Early antiquarians often misidentified these remains as being relics of legendary figures or lost civilizations rather than pieces of indigenous Japanese prehistory.

During the early Meiji period (1868–1912), the emergence of modern archaeology in Japan led to a more systematic study of prehistoric remains. The first significant scholarly recognition of Jōmon culture came in 1877, when Edward S. Morse, an American zoologist and orientalist, excavated the Ōmori Shell Mound near Tokyo. Morse coined the term Jōmon (縄文, "cord-marked") to describe the distinctive pottery he uncovered, characterized by impressions made using twisted cords.^[3] Morse's work marked the beginning of formal archaeological study of the Jōmon period.

Early 20th-century theories and discoveries

By the early 20th century, Japanese archaeologists began conducting their own excavations, with the main force behind archaeology in Japan shifting from foreign-led expeditions to national research initiatives. Scholars such as Tsuboi Shōgorō and Torii Ryūzō conducted further investigations of shell middens, burial sites, and Jōmon settlements. Nationalist Kokugaku ("National Learning") scholars sought to frame Jōmon culture within Japan's historical narrative, often contrasting it with the agriculturalists of the Yayoi period, whose lifestyle centered on rice cultivation was more clearly Sinitic in influence.^[12] During the 1920s–30s, Kojima Gizaemon and Hamada Kōsaku led efforts to establish regional typologies of Jōmon pottery, classifying styles into chronological phases based on stratigraphy, the study of sediment layers and their effects on artifacts over time. Excavations at sites such as Kasori Shell Midden in Chiba have shed light on Jōmon long-term settlement and subsistence patterns.^[13]

Post-war expansion and new interpretations (1945–1990s)

Between the 1950s and 1970s, the need for archaeological work in Japan expanded rapidly due to post-war reconstruction projects and large-scale public works. The Cultural Properties Protection Law (1950) required archaeological investigations before construction, leading to the excavation of thousands of Jōmon sites.

This resulted in newfound academic interest in the Jōmon. Researchers such as Serizawa Chōsuke and Yamanouchi Sugao played key roles in redefining Jōmon chronology, refining pottery typologies, and identifying major Jōmon sub-periods (Incipient, Initial, Early, Middle, Late, Final).^[14] The discovery of large settlements, such as Sannai Maruyama (Aomori) in the 1990s, revealed that Jōmon groups lived in permanent or semi-permanent villages, contradicting earlier assumptions that they were exclusively nomadic hunter-gatherers.^[15]

By the late 20th century, new perspectives emerged regarding Jōmon social complexity. The "Complex hunter-gatherers" theory became widely accepted, recognizing Jōmon societies as displaying features typically associated with neolithic, agricultural civilization such as long-term settlement patterns, the development social hierarchy, and the development of a division of labor/advanced craft specialization (e.g., lacquerware, jade ornaments, figurines) despite their hunter-gather lifestyle.^[16] By the new millenium, international collaboration also increased, with researchers drawing comparisons between the Jōmon and other prehistoric cultures, such as those Paleo- and Mesolithic cultures found in the American Pacific Northwest and Europe.

21st-century developments

The 21st century has seen major advancements in Jōmon archaeology, driven by scientific dating techniques, DNA Analysis, and interdisciplinary studies.

Chronological Refinements: Advances in radiocarbon dating (AMS C-14 dating) have refined the Jōmon timeline, pushing back the origins of pottery to 16,500 BCE at sites like Ōdai Yamamoto I in Aomori.^[17] This would corroborate the theory that Japan was among the earliest centers of pottery production in the world.
Ancient DNA Analysis: Genetic studies of Jōmon skeletal remains (e.g., those found in the Funadomari Shell Midden) provide insights into their genetic characteristics and modern legacy.^[18]
Environmental Adaptation Studies: Climate reconstructions suggest that Jōmon societies adapted to Holocene climate fluctuations by migrating between coastal and inland settlements as sea levels changed.^[19]
Jōmon Ritual Symbolism: Research into ceremonial sites, such as the Ōyu Stone Circles in Akita and Omori Katsuyama Stone Circle in Aomori, indicates that the Jōmon constructed large-scale ritual landscapes from stone, challenging the common assumption that only agricultural societies are capable of monumental architecture.^[20]
UNESCO Recognition: In 2021, 17 Jōmon sites across Hokkaidō and northern Honshū were declared UNESCO World Heritage sites, recognizing Jōmon culture as one of the world's longest-lasting hunter-gather traditions.^[21]

Lifestyle

Like many hunter-gatherer societies, the day to day life of the Jōmon was largely centered around activities like hunting, fishing, foraging for tree nuts, and catching shellfish. However, it has also been suggested that the Jōmon people practiced forms of early agriculture,^[22] such as the regular cultivation of adzuki beans and soybeans.^[23] The Jōmon people also used pottery, and generally lived in semi-permanent pit dwellings, characteristics more typically associated with late mesolithic or early neolithic agriculturalists.^[24]

Settlements

The modern Jōmon chronology commonly accepted by scholars generally follows that first laid out by Serizawa in Jōmon Pottery Classification and Chronology, published in 1956. Archaeological evidence suggests that settlements changed throughout the different phases of the Jōmon Period.

Incipient Jōmon settlements were the first sedentary settlements in Japan and consisted only of dwellings. An example of this type of settlement is the Odai Yamamoto 1 Site.
Initial Jōmon settlements begin to show signs of cultural complexity on account of the appearance of gravesites during this period. The residential area and the cemetery were separated. An example of such settlement is the Kakinoshima site.
Early Jōmon settlements gained more use-specific features: the storage area and the dump area. Sites representative of this period are the Kitakogane site, Tagoyano site, and Futatsumori Site.
Middle Jōmon saw the development of hub settlements and the division of dump and ritual spaces. Sites representative of this period are the Sannai-Maruyama Site, Ōfune Site, and Goshono site.
Late Jōmon saw the dissolution of hub settlements into smaller ones with a shared ritual center which also functioned as its cemetery. Some of the sites of this period include the Irie site, Komakino Site, Isedōtai Ruins, and Ōyu Stone Circles.
Final Jōmon saw the separation of the ritual site and the cemetery into two separate sites shared by multiple settlements. Some of the sites in this period include the Kiusu Earthwork Burial Circles, Ōmori Katsuyama Site, Takasago Burial Site, Kamegaoka Stone Age Site, and Korekawa Site.^[25]

The excavation of Sannai Maruyama Site has revealed networks of what are believed to be unpaved, Jōmon-era roadways. In addition to connecting the areas, buildings, and ritual spaces within the settlement itself, it theorized these paths may have also extended to other settlements. On both sides of the roads were aligned graves of various types and characteristics, including pit graves, tumuli, the graves of children, and stone circle graves. Further excavations along these long-forgotten pathways have also revealed both standard and large pit dwellings, dumping grounds, storage pits, unknown pillar-supported structures of various sizes, and a watering place used for soaking Japanese horse chestnuts.

As mentioned, Jōmon people typically resided in pit dwellings, semi-subterranean buildings built by digging a shallow hole in the ground, constructing a roof extending upwards from each side, and placing a hearth in its center. As Jōmon pit dwellings are relatively small compared to other prehistoric cultures, it is believed that each dwelling would have housed a family of four to six people for as long as two to three generations. The roofs enclosing these spaces were made of bark or thatch and may have been covered with soil to provide an extra layer of insulation. Altars may have also been installed in some of them. Pit dwellings longer than 10m are classified as large pit dwellings, which most likely functioned as communal spaces like meeting places, workshops, or shared winter residences^[26] comparable to contemporaneous Meso- and Neolithic structures found in Europe and the Americas.

Tools

Like other Paleolithic cultures, Jōmon sites display widespread evidence of the use and production of stone tools. Jōmon tools were most commonly fashioned from chipped stone, made of siliceous shale. However, tools made from other types of stone, wood, and rarer materials such as obsidian and jade have also been discovered in Jōmon-period sites.^[27]

These types of tools included but were not limited to: knives, stone drills, spearheads, arrowheads, scrapers sometimes with barbs or stemmed, semi-circular flat chipped stone tools believed to have been used in the preparation of food. In the case of tools built from multiple parts such as spears or arrows, Jōmon toolmakers used bitumen as an adhesive to bind the stone point with its wooden shaft.

However, some stone implements appear to have been made without the normal chipping process. This includes ground stone axes, made from granodiorite, greenstone, or blueschist, abrasion cutting stone tools, whetstones, grindstones with or without grooves, hammer stones, saddle querns, and stone weights.

Antlers and bones were also used for tools such as spatulas, fish hooks, harpoon heads, drills, and needles. Exclusive to antlers were hammers, where the base of the antler was used as the impact surface. Wood was used for making shafts of spears, arrows, harpoons, bows, and digging sticks while strips of bark were used to weave baskets.

Hunting

The Jōmon people were incredibly skilled, likely opportunistic hunters capable of tracking, catching, and killing a wide variety of both large and small game endemic to their environment. These included flying squirrels, hares, weasels, martens, foxes, squirrels, tanuki (raccoon dogs), wild boar, deer, bears, sea lions, badgers, apes, snow monkeys, otters, cormorants, albatrosses, pheasants, grebes, geese, and ducks. Hunting techniques included the use of projectile weapons like bows and spears, pitfall traps, and hunting dogs.^[26]

The percentage of prey hunted varies from site to site, but generally wild boars and deer were the staple of what was, in the case of the Jōmon, a largely carnivorous diet. However, in the Sannai Maruyama site, flying squirrels and hares are the dominant sources of meat most likely as a result of environmental factors.

Fishing

Archaeologists have uncovered the bones of many species of fish and other types of seafood in Jōmon dumping grounds. Given the variety of the species consumed, some of which would have required considerable travel to catch, it has been postulated that the Jōmon were adept fishermen and mariners. Some of the marine species found at Jōmon sites include yellowtail amberjack, right-eyed flounder, various types of shark, mackerel, herring, flounder, scorpion fish, globefish, greenling, Pacific sea bream, and Pacific cod. The Jōmon also gathed shellfish, including Japanese oysters, Ezo abalones, clams, crabs, octopi, squid, mantis shrimp, and other types of crustacean.^[26]

The Jōmon fished using harpoons, spears, lines, and nets. Jōmon harpoon heads were detachable and could be reeled in using ropes tied through their base. Harpoons and spears were used to catch larger prey, line fishing for smaller prey was done using fish hooks fashioned from antler or bone. Jōmon fish hooks generally fall into two categories fish hooks: single-ended hooks and coupled/combined hooks. The main difference between the two was that coupled fish hooks were barbed while single-ended hook did not. However, both types had notches to tie the line. Stone weights were attached to nets to act as sinkers.

There is evidence that the Jōmon people built ships out of large trees and used them for fishing and traveling. However, it is still debated whether Jōmon watercraft used sails or paddles as their primary means of propulsion.^[28]

Plant foraging and domestication

The Jōmon grew trees close to their settlements and gathered edible wild plants. Chestnuts were an especially common part of Jōmon diets, while trees themselves were frequently used as fuel and building material. Other types of flora regularly consumed by the Jōmon include walnuts, Japanese horse chestnuts, adzuki beans, Udo, silver vines, elderberries, wild grapes, mulberries, raspberries, and yams. Roots, tubers such as yams, and other subterranean forage was dug up using digging sticks.^[26] However, plant genomics studies have indicated that the adzuki bean was domesticated in eastern Japan between 3,000 and 5,000 years ago, suggesting that, in addition to gathering and cultivating wild plant species, the Jōmon were engaged in early plant domestication.^[29]

Food processing

Nuts, walnuts, and chestnuts were collected during autumn and were kept in storage pits or indoor inside large earthenware pots. Before use, they were crushed with hammer stones or grinding stone on top of saddle querns. Japanese horse chestnut and other chestnuts with strong scents were soaked in water to mellow their taste. At the Sannai Maruyama Site, archaeologists discovered a reservoir, filled and emptied by a spring, that may have been used to process nuts through soaking.^[26] The Jōmon might have also been able to distill alcohol using elderberries.

Cooking

Cooking was done on the pit dwelling's central hearth using smaller, purpose-made earthenware pots distinct from the those used for storage. During the Middle Jōmon period, earthenware was made in various shapes including pedestal dishes and bowls used to serve food. Round wooden containers are thought to have been held in one hand while pouring liquids, although the purpose of the custom remains a mystery.^[26]

Trade networks

The Jōmon maintained extensive trade networks that extended several hundred kilometers across the Japanese archipelago. Key trade items included obsidian, gemstones such as jade, amber, asphalt, red pigments, and various types of stone materials used to produce polished stone axes including granodiorite, greenstone, and blueschist.

Some materials were transported in raw form, while others were traded as refined or finished goods. Certain Jōmon sites appear to have specialized in the production of specific raw materials or crafted items. For example, the Sannai Maruyama site, a major trading hub, was particularly known for its jade artifacts. It inhabitants also engaged in the exchange of finished obsidian tools raw obsidian sourced, in some cases, from as far away as Hokkaido and Nagano. These tools, made of high-quality obsidian, have been found over 700 kilometers from their origin points.

Evidence of trade between the Jōmon of Hokkaido and Honshu, as well as between those living on the Kyushu and Ryukyu Islands, would further suggest that the Jōmon were skilled navigators and seafarers capable of long-distance maritime travel.^[26] According to a 2006 study, it is also possible that the Jōmon traded with southern Chinese and Southeast Asians via Fujian.^[30]

Culture

Elements of Jōmon culture are believed to be preserved in various aspects of modern Japanese culture. These include early forms of spiritual beliefs that preceded Shinto, as well as marriage customs, architectural styles, festivals, and traditional crafts such as lacquerware and pottery. These cultural traits are considered integral to the development of Japanese cultural identity.^[31]

Other examples of Jōmon influence in present Japanese culture, especially in Kyūshū, include the worship of Ame-no-Uzume (アメノウズメ) in Miyazaki Prefecture, Ta no Kami-sa (田の神さぁ) in the Aso region of Kumamoto Prefecture, and the Mishaguji (ミシャグジ) belief system.^[32]^[33]^[34]

Pottery

Jōmon pottery is identifiable by its distinctive cord-marked patterns, a style in which ropes were pressed into the surface of wet clay to create decorative designs. This technique, characteristic of the early Jōmon period, is widely regarded as one of the oldest forms of pottery in East Asia and the world. Among the most famous examples is the kaen-style pottery (火焔型土器, kaen-gata doki) from the Middle Jōmon period, noted for its elaborate patterns and dynamic forms.^[35]

In addition to pottery and jars, the Jōmon people also produced a large number of highly stylized clay figurines (dogū) and clay masks, reflecting a rich tradition of symbolic and ritualistic art.^[36]

Lacquerware

Lacquerware included wooden bowls, dishes, and combs. It was mixed with red pigments to give it a red color. Lacquer tree sap was collected from cultivated and managed areas. The steps to make lacquerware were:

Collect the sap
Remove the excess moisture
Purify the sap
Mix it with red pigments
Apply the lacquer by hand to the ware

Red pigments were made from ferrous quartz, then ground into powder before mixing it with lacquer. Some pottery was directly painted with red pigments instead of lacquering it.^[26]

Clothing

Fabric made with twisted warp called angin were found at Sannai Maruyama. It is believed that cloth and clothings were made of weaved twisted plant fiber such as hemp in this way.

The Jōmon people also practiced sewing using bone and antlers needles.^[26]

Jewelry and accessories

*Magatama* – kidney-shaped beads – are commonly found in Jōmon period Japanese finds, as well as in parts of Northeast Asia and Siberia.

A wide variety of materials were used in the creation of Jōmon accessories, including clay, stone, bone, shells, and lacquered wood. These ornaments are believed to have been used not only for special occasions but also in everyday life.^[37]

Excavations have uncovered bone hairpins and lacquered wooden combs, which were likely used to fasten and decorate tied hair. Cylindrical or drum-shaped earrings made of clay were worn by inserting them into pierced earlobes, while slender stone earrings were also passed through ear holes.^[38]

Many of these ornament styles show notable similarities to accessories found in later periods of Japanese history, suggesting a lasting influence of Jōmon aesthetics on subsequent Japanese decorative traditions.^[37]

Magatama

Magatama are curved, comma-shaped beads with a distinctive C-shape and a hole at one end, typically used as ornaments or ceremonial objects. They are believed to have been invented by the Jōmon people and have been excavated from archaeological sites throughout Japan.^[39]

Magatama continued to be widely used not only during the Jōmon period but also throughout the Yayoi and Kofun periods, remaining an important accessory in Japanese culture. Today, magatama are still revered as sacred objects in various Shinto shrines and also appear in Japanese mythology. One of the Imperial Regalia of Japan, the Yasakani no Magatama (八尺瓊勾玉), is considered a symbol of the Japanese monarchy.^[40]

These artifacts were most commonly made from jade (jadeite), but examples crafted from stone, clay, and boar tusks have also been discovered. The materials and production techniques varied by region and era, reflecting both local resources and cultural influences.^[39]

Religion

It is suggested that the religion of the Jōmon people was similar to early Shinto, specifically Ko-Shintō. It was largely based on animism, and possibly shamanism. Other similar religions are the Ryukyuan and Ainu religions.^[41] Certain strange stone implements in various shapes are thought to have been used as talisman.^[26]

Rituals and festivals

Accessories and jewelry are thought to have been worn more during special occasions such as festivals, burials, and rituals than in everyday life.^[26]

Central ritual sites outside settlements and belonging to multiple villages have started to appear during the Late Jōmon period^[25] but hub settlements also acting as central ritual hubs appeared during the Middle Jōmon period.

Mounds were built using refuse from soil excavation and daily life activities, but were not merely dumping grounds; instead, they had special significance as places of rituals.

Stone and clay figurines are believed to have been used for festivals. Many represented women with breasts and parts or holes possibly representing genitalia. They are thought to have been a way of praying for fertility in festivals. Asphalt has been used on some of them to attempt to repair them.

Miniature pottery are earthenware in extremely small sized modelled after utilitarian-sized vessels such as deep bowls for cooking and storing and shallow bowls for serving food. They are thought to have been used in ceremonies rather than as toys due to their excavations in ceremonial mounds.

Other objects found in ceremonial mounds include triangular pottery (theorized to be simplified versions of clay figurines), stick-shaped clay objects (thought to be a miniature pottery version of stone rods), stamp-shaped stones (thought to be modelled after female genitalia), walnut clay objects (created by pressing clay against inner shell of walnuts), and pottery with human figure (theorized to be shamans with head ornaments and tools).

Sword-shaped artefacts made of whale bone have been excavated and are thought to have been used in fire related rituals as most have burned marks.^[26] The Jōmon also crafted stone batons or rods and swords^[36] which are thought to have been used for rituals and festivals as many have been exposed to fire. Other artefacts such as large jade beads have also been exposed to fire.

In Sannai Maruyama, a large structure made of 6 great pillars of chestnuts between 1 and 2 meters in diameter has been repeatedly built through the ages. It is thought to have played multiple roles such as a ritual venue, totem pole, observatory, lighthouse, and watchtower.^[26]

Burials

Graves were different for different people with adult graves being different from children's and from a few important people.

Adults were buried in pit graves, some with pebbles acting as grave markers or soil mounds on top of them.
Important people were buried in pit graves surrounded by stone circles.
Children were buried in reused everyday pottery and placed together away from the other graves: some had modifications done to the pottery such as breaking the rim or piercing holes at the bottom or side of it. It is possible that only infant were buried in this fashion. Some of them had fist-sized circular pebbles or flaking tools in them.

Most graves did not contain grave goods. For those that had them, it is believed that men and women were buried with different objects: hunting tools and stone arrowheads, and cooking utensils such as saddle quern respectively.

In Sannai Maruyama, pit graves have been excavated on both sides of roads, feet towards the road at slight angles. At this same site, pillar-supported structures may have been used for temporary resting place for the deceased.^[26]

Languages

It is not known what language or languages were spoken in Japan during the Jōmon period. Suggested languages are: the Ainu language, Japonic languages, Austronesian languages, or unknown and today extinct languages.^[42]^[43] While the most supported view is to equate the Ainu language with the Jōmon language, this view is not uncontroversial or easily acceptable as there were probably multiple distinct language families spoken by the Jōmon period population of the Japanese archipelago.^[44]

Alexander Vovin (1993) argues that the Ainu languages originated in central Honshu, and were later pushed northwards into Hokkaido, where the early Ainu-speakers merged with local groups, forming the historical Ainu ethnicity. Bilingualism between Ainu and Japanese was common in Tohoku until the 10th century.^[45]^[46] According to Vovin (2021) there is also some evidence for the presence of Austronesian languages close to the Japanese archipelago, which may have contributed some loanwords to early Japanese.^[46]

Some linguists suggest that the Japonic languages may have been already present within the Japanese archipelago and coastal Korea, before the Yayoi period, and can be linked to one of the Jōmon populations of southwestern Japan, rather than the later Yayoi or Kofun period rice-agriculturalists. Japonic-speakers rapidly grew during the Yayoi period by assimilating the newcomers, adopting rice growing, and fusing mainland Asian technologies with local traditions.^[47]

Origins

The Jōmon people represent the descendants of the Paleolithic inhabitants of the Japanese archipelago, which became isolated from other mainland Asian groups some 22,000 to 25,000 years ago. They have been described as "one of the most deeply diverged populations in East Asia".^[48]^[49]^[50]^[51]

Genetics

Phylogenetic position of the Jōmon lineage among other East Eurasians

Demographic history of the Jomon lineage (A) Maximum likelihood phylogenetic tree reconstructed by TreeMix under a model of two migrations

Principal component analysis (PCA) of ancient and present-day individuals from worldwide populations

The Jōmon lineage is inferred to have diverged from Ancient East Asians between 25 and 38,000 years ago, after the divergence of the Basal East Asian Tianyuan and Hoabinhian lineages but before the divergence of Ancient Northern East Asians and Ancient Southern East Asians.^[52]^[53]^[49] Like other East Asian populations, the ancestors of the Jōmon people originated from Southeast Asia and expanded to East Asia via a coastal route. They represent one of the "earliest waves of migration".^[49]^[54]^[55]^[56]

The Jōmon lineage displays a closer genetic affinity to Ancient Northern and Southern East Asian lineages, compared to the Tianyuan or Hoabinhian lineages, and have a similar divergence date as the closely related "Longlin" ancestry from Guangxi. ^[49]However, there is evidence of Jōmon individuals having affinities with Hoabinhians^[57]^[58] and Aboriginal Australians.^[59] Beyond their genetic affinity with other Eastern Asian lineages, the Jōmon also display a weak genetic affinity with the Yana Rhinoceros Horn Site specimen, associated with Ancient North Eurasians (or Ancient North Siberians), which may point to gene flow between both groups prior to their isolation from other East Eurasian populations.^[53] According to Bennet et al., "one explanation may be that Tianyuan-like early ancestors of the Jōmon interacted with groups that entered Siberia through a northern migration route".^[60] This gene flow may be associated with the introduction of microblade technology to northern Japan^[61] but so far, there is no evidence for direct gene flow from ANE-like (MA-1) sources into the Jōmon, suggesting instead a non-demic diffusion.^[62]^[63]^[64] However, the Jōmon have genetic affinities with lowland coastal East Asians and northeast Siberians.^[65]^[66]^[67]^[68]These affinities imply later contact episodes between the Jōmon and other East Eurasian populations.^[30]^[65]^[67]^[69]^[70]^[68] Alternatively, they reflect a shared origin in a metapopulation that expanded from south to north along the coasts of Eastern Asia.^[71] Nonetheless, there is no evidence for coastal East Asian affinities for the Ryukyuan Jōmon.^[72]^[73]^[74]^[75]

Overall, the Jōmon overwhelmingly share an ancestral component with the Yokchido individual from ancient Korea, who have about 95-100% Jōmon ancestry.^[76]^[77]^[78] To a lesser extent, they share an ancestral component with southern Chinese, Southeast Asians and Oceanians, which is further maximized in Papuans and Vanuatuans, especially Mainland and Hokkaido Jōmon. This component is shared by Yayoi peoples too, suggesting an origin from another deeply diverged old Asian lineage.^[76] The Jōmon also mixed with southern East Asians, as well as Siberians for Hokkaido Jōmon,^[79] except for Ryukyuan Jōmon.^[72]^[73]^[74]^[75]

Full genome studies on multiple Jōmon remains revealed them to carry gene alleles associated with a higher alcohol tolerance, wet earwax, no derived variant of the EDAR gene, and that they likely frequently consumed fatty sea and land animals. They also carried alleles for medium to light skin, dark and fine/thin hair, and brown eyes. Some samples also displayed a higher risk of developing liver spots as a result of excessive sun exposure.^[54]^[80]^[81]

Genetic data further indicates that the Jōmon peoples were genetically predisposed for higher triglyceride and blood sugar levels, increasing the risk of obesity. At the same time, it gave them resistance to starvation. Modern Japanese share these alleles with the Jōmon period population, although at lower and variable frequency, in line with the inferred admixture among modern Japanese peoples. Watanabe et al. stated that the genetic predisposition for shorter stature among Japanese people often correlates with high Jōmon ancestry, with the opposite correlating with high continental East Asian ancestry.^[54] However, Yamamoto et al. (2024) stated that the association of Jōmon ancestry with the decrease of height is observable only if principal components are not accounted for in the test, indicating that this association can be confounded by population stratification. They also found indications for an influence on the Body mass index, including a higher risk of obesity among modern Japanese, but also higher frequency of "active functions in skeletal muscle cells" and "increased bone mineral density", which may have been related to the hunter-gatherer lifestyle of the Jōmon people.^[82]

Haplogroups

It is thought that the haplogroups D-M55 (D1a2a) and C1a1 were frequent among the historical Jōmon period people of Japan. One 3,800-year-old Jōmon man excavated from Rebun Island was found to belong to Haplogroup D1a2b1(D-CTS 220).^[83] Today, haplogroup D-M55 is found in about 35%^[84] and haplogroup C1a1 in about 6% of modern Japanese people. D-M55 is found regularly only in Japanese (Ainu, Ryukyuans, and Yamato), and Koreans (albeit with much lower frequency).^[85] D-M55 also has been observed in Micronesia 5.1%, Timor 0.2%, China 0–0.4%, this is explained by recent admixture, dating back to the Japanese empire (1868–1945) occupation of those regions.^[85] Haplogroup C1a1 has been found regularly in about 6% of modern Japanese. Elsewhere, it has been observed sporadically in individuals from South Korea, North Korea (South Hwanghae Province), and China (ethnic Korean in Ning'an and Han Chinese in Linghai, Guancheng Hui District, Haigang District, and Dinghai District).^[86] A 2021 study estimated that the frequency of the D-M55 clade increased during the late Jōmon period.^[87] The divergence between the D1a2-M55 and the D1a-F6251 subclades (the latter of which is common in Tibetans, other Tibeto-Burmese groups, and Altaians, and has a moderate distribution in the rest of East Asia, Southeast Asia, and Central Asia) may have occurred near the Tibetan Plateau.^[84]

The MtDNA haplogroup diversity of the Jōmon people is characterized by the presence of haplogroups M7a and N9b.^[88]^[89]^[90] Studies published in 2004 and 2007 show the combined frequency of M7a and N9b observed in modern Japanese to be from 12~15% to 17% in mainstream Japanese.^[91]^[92] N9b is frequently found among the Hokkaido Jōmon while M7a is found frequently among the Honshu Jōmon.^[93] However N9b is found only at very low percentage among the Honshu Jōmon.^[93] Both M7a and N9b have coalescent times about 10,000 years ago. Studies have suggested that M7a originated from westward migrations from the Korean peninsula while N9b was introduced from Northeast Asia via Sakhalin and Hokkaido. However, it is likely that these haplogroups were indigenous to the Japanese archipelago, with early Jōmon being "located on branches closer to the root".^[94] Haplogroup M7a now has its highest frequency in Okinawa.^[95]

Using the Fossa Magna as the boundary line, M7a was more common in western Jōmon while N9b was more common in eastern Jōmon, which can be explained by genetic drift.^[94] Other studies state that M7a was present at all sites in Early Jōmon Japan, whether northern or southern, although N9b was not found at any site below Kyushu. In Middle Jōmon Japan, M7a and N9b were both observed, especially at the Chiba Prefecture. In Late Jōmon Japan, M7a was present in Hokkaido and Okinawa. N9b was common in Funadomari while D4b2 and D4h2 were common in the Shomyoji shell midden and Funadomari respectively. In the Final Jōmon, N9b prevailed in Hokkaido while N9b and M7a were both observed in Honshu. The following sites in Hokkaido have these common haplogroups; G1b at Usu-Moshiri, G1b and D4h2 at Usu-Moshiri, G1b at Minami-Usu 6 and D4h2 at Onkoromanai.^[96]

Morphological characteristics

Dental morphology suggests that the Jōmon had Sundadont dental structure which is more common among modern Southeast Asians and indigenous Taiwanese, and is ancestral to the Sinodont dental structure commonly found among modern Northeast Asians, suggesting that the Jōmon split from the common "Ancestral East Asians" prior to the formation of modern Northeast Asians.^[97]

Kondo et al. analyzed the regional morphological and craniometric characteristics of the Jōmon-era population of Japan, and found that they were morphologically heterogeneous and displayed differences along a Northeast to Southwest cline. Differences were based on the cranial index, with Hokkaido Epi- Jōmon crania being mesocephalic and Okinawan crania being brachycephalic. They concluded that the "Jōmon skulls, especially in the neurocranium, exhibit a discernible level of northeast-to-southwest geographical cline across the Japanese archipelago, placing the Hokkaido and Okinawa samples at both extreme ends. The following scenarios can be hypothesized with caution: (a) the formation of Jōmon population seemed to proceed in eastern or central Japan, not western Japan (Okinawa or Kyushu regions); (b) the Kyushu Jōmon could have a small-sized and isolated population history; and (c) the population history of Hokkaido Jōmon could have been deeply rooted and/or affected by long-term extrinsic gene flows." They also suggested that regional differences in cranial length is based on genetic, or phylogenetic, and environmental effects.^[98] But Gakuhari et al. clarifies that Hokkaido and Honshu Jōmon cluster together and form a clade to the exclusion of other groups.^[81]

Chatters, citing anthropologist C. Loring Brace, classified Jōmon and Polynesians as a single craniofacial "Jōmon -Pacific" cluster.^[99] Chatters, citing Powell, argues that the Jōmon most resembled the Native American Kennewick Man and Polynesians. According to him, the Ainu descend from the Jōmon people, an East Asian population with "closest biological affinity with south-east Asians rather than western Eurasian peoples".^[100]^[101] Powell further describes the dental structure of the Jōmon to be of the Sundadont type,^[99] while also displaying some similarities to the Native American Kennewick Man.^[100] There were also close morphological similarities between the ~33,000 to 23,000 years old Liujiang man from Guangxi, China and the Minatogawa Man from Okinawa.^[102]^[103]

The Jōmon also displayed affinities with Australo-Papuan groups, similar to prehistoric populations from southern China and Southeast Asia, especially Hoabinhian hunter-gatherers, along with the Zhoukoudian remains from Beijing, China. They possessed traits such as 'dolichocephalic calvaria, large zygomatic bones, remarkably prominent glabellae and superciliary arches, concave nasal roots, and low and wide faces',^[104]^[105]^[106] yet were genetically closer or ancestral to later East Asians despite phenotypic discontinuities, pointing to a legacy of Paleolithic variations lost in modern Eastern Asian populations.^[107]^[108] However, they were preserved in some populations like the Bo people, an extinct ethnic group from Yunnan, China.^[109] Typical Jōmon features were also common in Eurasian Upper Paleolithic hunter-gatherers.^[110]

Craniofacial features of the Jōmon people were significantly retained by the Ainu and Okinawans/Ryukyuans.^[111] The Ainu have 2 genes "associated with facial structure in Europeans" but still possessed hair and teeth morphology found in East Asians.^[112] In regards to facial flatness, the Ainu were intermediate between Caucasoids and Mongoloids^[113] but another study states that they were well within the Mongoloid range.^[114]Ainu also exhibit strong influence from northeast Asian populations.^[74]Meanwhile, Okinawans/Ryukyuans have a "well-defined and less flat upper face", which is characterized by a prominent glabella and nasal root.^[111] Among contemporary Japanese subpopulations, Kinki populations phenotypically differ the most from Jōmon people, especially Hokkaido Ainu. Other subpopulations were more intermediate although morphological similarities exist between Hokkaido Ainu and contemporary Tohoku populations.^[115] Southern Japanese also exhibit strong similarities with Jōmon and Ainu groups, as well as Yayoi groups, and are relatively less impacted by northeast Asian groups.^[74]

ATL retrovirus

A gene common in Jōmon people is a retrovirus of ATL (human T lymphotropic virus, HTVL-I). This virus was discovered as a cause of adult T cell leukemia (ATL), and research was advanced by Yorio Hinuma of Kyoto University Virus Research Institute.^[116]

Although it was known that many virus carriers existed in Japan, it was not found at all in neighboring countries of East Asia. Meanwhile, it has been found in many Africans, Native Americans, Tibetans, Siberians, Burmese people, Indigenous people of New Guinea, Polynesians, etc. Looking at distribution in Japan, it is seen particularly frequently in southern Kyushu, Nagasaki Prefecture, Okinawa and among the Ainu. And it is seen at medium frequency in the southern part of Shikoku, southern part of the Kii Peninsula, the Pacific side of the Tōhoku region (Sanriku) and Oki Islands. Overall, carriers of the ATL retrovirus were found to be more common in remote areas and remote islands. When examining the well-developed areas of ATL in each region of Kyushu, Shikoku, and Tōhoku in detail, carriers are preserved at high rates in small settlements that were isolated from the surroundings and inconvenient for traffic.^[117]^[116]

The path of natural infection of this virus is limited to vertical infection between women and children (most often through breastfeeding) and horizontal infection between males and females (most often from males to females through sexual intercourse).^[118]

Based on the above, Hinuma concluded that the high frequency area of this virus indicates that high density remains of Jōmon people.^[117]

Contributions to other populations

Historical groups

Full genome analyses of Okhotsk culture remains on Sakhalin found them to be derived from three major sources, notably Ancient Northeast Asians, Ancient Paleo-Siberians, and Jōmon people of Japan. An admixture analysis revealed them to carry c. 54% Ancient Northeast Asian, c. 22% Ancient Paleo-Siberian, and c. 24% Jōmon ancestries respectively.^[119]

Genetic analyses on ancient remains from the southern Korean Peninsula during the Three Kingdoms period reveal elevated Jōmon ancestry. This ancestry was most likely local to Korea. Around 500 CE, migrations led by northern Chinese virtually erased Jōmon ancestry among Koreans, with the latter becoming genetically homogenous.^[120]

Modern groups

The Ainu have the highest proportion of Jōmon ancestry among modern populations, estimated at up to 70%, followed by the Ryukyuan/Okinawan people at around 30%, and mainland Japanese at approximately 10–20%. The proportion of Jōmon ancestry varies regionally, being highest in the Tōhoku and Kyūshū regions, and lowest in Kinki and Shikoku, where Yayoi ancestry is more dominant. Residents of Tōhoku, Kantō, and Kyūshū show closer genetic affinity with Ryukyuans. Genetic relatedness between the Ainu and mainland Japanese is particularly strong in western Hokkaidō and Aomori. It is also believed that mainland Japanese primarily derive their Jōmon ancestry from western Jōmon populations.^[115]^[121]^[122]

Low levels of Jōmon ancestry are found in present Koreans (approximately 1–5%), as well as in some Northeast Asian and coastal East Asian populations. For example, Taiwanese aborigines like Ami and Atayal, along with Kra-Dai populations, have some genetic affinities with the Jōmon.^[121]^[71]^[123] However, the affinities between Jōmon and groups like Taiwanese aborigines and coastal Siberians is more likely due to their ancestors belonging to the same metapopulation that colonized Eastern Asia from south to north. That said, there is strong evidence of intermixing between Siberians and Ainu.^[71]

In popular culture

Aspects of the Jōmon culture and pottery were used in the video game The Legend of Zelda: Breath of the Wild. Nintendo's art director Takizawa Satoru said that the Jōmon culture was the inspiration for the "Sheikah Slates, shrines and other ancient objects" in the game.^[124]

A recreated Jōmon village in the form of an experience park (Sarashina no Sato), which offers different activities, can be visited in Chikuma, Nagano.^[125]

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The dual nature of Japanese population structure was advanced by Miller, who proposed that the resident Jōmon population spoke an Altaic language ancestral to modern Japanese, and this Altaic tongue underwent Austronesian influence when the islanders absorbed the bearers of the incursive Yayoi culture.
^ Adachi, Noboru; Kanzawa-Kiriyama, Hideaki; Nara, Takashi; Kakuda, Tsuneo; Nishida, Iwao; Shinoda, Ken-Ichi (2021). "Ancient genomes from the initial Jomon period: new insights into the genetic history of the Japanese archipelago". Anthropological Science. 129 (1): 13–22. doi:10.1537/ase.2012132. As mentioned above, Jomon people are descendants of a common ancestor, although the process of their formation is still unknown. However, their origin dates back to the Paleolithic period based on the distribution of mitochondrial DNA haplogroups of the Jomon people and the age of divergence, which was 22000–23000 YBP (Adachi et al., 2011), and their phylogenetic basal position in the nuclear genome analysis (Kanzawa-Kiriyama et al., 2019).
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^ Jeong, Gichan; Gill, Haechan; Moon, Hyungmin; Jeong, Choongwon (11 December 2023). "An ancient genome perspective on the dynamic history of the prehistoric Jomon people in and around the Japanese archipelago". Human Population Genetics and Genomics: 1–21. doi:10.47248/hpgg2303040008.
^ Cooke, Niall P.; Murray, Madeleine; Cassidy, Lara M.; Mattiangeli, Valeria; Okazaki, Kenji; Kasai, Kenji; Gakuhari, Takashi; Bradley, Daniel G.; Nakagome, Shigeki (June 2024). "Genomic imputation of ancient Asian populations contrasts local adaptation in pre- and post-agricultural Japan". iScience. 27 (6): 110050. Bibcode:2024iSci...27k0050C. doi:10.1016/j.isci.2024.110050. PMC 11176660. PMID 38883821.
^ Osada, Naoki; Kawai, Yosuke (2021). "Exploring models of human migration to the Japanese archipelago using genome-wide genetic data". Anthropological Science. 129 (1): 45–58. doi:10.1537/ase.201215. Most Southeast, East, and Northeast Asian populations, including Jomon, are nearly equally distant from the Tianyuan individual, supporting the hypothesis that the Tianyuan population are diverged from the lineage basal to all East and Northeast Asians.
^ ^a ^b Cooke, Niall P.; Mattiangeli, Valeria; Cassidy, Lara M.; Okazaki, Kenji; Stokes, Caroline A.; Onbe, Shin; Hatakeyama, Satoshi; Machida, Kenichi; Kasai, Kenji; Tomioka, Naoto; Matsumoto, Akihiko; Ito, Masafumi; Kojima, Yoshitaka; Bradley, Daniel G.; Gakuhari, Takashi; Nakagome, Shigeki (2021). "Ancient genomics reveals tripartite origins of Japanese populations". Science Advances. 7 (38): eabh2419. Bibcode:2021SciA....7.2419C. doi:10.1126/sciadv.abh2419. PMC 8448447. PMID 34533991. However, we note no dilution of Jomon ancestry in the Japanese population (15.0 ± 3.8%), relative to the Kofun individuals (13.1 ± 3.5%) (fig. S22).
^ ^a ^b ^c Watanabe, Yusuke; Ohashi, Jun (June 2023). "Modern Japanese ancestry-derived variants reveal the formation process of the current Japanese regional gradations". iScience. 26 (3): 106130. Bibcode:2023iSci...26j6130W. doi:10.1016/j.isci.2023.106130. PMC 9984562. PMID 36879818. Whole-genome analyses extracted from the remains of the Jomon people showed that they were highly differentiated from other East Asians, forming a basal lineage to East and Northeast Asians.8,10,11 The genetic relationship between Jomon individuals and other East Asians suggests that the ancestral population of the Jomon people is one of the earliest wave migrants who might have taken a coastal route from Southeast Asia toward East Asia.11 It was also revealed that the Jomon people are genetically closely related to the Ainu/Ryukyuan population and that 10–20% of the genomic components found in mainland Japanese are derived from the Jomon people.8,10 Recent studies have found that, in addition to the "East Asian" population, which is closely related to modern Han Chinese, the "Northeast Asian" population also contributed to the ancestry of modern Japanese people.12,13 Cooke et al. 202113 showed the deep divergence of the Jomon people from continental populations, including the "East Asians" and "Northeast Asians"; thus, it can be concluded that the modern mainland Japanese are a population with genomic components derived from a basal East Asian lineage (i.e., the Jomon people) and from continental East Asians.
^ Aoki, Kenichi; Takahata, Naoyuki; Oota, Hiroki; et al. (30 August 2023). "Infectious diseases may have arrested the southward advance of microblades in Upper Palaeolithic East Asia". Proceedings of the Royal Society B: Biological Sciences. 290 (2005). doi:10.1098/rspb.2023.1262. PMC 10465978. PMID 37644833. These observations are consistent with the view that soon after the single eastward migration of modern humans, East Asians diverged in southern East Asia and dispersed northward across the continent.
^ Yamamoto, Kenichi; Namba, Shinichi; Sonehara, Kyuto; Suzuki, Ken; Sakaue, Saori; Cooke, Niall P.; Higashiue, Shinichi; Kobayashi, Shuzo; Afuso, Hisaaki; Matsuura, Kosho; Mitsumoto, Yojiro; Fujita, Yasuhiko; Tokuda, Torao; Matsuda, Koichi; Gakuhari, Takashi; Yamauchi, Toshimasa; Kadowaki, Takashi; Nakagome, Shigeki; Okada, Yukinori (12 November 2024). "Genetic legacy of ancient hunter-gatherer Jomon in Japanese populations". Nature Communications. 15 (1): 9780. Bibcode:2024NatCo..15.9780Y. doi:10.1038/s41467-024-54052-0. PMC 11558008. PMID 39532881.
^ Gakuhari, Takashi; Nakagome, Shigeki; Rasmussen, Simon; et al. (2020). "Ancient Jomon genome sequence analysis sheds light on migration patterns of early East Asian populations". Communications Biology. 3 (437) – via Nature.
^ Watanabe, Yusuke; Wakiyama, Yoshiki; Waku, Daisuke; et al. (2024). Cold adaptation in Upper Paleolithic hunter-gatherers of eastern Eurasia (Preprint). doi:10.1101/2024.05.03.591810.
^ Kanzawa-Kiriyama, Hideaki; Jinam, Timothy A.; Kawai, Yosuke; et al. (2019). "Late Jomon male and female genome sequences from the Funadomari site in Hokkaido, Japan". Anthropological Science. 127 (2): 83–108 – via J-STAGE.
^ Bennett, Andrew E.; Liu, Yichen; Fu, Qiaomei (2025). Reconstructing the Human Population History of East Asia through Ancient Genomics. doi:10.1017/9781009246675. ISBN 978-1-009-24667-5.^{[page needed]}
^ Natsuki, Daigo (January 2022). "Migration and adaptation of Jomon people during Pleistocene/Holocene transition period in Hokkaido, Japan". Quaternary International. 608–609: 49–64. Bibcode:2022QuInt.608...49N. doi:10.1016/j.quaint.2021.01.009.
^ de Boer, Elisabeth; Yang, Melinda A.; Kawagoe, Aileen; Barnes, Gina L. (2020). "Japan considered from the hypothesis of farmer/language spread". Evolutionary Human Sciences. 2: e13. doi:10.1017/ehs.2020.7. PMC 10427481. PMID 37588377. Ancient northern Siberian ancestry prevalent during the Palaeolithic notable for both its closer relationship with European-related rather than Asian-related ancestry and its impact on Native American ancestry is not found in mainland East Asians or the Jōmon, which emphasizes that the connections are specific to coastal mainland East Asians and the Jōmon.
^ Gakuhari, Takashi; Nakagome, Shigeki; Rasmussen, Simon; Allentoft, Morten E.; Sato, Takehiro; Korneliussen, Thorfinn; Chuinneagáin, Blánaid Ní; Matsumae, Hiromi; Koganebuchi, Kae; Schmidt, Ryan; Mizushima, Souichiro; Kondo, Osamu; Shigehara, Nobuo; Yoneda, Minoru; Kimura, Ryosuke; Ishida, Hajime; Masuyama, Tadayuki; Yamada, Yasuhiro; Tajima, Atsushi; Shibata, Hiroki; Toyoda, Atsushi; Tsurumoto, Toshiyuki; Wakebe, Tetsuaki; Shitara, Hiromi; Hanihara, Tsunehiko; Willerslev, Eske; Sikora, Martin; Oota, Hiroki (25 August 2020). "Ancient Jomon genome sequence analysis sheds light on migration patterns of early East Asian populations". Communications Biology. 3 (1): 437. doi:10.1038/s42003-020-01162-2. PMC 7447786. PMID 32843717. Therefore, there was no detectable signature of gene flow from MA-1 to the ancient/present-day Southeast/East Asians including IK002.
^ Abood, Steven; Oota, Hiroki (14 February 2025). "Human dispersal into East Eurasia: ancient genome insights and the need for research on physiological adaptations". Journal of Physiological Anthropology. 44 (1): 5. doi:10.1186/s40101-024-00382-3. PMC 11829451. PMID 39953642. However, the fact that no evidence of gene flow from Mal'ta was detected in the genome of the Ikawazu Jomon individual was a novel discovery. To what extent did the genome of the northern route influence the Jomon people? In the genome of the Ikawazu Jomon individual, no evidence of gene flow from the northern route was detected. Sufficient DNA was extracted from one of the two Jomon skeletons excavated from the Funadomari site in Hokkaido, allowing for the determination of a complete genome sequence. The Funadomari Jomon genome sequence had a high depth of coverage, and analysis revealed a remarkable genetic similarity to the Ikawazu Jomon. Including this Funadomari Jomon sequence, genome sequence data from approximately 10 Jomon individuals have been registered in public databases and are available for analysis. To date, the conclusion remains unchanged.
^ ^a ^b Jeong, Choongwon; Nakagome, Shikegi; Rienzo, Anna Di (2016). "Deep History of East Asian Populations Revealed Through Genetic Analysis of the Ainu". Genetics. 202 (1): 261–272. doi:10.1534/genetics.115.178673. PMC 4701090. PMID 26500257.
^ Kanzawa-Kiriyama, Hideaki; Kryukov, Kirill; Jinam, Timothy A; Hosomichi, Kazuyoshi; Saso, Aiko; Suwa, Gen; Ueda, Shintaroh; Yoneda, Minoru; Tajima, Atsushi; Shinoda, Ken-ichi; Inoue, Ituro; Saitou, Naruya (February 2017). "A partial nuclear genome of the Jomons who lived 3000 years ago in Fukushima, Japan". Journal of Human Genetics. 62 (2): 213–221. doi:10.1038/jhg.2016.110. PMC 5285490. PMID 27581845 – via Nature. Allele sharing analysis using 5392 SNP sites showed that the Ainu had the highest percentage of allele sharing with the Sanganji Jomon, followed by the Ryukyuan, the mainland Japanese and CHB, similar to the projection of PC1 in Figure 2b. Using the HGDP East Eurasian data set with 7081 SNP sites, the mainland Japanese had the highest allele sharing with the Sanganji Jomon. Interestingly, southern East Eurasians had slightly higher allele-sharing percentages than northern East Eurasians, although we have to be careful with the effect of post-mortem changes.
^ ^a ^b Yang, Melinda A.; Fan, Xuechun; Sun, Bo; Chen, Chungyu; Lang, Jianfeng; Ko, Ying-Chin; Tsang, Cheng-hwa; Chiu, Hunglin; Wang, Tianyi; Bao, Qingchuan; Wu, Xiaohong; Hajdinjak, Mateja; Ko, Albert Min-Shan; Ding, Manyu; Cao, Peng; Yang, Ruowei; Liu, Feng; Nickel, Birgit; Dai, Qingyan; Feng, Xiaotian; Zhang, Lizhao; Sun, Chengkai; Ning, Chao; Zeng, Wen; Zhao, Yongsheng; Zhang, Ming; Gao, Xing; Cui, Yinqiu; Reich, David; Stoneking, Mark; Fu, Qiaomei (17 July 2020). "Ancient DNA indicates human population shifts and admixture in northern and southern China". Science. 369 (6501): 282–288. Bibcode:2020Sci...369..282Y. doi:10.1126/science.aba0909. PMID 32409524. Instead, we find that Jōmon individual shows affinities to several coastal Neolithic populations in Siberia, as well as southern East Asia. The patterns demonstrated here show that coastal regions were areas of interconnectivity and gene flow rather than isolation.
^ ^a ^b Bennett, Andrew E.; Liu, Yichen; Fu, Qiaomei (2025). Reconstructing the Human Population History of East Asia through Ancient Genomics. Cambridge University Press. ISBN 978-1-009-24667-5. The current understanding is that the Jōmon represent a distinct East Asian lineage that separated from the basal East Asian lineage between 38,000 and 25,000 years ago, after the divergence of Tianyuan-related and Önge-related lineages, but prior to the separation of northern and eastern Asians and groups that would contribute to Native Americans. They appear to have remained in relative isolation, although possibly periodically interacting with neighboring mainland coastal groups.
^ de Boer, Elisabeth; Yang, Melinda A.; Kawagoe, Aileen; Barnes, Gina L. (2020). "Japan considered from the hypothesis of farmer/language spread". Evolutionary Human Sciences. 2: e13. doi:10.1017/ehs.2020.7. PMC 10427481. PMID 37588377. One explanation for a connection between the Jōmon and coastal East Asians could be that the Jōmon were not completely isolated from mainland East Asians. By 3900 years ago, the date of the oldest Jōmon nuclear genome sampled, Austronesians were rapidly expanding into islands in the Pacific. The main patterns observed both in past mtDNA studies and in recent genome-wide studies of the Jōmon all seem to highlight coastal connections, which may suggest that the Jōmon experienced gene flow with populations deriving from mainland East Asia prior to any contact associated with migration of Mumun immigrants from the Korean peninsula.
^ Wang, Mengge; He, Guanglin; Zou, Xing; et al. (2021). "New insights from the combined discrimination of modern/ancient genome-wide shared alleles and haplotypes: Differentiated demographic history reconstruction of Tai-Kadai and Sinitic people in South China". bioRxiv – via bioRxiv. The ancestry of jacinth color maximized in Iron Age Hanben and Gongguan people was widely distributed among coastal Neolithic southern East Asians from Fujian province, Jomon people and modern East Asians.
^ ^a ^b ^c Gakuhari, Takashi; Nakagome, Shigeki; Rasmussen, Simon; et al. (2020). "Ancient Jomon genome sequence analysis sheds light on migration patterns of early East Asian populations". Communications Biology. 3 (437) – via NCBI.
^ ^a ^b Matsukusa, Hirotaka; Oota, Hiroki; Haneji, Kuniaki; et al. (2010). "A Genetic Analysis of the Sakishima Islanders Reveals No Relationship With Taiwan Aborigines but Shared Ancestry With Ainu and Main-Island Japanese". American Journal of Physical Anthropology. 142 (2): 211–223 – via NCBI. This study reveals that the Sakishima islanders are not related to Taiwan aborigines, but exhibit affinity with the Hokkaido Ainu. These results confirm that the Austronesian expansion did not contribute to modern Sakishima, main-island Okinawa, and Honshu Japanese people.
^ ^a ^b Sato, Takehiro; Nakagome, Shigeki; Watanabe, Chiaki; Yamaguchi, Kyoko (2014). "Genome-Wide SNP Analysis Reveals Population Structure and Demographic History of the Ryukyu Islanders in the Southern Part of the Japanese Archipelago". Molecular Biology and Evolution. 31 (11): 2929–2940 – via Oxford Academic. A previous study based on mtDNA, Y chromosomal STRs, and autosomal STRs also showed that there was no evidence of any contribution from the aboriginal Taiwanese populations to the gene pool of the Ryukyu Islanders. Similarly, using a large number of SNP markers, this study verified that there is a clear genetic gap between Taiwan and the Ryukyu Islands.
^ ^a ^b ^c ^d Dudzik, Beatrix (2015). "Investigating Cranial Variation in Japanese Populations Using Geometric Morphometrics". University of Tennessee – via TRACE: Tennessee Research and Creative Exchange.
^ ^a ^b Koganebuchi, Kae; Matsunami, Masatoshi; Imamura, Minako; Kawai, Yosuke; Hitomi, Yuki; Tokunaga, Katsushi; Maeda, Shiro; Ishida, Hajime; Kimura, Ryosuke (20 July 2023). "Demographic history of Ryukyu islanders at the southern part of the Japanese Archipelago inferred from whole-genome resequencing data". Journal of Human Genetics. 68 (11): 759–767. doi:10.1038/s10038-023-01180-y. ISSN 1435-232X. PMC 10597838. PMID 37468573.
^ ^a ^b Ishiya, Koji; Mizuno, Fuzuki; Gojobori, Jun; et al. (2024). High-coverage genome sequencing of Yayoi and Jomon individuals shed light on prehistoric human population history in East Eurasian (Preprint). doi:10.1101/2024.08.09.606917.
^ Robbeets, Martine; Bouckaert, Remco; Conte, Matthew; Savelyev, Alexander; Li, Tao; An, Deog-Im; Shinoda, Ken-ichi; Cui, Yinqiu; Kawashima, Takamune; Kim, Geonyoung; Uchiyama, Junzo; Dolińska, Joanna; Oskolskaya, Sofia; Yamano, Ken-Yōjiro; Seguchi, Noriko; Tomita, Hirotaka; Takamiya, Hiroto; Kanzawa-Kiriyama, Hideaki; Oota, Hiroki; Ishida, Hajime; Kimura, Ryosuke; Sato, Takehiro; Kim, Jae-Hyun; Deng, Bingcong; Bjørn, Rasmus; Rhee, Seongha; Ahn, Kyou-Dong; Gruntov, Ilya; Mazo, Olga; Bentley, John R.; Fernandes, Ricardo; Roberts, Patrick; Bausch, Ilona R.; Gilaizeau, Linda; Yoneda, Minoru; Kugai, Mitsugu; Bianco, Raffaela A.; Zhang, Fan; Himmel, Marie; Hudson, Mark J.; Ning, Chao (25 November 2021). "Triangulation supports agricultural spread of the Transeurasian languages". Nature. 599 (7886): 616–621. Bibcode:2021Natur.599..616R. doi:10.1038/s41586-021-04108-8. PMC 8612925. PMID 34759322.
^ Kim, Jonghyun; Mizuno, Fuzuki; Matsushita, Takayuki; Matsushita, Masami; Aoto, Saki; Ishiya, Koji; Kamio, Mami; Naka, Izumi; Hayashi, Michiko; Kurosaki, Kunihiko; Ueda, Shintaroh; Ohashi, Jun (January 2025). "Genetic analysis of a Yayoi individual from the Doigahama site provides insights into the origins of immigrants to the Japanese Archipelago". Journal of Human Genetics. 70 (1): 47–57. doi:10.1038/s10038-024-01295-w. PMC 11700843. PMID 39402381.
^ de Boer, Elisabeth; Yang, Melinda A.; Kawagoe, Aileen; Barnes, Gina L. (2020). "Japan considered from the hypothesis of farmer/language spread". Evolutionary Human Sciences. 2: e13. doi:10.1017/ehs.2020.7. PMC 10427481. PMID 37588377.
^ Kanzawa-Kiriyama, Hideaki; Jinam, Timothy A.; Kawai, Yosuke; Sato, Takehiro; Hosomichi, Kazuyoshi; Tajima, Atsushi; Adachi, Noboru; Matsumura, Hirofumi; Kryukov, Kirill; Saitou, Naruya; Shinoda, Ken-Ichi (2019). "Late Jomon male and female genome sequences from the Funadomari site in Hokkaido, Japan". Anthropological Science. 127 (2): 83–108. doi:10.1537/ase.190415.
^ ^a ^b Gakuhari, Takashi; Nakagome, Shigeki; Rasmussen, Simon; Allentoft, Morten E.; Sato, Takehiro; Korneliussen, Thorfinn; Chuinneagáin, Blánaid Ní; Matsumae, Hiromi; Koganebuchi, Kae; Schmidt, Ryan; Mizushima, Souichiro; Kondo, Osamu; Shigehara, Nobuo; Yoneda, Minoru; Kimura, Ryosuke (25 August 2020). "Ancient Jomon genome sequence analysis sheds light on migration patterns of early East Asian populations". Communications Biology. 3 (1): 437. doi:10.1038/s42003-020-01162-2. PMC 7447786. PMID 32843717. Subsequently, we carried out model-based unsupervised clustering using ADMIXTURE44 (Supplementary Fig. 6). Assuming K = 15 ancestral clusters (Fig. 1b), an ancestral component unique to IK002 appears, which is the most prevalent in the Hokkaido Ainu (average 79.3%). This component is also shared with present-day Honshu Japanese as well as Ulchi (9.8% and 6.0%, respectively) (Fig. 1b).
^ Yamamoto, Kenichi; Namba, Shinichi; Sonehara, Kyuto; Suzuki, Ken; Sakaue, Saori; Cooke, Niall P.; Higashiue, Shinichi; Kobayashi, Shuzo; Afuso, Hisaaki; Matsuura, Kosho; Mitsumoto, Yojiro; Fujita, Yasuhiko; Tokuda, Torao; Matsuda, Koichi; Gakuhari, Takashi (12 November 2024). "Genetic legacy of ancient hunter-gatherer Jomon in Japanese populations". Nature Communications. 15 (1): 9780. Bibcode:2024NatCo..15.9780Y. doi:10.1038/s41467-024-54052-0. PMC 11558008. PMID 39532881. In the whole BBJ dataset, the proportions of the three distinct ancestral components closely align with those reported in the previous study (Jomon: 12.4%, Northeast Asia: 21.2%, and East Asia: 66.4%)14. However, Jomon ancestry exhibits regional variation, ranging from 9.8% in Kinki to 26.1% in Okinawa (Fig. 2a). Within the Ryukyu Islands, there is an elevated level of Jomon ancestry, with the highest proportion observed on Yoron Island (Fig. 2b). Jomon ancestry is even higher in one of the genetically-defined populations, Hokkaido_sub (31.6%, Fig. 2c and Supplementary Data 3), which primarily includes a subset of individuals from Hokkaido.
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[10] "縄文", Wiktionary, the free dictionary, 12 January 2025, retrieved 22 February 2025

[11] Mizoguchi, Koji (2013). The Archaeology of Japan. doi:10.1017/CBO9781139034265. ISBN 978-1-139-03426-5.^{[page needed]}

[12] Tsuboi, S. (1921). On the Origins of Japanese Pottery. Tokyo Anthropological Society.

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[15] Habu, J. (2004). Ancient Jomon of Japan. Cambridge University Press.^{[page needed]}

[16] Hudson, M. (2022). Reconsidering Jōmon Complexity: New Evidence from Interdisciplinary Studies. Asian Perspectives, 61(1), 34–57.

[17] Kuzmin, Y. (2017). Radiocarbon Dating of Early Pottery in East Asia: Implications for Jōmon Chronology. Antiquity, 91(356), 1472–1484.

[18] McColl, H. et al. (2019). Ancient Genomes Reveal Jōmon Contributions to Modern Japanese Populations. Nature Communications, 10(1), 1005.

[19] Shitara, H. (2020). Holocene Climate Change and the Jōmon Adaptation in the Japanese Archipelago. Quaternary International, 568, 79–93.

[20] Kaner, S. (2018). Jōmon Monuments and Ritual Practices in Prehistoric Japan. Journal of World Prehistory, 31(2), 103–126.

[21] UNESCO (2021). Jōmon Prehistoric Sites of Northern Japan. Official World Heritage Listing.

[22] Crawford, Gary W. (October 2011). "Advances in Understanding Early Agriculture in Japan". Current Anthropology. 52 (S4): S331 – S345. doi:10.1086/658369.

[23] Takahashi, Yu; Nasu, Hiroo; Nakayama, Seiji; Tomooka, Norihiko (2023). "Domestication of azuki bean and soybean in Japan: From the insight of archeological and molecular evidence". Breeding Science. 73 (2): 117–131. Bibcode:2023BrSci..73..117T. doi:10.1270/jsbbs.22074. PMC 10316305. PMID 37404345.

[24] Crawford, Gary W. (2011). "Advances in Understanding Early Agriculture in Japan". Current Anthropology. 52 (S4): S331 – S345. doi:10.1086/658369. JSTOR 10.1086/658369. S2CID 143756517.

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[:9-26] ^ ^a ^b ^c ^d ^e ^f ^g ^h ⁱ ^j ^k ^l ^m ⁿ Visitor's Guide to the Sannai Maruyama Site (1st ed.). Sannai Maruyama Jomon Culture Center. 27 January 2023.

[27] 本節の典拠は橋口、前掲書、158–172ページ

[28] 堤隆は旧石器時代の神津島での黒曜石採取については、丸木舟を建造出来るような石器が存在しなかったことから考えて、カヤックのようなスキンボートを使用したのではないかと指摘している（堤隆『黒曜石3万年の旅』NHKブックス、2004年、93ページ）

[29] Chien, Chih-Cheng; Seiko, Takashi; Muto, Chiaki; Ariga, Hirotaka; Wang, Yen-Chiao; Chang, Chuan-Hsin; Sakai, Hiroaki; Naito, Ken; Lee, Cheng-Ruei (29 May 2025). "A single domestication origin of adzuki bean in Japan and the evolution of domestication genes". Science. 388 (6750): eads2871. doi:10.1126/science.ads2871. ISSN 0036-8075. PMID 40440382.

[:10-30] Lapteff, Sergey (2006). "Relationships between Jōmon Culture and the Cultures of the Yangtze, South China, and Continental Southeast Asian Areas". Japan Review (18): 261. JSTOR 25791304. Especially, the similarities are numerous between Jomon and the Fujian region, showing that Fujian was probably one of the main bridges connecting Japan with Asian continent for migrations of human groups and possibly for trade.

[31] "縄文時代のリアルを紐解くと、現代社会のルーツが見えてくる。 | 東京都立大学総合研究推進機構 TMU Research Portal". research-miyacology.tmu.ac.jp (in Japanese). 1 November 2021. Retrieved 6 May 2025.

[:20-32] "ミシャグジとは何？わかりやすく解説 Weblio辞書". www.weblio.jp (in Japanese). Retrieved 6 May 2025.

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[:29-34] "【ホームメイト】神社に祀られている神様「第七回・アメノウズメ（芸能の女神）」". www.homemate-research-religious-building.com. Retrieved 6 May 2025.

[35] "火焔型土器とは？新潟の国宝に隠された縄文の謎、火焔土器との違い". 日本神話と歴史 (in Japanese). 22 October 2024. Retrieved 6 May 2025.

[heritageofjapan-36] "Jomon crafts and what they were for". Heritage of Japan. 12 July 2007. Retrieved 26 August 2019.

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[38] "さいたま市立博物館展示web解説（縄文時代その2）". 埼玉県さいたま市役所公式ホームページ (in Japanese). Retrieved 6 May 2025.

[:27-39] "神聖視された「勾玉」の実態人々がその貴重さに魅せられたわけ". 國學院大學 (in Japanese). Retrieved 6 May 2025.

[40] "【解説】「三種の神器」、皇室が持つ謎の宝物". BBCニュース (in Japanese). Retrieved 6 May 2025.

[41] Pilgrim, Richard; Ellwood, Robert (1985). Japanese Religion (1st ed.). Englewood Cliffs, New Jersey: Prentice Hall Inc. pp. 18–19. ISBN 978-0-13-509282-8.

[42] 小泉保（1998）『縄文語の発見』青土社 (in Japanese)

[43] 『古代に真実を求めて第七集（古田史学論集）』2004年、古田史学の会（編集） (in Japanese)

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[45] Vovin, Alexander (1993). A Reconstruction of Proto-Ainu. BRILL. doi:10.1163/9789004644823. ISBN 978-90-04-09905-0.^{[page needed]}

[Vovin_272–300-46] Vovin, Alexander (21 December 2021). "Austronesians in the Northern Waters?". International Journal of Eurasian Linguistics. 3 (2): 272–300. doi:10.1163/25898833-00320006.

[47] Chaubey, Gyaneshwer; Driem, George van (2020). "Munda languages are father tongues, but Japanese and Korean are not". Evolutionary Human Sciences. 2: e19. doi:10.1017/ehs.2020.14. PMC 10427457. PMID 37588351. The Japonic-speaking Early Jōmon people must have been drawn in to avail themselves of the pickings of Yayoi agricultural yields, and the Yayoi may have prospered and succeeded in multiplying their paternal lineages precisely because they managed to accommodate the Jōmon linguistically and in material ways.
The dual nature of Japanese population structure was advanced by Miller, who proposed that the resident Jōmon population spoke an Altaic language ancestral to modern Japanese, and this Altaic tongue underwent Austronesian influence when the islanders absorbed the bearers of the incursive Yayoi culture.

[48] Adachi, Noboru; Kanzawa-Kiriyama, Hideaki; Nara, Takashi; Kakuda, Tsuneo; Nishida, Iwao; Shinoda, Ken-Ichi (2021). "Ancient genomes from the initial Jomon period: new insights into the genetic history of the Japanese archipelago". Anthropological Science. 129 (1): 13–22. doi:10.1537/ase.2012132. As mentioned above, Jomon people are descendants of a common ancestor, although the process of their formation is still unknown. However, their origin dates back to the Paleolithic period based on the distribution of mitochondrial DNA haplogroups of the Jomon people and the age of divergence, which was 22000–23000 YBP (Adachi et al., 2011), and their phylogenetic basal position in the nuclear genome analysis (Kanzawa-Kiriyama et al., 2019).

[Yang_A_genetic_history_of_migration-49] Yang, Melinda A. (6 January 2022). "A genetic history of migration, diversification, and admixture in Asia". Human Population Genetics and Genomics: 1–32. doi:10.47248/hpgg2202010001.

[:6-50] Jeong, Gichan; Gill, Haechan; Moon, Hyungmin; Jeong, Choongwon (11 December 2023). "An ancient genome perspective on the dynamic history of the prehistoric Jomon people in and around the Japanese archipelago". Human Population Genetics and Genomics: 1–21. doi:10.47248/hpgg2303040008.

[51] Cooke, Niall P.; Murray, Madeleine; Cassidy, Lara M.; Mattiangeli, Valeria; Okazaki, Kenji; Kasai, Kenji; Gakuhari, Takashi; Bradley, Daniel G.; Nakagome, Shigeki (June 2024). "Genomic imputation of ancient Asian populations contrasts local adaptation in pre- and post-agricultural Japan". iScience. 27 (6): 110050. Bibcode:2024iSci...27k0050C. doi:10.1016/j.isci.2024.110050. PMC 11176660. PMID 38883821.

[52] Osada, Naoki; Kawai, Yosuke (2021). "Exploring models of human migration to the Japanese archipelago using genome-wide genetic data". Anthropological Science. 129 (1): 45–58. doi:10.1537/ase.201215. Most Southeast, East, and Northeast Asian populations, including Jomon, are nearly equally distant from the Tianyuan individual, supporting the hypothesis that the Tianyuan population are diverged from the lineage basal to all East and Northeast Asians.

[Cooke_Mattiangeli_Cassidy_et_al_Ancient_genomics_reveals_tripartite-53] Cooke, Niall P.; Mattiangeli, Valeria; Cassidy, Lara M.; Okazaki, Kenji; Stokes, Caroline A.; Onbe, Shin; Hatakeyama, Satoshi; Machida, Kenichi; Kasai, Kenji; Tomioka, Naoto; Matsumoto, Akihiko; Ito, Masafumi; Kojima, Yoshitaka; Bradley, Daniel G.; Gakuhari, Takashi; Nakagome, Shigeki (2021). "Ancient genomics reveals tripartite origins of Japanese populations". Science Advances. 7 (38): eabh2419. Bibcode:2021SciA....7.2419C. doi:10.1126/sciadv.abh2419. PMC 8448447. PMID 34533991. However, we note no dilution of Jomon ancestry in the Japanese population (15.0 ± 3.8%), relative to the Kofun individuals (13.1 ± 3.5%) (fig. S22).

[Watanabe2023-54] Watanabe, Yusuke; Ohashi, Jun (June 2023). "Modern Japanese ancestry-derived variants reveal the formation process of the current Japanese regional gradations". iScience. 26 (3): 106130. Bibcode:2023iSci...26j6130W. doi:10.1016/j.isci.2023.106130. PMC 9984562. PMID 36879818. Whole-genome analyses extracted from the remains of the Jomon people showed that they were highly differentiated from other East Asians, forming a basal lineage to East and Northeast Asians.8,10,11 The genetic relationship between Jomon individuals and other East Asians suggests that the ancestral population of the Jomon people is one of the earliest wave migrants who might have taken a coastal route from Southeast Asia toward East Asia.11 It was also revealed that the Jomon people are genetically closely related to the Ainu/Ryukyuan population and that 10–20% of the genomic components found in mainland Japanese are derived from the Jomon people.8,10 Recent studies have found that, in addition to the "East Asian" population, which is closely related to modern Han Chinese, the "Northeast Asian" population also contributed to the ancestry of modern Japanese people.12,13 Cooke et al. 202113 showed the deep divergence of the Jomon people from continental populations, including the "East Asians" and "Northeast Asians"; thus, it can be concluded that the modern mainland Japanese are a population with genomic components derived from a basal East Asian lineage (i.e., the Jomon people) and from continental East Asians.

[55] Aoki, Kenichi; Takahata, Naoyuki; Oota, Hiroki; et al. (30 August 2023). "Infectious diseases may have arrested the southward advance of microblades in Upper Palaeolithic East Asia". Proceedings of the Royal Society B: Biological Sciences. 290 (2005). doi:10.1098/rspb.2023.1262. PMC 10465978. PMID 37644833. These observations are consistent with the view that soon after the single eastward migration of modern humans, East Asians diverged in southern East Asia and dispersed northward across the continent.

[56] Yamamoto, Kenichi; Namba, Shinichi; Sonehara, Kyuto; Suzuki, Ken; Sakaue, Saori; Cooke, Niall P.; Higashiue, Shinichi; Kobayashi, Shuzo; Afuso, Hisaaki; Matsuura, Kosho; Mitsumoto, Yojiro; Fujita, Yasuhiko; Tokuda, Torao; Matsuda, Koichi; Gakuhari, Takashi; Yamauchi, Toshimasa; Kadowaki, Takashi; Nakagome, Shigeki; Okada, Yukinori (12 November 2024). "Genetic legacy of ancient hunter-gatherer Jomon in Japanese populations". Nature Communications. 15 (1): 9780. Bibcode:2024NatCo..15.9780Y. doi:10.1038/s41467-024-54052-0. PMC 11558008. PMID 39532881.

[57] Gakuhari, Takashi; Nakagome, Shigeki; Rasmussen, Simon; et al. (2020). "Ancient Jomon genome sequence analysis sheds light on migration patterns of early East Asian populations". Communications Biology. 3 (437) – via Nature.

[:32-58] Watanabe, Yusuke; Wakiyama, Yoshiki; Waku, Daisuke; et al. (2024). Cold adaptation in Upper Paleolithic hunter-gatherers of eastern Eurasia (Preprint). doi:10.1101/2024.05.03.591810.

[59] Kanzawa-Kiriyama, Hideaki; Jinam, Timothy A.; Kawai, Yosuke; et al. (2019). "Late Jomon male and female genome sequences from the Funadomari site in Hokkaido, Japan". Anthropological Science. 127 (2): 83–108 – via J-STAGE.

[:4-60] Bennett, Andrew E.; Liu, Yichen; Fu, Qiaomei (2025). Reconstructing the Human Population History of East Asia through Ancient Genomics. doi:10.1017/9781009246675. ISBN 978-1-009-24667-5.^{[page needed]}

[61] Natsuki, Daigo (January 2022). "Migration and adaptation of Jomon people during Pleistocene/Holocene transition period in Hokkaido, Japan". Quaternary International. 608–609: 49–64. Bibcode:2022QuInt.608...49N. doi:10.1016/j.quaint.2021.01.009.

[62] Boer, Elisabeth; Yang, Melinda A.; Kawagoe, Aileen; Barnes, Gina L. (2020). "Japan considered from the hypothesis of farmer/language spread". Evolutionary Human Sciences. 2: e13. doi:10.1017/ehs.2020.7. PMC 10427481. PMID 37588377. Ancient northern Siberian ancestry prevalent during the Palaeolithic notable for both its closer relationship with European-related rather than Asian-related ancestry and its impact on Native American ancestry is not found in mainland East Asians or the Jōmon, which emphasizes that the connections are specific to coastal mainland East Asians and the Jōmon.

[63] Gakuhari, Takashi; Nakagome, Shigeki; Rasmussen, Simon; Allentoft, Morten E.; Sato, Takehiro; Korneliussen, Thorfinn; Chuinneagáin, Blánaid Ní; Matsumae, Hiromi; Koganebuchi, Kae; Schmidt, Ryan; Mizushima, Souichiro; Kondo, Osamu; Shigehara, Nobuo; Yoneda, Minoru; Kimura, Ryosuke; Ishida, Hajime; Masuyama, Tadayuki; Yamada, Yasuhiro; Tajima, Atsushi; Shibata, Hiroki; Toyoda, Atsushi; Tsurumoto, Toshiyuki; Wakebe, Tetsuaki; Shitara, Hiromi; Hanihara, Tsunehiko; Willerslev, Eske; Sikora, Martin; Oota, Hiroki (25 August 2020). "Ancient Jomon genome sequence analysis sheds light on migration patterns of early East Asian populations". Communications Biology. 3 (1): 437. doi:10.1038/s42003-020-01162-2. PMC 7447786. PMID 32843717. Therefore, there was no detectable signature of gene flow from MA-1 to the ancient/present-day Southeast/East Asians including IK002.

[64] Abood, Steven; Oota, Hiroki (14 February 2025). "Human dispersal into East Eurasia: ancient genome insights and the need for research on physiological adaptations". Journal of Physiological Anthropology. 44 (1): 5. doi:10.1186/s40101-024-00382-3. PMC 11829451. PMID 39953642. However, the fact that no evidence of gene flow from Mal'ta was detected in the genome of the Ikawazu Jomon individual was a novel discovery. To what extent did the genome of the northern route influence the Jomon people? In the genome of the Ikawazu Jomon individual, no evidence of gene flow from the northern route was detected. Sufficient DNA was extracted from one of the two Jomon skeletons excavated from the Funadomari site in Hokkaido, allowing for the determination of a complete genome sequence. The Funadomari Jomon genome sequence had a high depth of coverage, and analysis revealed a remarkable genetic similarity to the Ikawazu Jomon. Including this Funadomari Jomon sequence, genome sequence data from approximately 10 Jomon individuals have been registered in public databases and are available for analysis. To date, the conclusion remains unchanged.

[:1-65] Jeong, Choongwon; Nakagome, Shikegi; Rienzo, Anna Di (2016). "Deep History of East Asian Populations Revealed Through Genetic Analysis of the Ainu". Genetics. 202 (1): 261–272. doi:10.1534/genetics.115.178673. PMC 4701090. PMID 26500257.

[:19-66] Kanzawa-Kiriyama, Hideaki; Kryukov, Kirill; Jinam, Timothy A; Hosomichi, Kazuyoshi; Saso, Aiko; Suwa, Gen; Ueda, Shintaroh; Yoneda, Minoru; Tajima, Atsushi; Shinoda, Ken-ichi; Inoue, Ituro; Saitou, Naruya (February 2017). "A partial nuclear genome of the Jomons who lived 3000 years ago in Fukushima, Japan". Journal of Human Genetics. 62 (2): 213–221. doi:10.1038/jhg.2016.110. PMC 5285490. PMID 27581845 – via Nature. Allele sharing analysis using 5392 SNP sites showed that the Ainu had the highest percentage of allele sharing with the Sanganji Jomon, followed by the Ryukyuan, the mainland Japanese and CHB, similar to the projection of PC1 in Figure 2b. Using the HGDP East Eurasian data set with 7081 SNP sites, the mainland Japanese had the highest allele sharing with the Sanganji Jomon. Interestingly, southern East Eurasians had slightly higher allele-sharing percentages than northern East Eurasians, although we have to be careful with the effect of post-mortem changes.

[:22-67] Yang, Melinda A.; Fan, Xuechun; Sun, Bo; Chen, Chungyu; Lang, Jianfeng; Ko, Ying-Chin; Tsang, Cheng-hwa; Chiu, Hunglin; Wang, Tianyi; Bao, Qingchuan; Wu, Xiaohong; Hajdinjak, Mateja; Ko, Albert Min-Shan; Ding, Manyu; Cao, Peng; Yang, Ruowei; Liu, Feng; Nickel, Birgit; Dai, Qingyan; Feng, Xiaotian; Zhang, Lizhao; Sun, Chengkai; Ning, Chao; Zeng, Wen; Zhao, Yongsheng; Zhang, Ming; Gao, Xing; Cui, Yinqiu; Reich, David; Stoneking, Mark; Fu, Qiaomei (17 July 2020). "Ancient DNA indicates human population shifts and admixture in northern and southern China". Science. 369 (6501): 282–288. Bibcode:2020Sci...369..282Y. doi:10.1126/science.aba0909. PMID 32409524. Instead, we find that Jōmon individual shows affinities to several coastal Neolithic populations in Siberia, as well as southern East Asia. The patterns demonstrated here show that coastal regions were areas of interconnectivity and gene flow rather than isolation.

[:23-68] Bennett, Andrew E.; Liu, Yichen; Fu, Qiaomei (2025). Reconstructing the Human Population History of East Asia through Ancient Genomics. Cambridge University Press. ISBN 978-1-009-24667-5. The current understanding is that the Jōmon represent a distinct East Asian lineage that separated from the basal East Asian lineage between 38,000 and 25,000 years ago, after the divergence of Tianyuan-related and Önge-related lineages, but prior to the separation of northern and eastern Asians and groups that would contribute to Native Americans. They appear to have remained in relative isolation, although possibly periodically interacting with neighboring mainland coastal groups.

[:12-69] Boer, Elisabeth; Yang, Melinda A.; Kawagoe, Aileen; Barnes, Gina L. (2020). "Japan considered from the hypothesis of farmer/language spread". Evolutionary Human Sciences. 2: e13. doi:10.1017/ehs.2020.7. PMC 10427481. PMID 37588377. One explanation for a connection between the Jōmon and coastal East Asians could be that the Jōmon were not completely isolated from mainland East Asians. By 3900 years ago, the date of the oldest Jōmon nuclear genome sampled, Austronesians were rapidly expanding into islands in the Pacific. The main patterns observed both in past mtDNA studies and in recent genome-wide studies of the Jōmon all seem to highlight coastal connections, which may suggest that the Jōmon experienced gene flow with populations deriving from mainland East Asia prior to any contact associated with migration of Mumun immigrants from the Korean peninsula.

[70] Wang, Mengge; He, Guanglin; Zou, Xing; et al. (2021). "New insights from the combined discrimination of modern/ancient genome-wide shared alleles and haplotypes: Differentiated demographic history reconstruction of Tai-Kadai and Sinitic people in South China". bioRxiv – via bioRxiv. The ancestry of jacinth color maximized in Iron Age Hanben and Gongguan people was widely distributed among coastal Neolithic southern East Asians from Fujian province, Jomon people and modern East Asians.

[:24-71] Gakuhari, Takashi; Nakagome, Shigeki; Rasmussen, Simon; et al. (2020). "Ancient Jomon genome sequence analysis sheds light on migration patterns of early East Asian populations". Communications Biology. 3 (437) – via NCBI.

[:34-72] Matsukusa, Hirotaka; Oota, Hiroki; Haneji, Kuniaki; et al. (2010). "A Genetic Analysis of the Sakishima Islanders Reveals No Relationship With Taiwan Aborigines but Shared Ancestry With Ainu and Main-Island Japanese". American Journal of Physical Anthropology. 142 (2): 211–223 – via NCBI. This study reveals that the Sakishima islanders are not related to Taiwan aborigines, but exhibit affinity with the Hokkaido Ainu. These results confirm that the Austronesian expansion did not contribute to modern Sakishima, main-island Okinawa, and Honshu Japanese people.

[:35-73] Sato, Takehiro; Nakagome, Shigeki; Watanabe, Chiaki; Yamaguchi, Kyoko (2014). "Genome-Wide SNP Analysis Reveals Population Structure and Demographic History of the Ryukyu Islanders in the Southern Part of the Japanese Archipelago". Molecular Biology and Evolution. 31 (11): 2929–2940 – via Oxford Academic. A previous study based on mtDNA, Y chromosomal STRs, and autosomal STRs also showed that there was no evidence of any contribution from the aboriginal Taiwanese populations to the gene pool of the Ryukyu Islanders. Similarly, using a large number of SNP markers, this study verified that there is a clear genetic gap between Taiwan and the Ryukyu Islands.

[:33-74] Dudzik, Beatrix (2015). "Investigating Cranial Variation in Japanese Populations Using Geometric Morphometrics". University of Tennessee – via TRACE: Tennessee Research and Creative Exchange.

[:02-75] Koganebuchi, Kae; Matsunami, Masatoshi; Imamura, Minako; Kawai, Yosuke; Hitomi, Yuki; Tokunaga, Katsushi; Maeda, Shiro; Ishida, Hajime; Kimura, Ryosuke (20 July 2023). "Demographic history of Ryukyu islanders at the southern part of the Japanese Archipelago inferred from whole-genome resequencing data". Journal of Human Genetics. 68 (11): 759–767. doi:10.1038/s10038-023-01180-y. ISSN 1435-232X. PMC 10597838. PMID 37468573.

[:242-76] Ishiya, Koji; Mizuno, Fuzuki; Gojobori, Jun; et al. (2024). High-coverage genome sequencing of Yayoi and Jomon individuals shed light on prehistoric human population history in East Eurasian (Preprint). doi:10.1101/2024.08.09.606917.

[77] Robbeets, Martine; Bouckaert, Remco; Conte, Matthew; Savelyev, Alexander; Li, Tao; An, Deog-Im; Shinoda, Ken-ichi; Cui, Yinqiu; Kawashima, Takamune; Kim, Geonyoung; Uchiyama, Junzo; Dolińska, Joanna; Oskolskaya, Sofia; Yamano, Ken-Yōjiro; Seguchi, Noriko; Tomita, Hirotaka; Takamiya, Hiroto; Kanzawa-Kiriyama, Hideaki; Oota, Hiroki; Ishida, Hajime; Kimura, Ryosuke; Sato, Takehiro; Kim, Jae-Hyun; Deng, Bingcong; Bjørn, Rasmus; Rhee, Seongha; Ahn, Kyou-Dong; Gruntov, Ilya; Mazo, Olga; Bentley, John R.; Fernandes, Ricardo; Roberts, Patrick; Bausch, Ilona R.; Gilaizeau, Linda; Yoneda, Minoru; Kugai, Mitsugu; Bianco, Raffaela A.; Zhang, Fan; Himmel, Marie; Hudson, Mark J.; Ning, Chao (25 November 2021). "Triangulation supports agricultural spread of the Transeurasian languages". Nature. 599 (7886): 616–621. Bibcode:2021Natur.599..616R. doi:10.1038/s41586-021-04108-8. PMC 8612925. PMID 34759322.

[78] Kim, Jonghyun; Mizuno, Fuzuki; Matsushita, Takayuki; Matsushita, Masami; Aoto, Saki; Ishiya, Koji; Kamio, Mami; Naka, Izumi; Hayashi, Michiko; Kurosaki, Kunihiko; Ueda, Shintaroh; Ohashi, Jun (January 2025). "Genetic analysis of a Yayoi individual from the Doigahama site provides insights into the origins of immigrants to the Japanese Archipelago". Journal of Human Genetics. 70 (1): 47–57. doi:10.1038/s10038-024-01295-w. PMC 11700843. PMID 39402381.

[79] Boer, Elisabeth; Yang, Melinda A.; Kawagoe, Aileen; Barnes, Gina L. (2020). "Japan considered from the hypothesis of farmer/language spread". Evolutionary Human Sciences. 2: e13. doi:10.1017/ehs.2020.7. PMC 10427481. PMID 37588377.

[:43-80] Kanzawa-Kiriyama, Hideaki; Jinam, Timothy A.; Kawai, Yosuke; Sato, Takehiro; Hosomichi, Kazuyoshi; Tajima, Atsushi; Adachi, Noboru; Matsumura, Hirofumi; Kryukov, Kirill; Saitou, Naruya; Shinoda, Ken-Ichi (2019). "Late Jomon male and female genome sequences from the Funadomari site in Hokkaido, Japan". Anthropological Science. 127 (2): 83–108. doi:10.1537/ase.190415.

[Gakuhari_Nakagome_Rasmussen_et_al_Ancient_Jomon_genome_sequence_analysis-81] Gakuhari, Takashi; Nakagome, Shigeki; Rasmussen, Simon; Allentoft, Morten E.; Sato, Takehiro; Korneliussen, Thorfinn; Chuinneagáin, Blánaid Ní; Matsumae, Hiromi; Koganebuchi, Kae; Schmidt, Ryan; Mizushima, Souichiro; Kondo, Osamu; Shigehara, Nobuo; Yoneda, Minoru; Kimura, Ryosuke (25 August 2020). "Ancient Jomon genome sequence analysis sheds light on migration patterns of early East Asian populations". Communications Biology. 3 (1): 437. doi:10.1038/s42003-020-01162-2. PMC 7447786. PMID 32843717. Subsequently, we carried out model-based unsupervised clustering using ADMIXTURE44 (Supplementary Fig. 6). Assuming K = 15 ancestral clusters (Fig. 1b), an ancestral component unique to IK002 appears, which is the most prevalent in the Hokkaido Ainu (average 79.3%). This component is also shared with present-day Honshu Japanese as well as Ulchi (9.8% and 6.0%, respectively) (Fig. 1b).

[:3-82] Yamamoto, Kenichi; Namba, Shinichi; Sonehara, Kyuto; Suzuki, Ken; Sakaue, Saori; Cooke, Niall P.; Higashiue, Shinichi; Kobayashi, Shuzo; Afuso, Hisaaki; Matsuura, Kosho; Mitsumoto, Yojiro; Fujita, Yasuhiko; Tokuda, Torao; Matsuda, Koichi; Gakuhari, Takashi (12 November 2024). "Genetic legacy of ancient hunter-gatherer Jomon in Japanese populations". Nature Communications. 15 (1): 9780. Bibcode:2024NatCo..15.9780Y. doi:10.1038/s41467-024-54052-0. PMC 11558008. PMID 39532881. In the whole BBJ dataset, the proportions of the three distinct ancestral components closely align with those reported in the previous study (Jomon: 12.4%, Northeast Asia: 21.2%, and East Asia: 66.4%)14. However, Jomon ancestry exhibits regional variation, ranging from 9.8% in Kinki to 26.1% in Okinawa (Fig. 2a). Within the Ryukyu Islands, there is an elevated level of Jomon ancestry, with the highest proportion observed on Yoron Island (Fig. 2b). Jomon ancestry is even higher in one of the genetically-defined populations, Hokkaido_sub (31.6%, Fig. 2c and Supplementary Data 3), which primarily includes a subset of individuals from Hokkaido.

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@@ Line 240: / Line 240: @@
 Full genome analyses of [[Okhotsk culture]] remains on [[Sakhalin]] found them to be derived from three major sources, notably [[Ancient Northeast Asian]]s, [[Ancient Paleo-Siberian]]s, and Jōmon people of Japan. An admixture analysis revealed them to carry c. 54% Ancient Northeast Asian, c. 22% Ancient Paleo-Siberian, and c. 24% Jōmon ancestries respectively.<ref name= "ReferenceA">{{Cite journal |last1=Sato |first1=Takehiro |last2=Adachi |first2= Noboru |last3=Kimura |first3= Ryosuke |last4=Hosomichi |first4= Kazuyoshi |last5=Yoneda |first5=Minoru |last6=Oota |first6=Hiroki |last7=Tajima |first7=Atsushi |last8=Toyoda |first8=Atsushi |last9= Kanzawa-Kiriyama |first9=Hideaki |last10=Matsumae |first10=Hiromi |last11=Koganebuchi |first11=Kae |last12=Shimizu |first12=Kentaro K |last13=Shinoda |first13=Ken-ichi |last14=Hanihara |first14=Tsunehiko |last15=Weber |first15=Andrzej |display-authors= 3|date=19 August 2021 |title= Whole-Genome Sequencing of a 900-Year-Old Human Skeleton Supports Two Past Migration Events from the Russian Far East to Northern Japan |url= |journal=Genome Biology and Evolution |volume=13 |issue=9 |doi=10.1093/gbe/evab192 |pmc=8449830 |pmid= 34410389}}</ref>
+Genetic analyses on ancient remains from the southern [[Korean Peninsula]] during the [[Three Kingdoms period of Korea|Three Kingdoms period]] reveal elevated Jōmon ancestry. This ancestry was most likely local to Korea. Around 500 CE, migrations led by northern Chinese virtually erased Jōmon ancestry among Koreans, with the latter becoming genetically homogenous.<ref>{{Cite journal |last=Gelabert |first=Pere |last2=Blazyte |first2=Asta |last3=Chang |first3=Yongjoon |last4=Fernandes |first4=Daniel M. |display-authors=3 |date=2022 |title=Northeastern Asian and Jomon-related genetic structure in the Three Kingdoms period of Gimhae, Korea |url=https://www.sciencedirect.com/science/article/pii/S0960982222009162#sec3 |journal=Current Biology |volume=32 |issue=15 |pages=3232-3244 |via=ScienceDirect}}</ref>
-Genetic analyses on ancient remains from the southern [[Korean Peninsula]] during the [[Three Kingdoms period of Korea|Three Kingdoms period]] reveal elevated Jōmon ancestry at c. 37%, while [[Yayoi people|Yayoi]] remains in Japan were found to carry nearly equal amounts of Jōmon ancestry (35–60%) and [[Ancient Northeast Asian]]-like ancestry (40–65%). These results suggest the presence of a Jōmon-like population on the Korean peninsula and their significant contribution to the formation of early [[Japonic languages|Japonic]]-speakers. As such, the "agricultural transition in prehistoric Japan involved the process of assimilation, rather than replacement, with almost equal genetic contributions from the indigenous Jōmon and mainland Asian migrants of the Mumun/Yayoi period". The Jōmon-like ancestry in Korea was 'diluted' over time due to subsequent arrivals of Neolithic [[West Liao River]] farmers from northeast China.<ref name="Cooke Mattiangeli Cassidy et al Ancient genomics reveals tripartite"/><ref name="Wang Wang Human genetics: The dual origin">{{cite journal |last1=Wang |first1=Rui |last2=Wang |first2=Chuan-Chao |date=August 2022 |title=Human genetics: The dual origin of Three Kingdoms period Koreans |journal=Current Biology |volume=32 |issue=15 |pages=R844–R847 |doi=10.1016/j.cub.2022.06.044 |pmid=35944486 |quote=Two main ancestry components were observed in ancient Koreans with different proportions: northern East Asian-related ancestry and indigenous Jomon-related ancestry. The northern East Asian ancestry was suggested to be related to the Neolithic West Liao River farmers in northeast China, who were an admixture of ANA and NYR ancestry. The finding indicated that West Liao River-related farmers might have spread the proto-Korean language as their ancestry was found to be predominant in extant Koreans. Proto-Korean groups, in turn, introduced West Liao River-like ancestry into the gene pool of present-day Japan. Present-day Japanese can be represented as a mixture of Koreans (91%) with a limited genetic heritage from a basal East Asian lineage related to Jomon (9%), except for the indigenous Ainu, who are considered direct descendants of the Jomon people. |doi-access=free|bibcode=2022CBio...32.R844W }}</ref>
 ==== Modern groups ====
@@ Line 246: / Line 246: @@
 The [[Ainu people|Ainu]] have the highest proportion of Jōmon ancestry among modern populations, estimated at up to 70%, followed by the [[Ryukyuans|Ryukyuan]]/Okinawan people at around 30%, and mainland Japanese at approximately 10–20%. The proportion of Jōmon ancestry varies regionally, being highest in the [[Tōhoku region|Tōhoku]] and [[Kyushu|Kyūshū regions]], and lowest in [[Kansai region|Kinki]] and [[Shikoku]], where Yayoi ancestry is more dominant. Residents of [[Tōhoku region|Tōhoku]], [[Kantō region|Kantō]], and [[Kyushu|Kyūshū]] show closer genetic affinity with [[Ryukyuans]]. Genetic relatedness between the Ainu and mainland Japanese is particularly strong in western [[Hokkaido|Hokkaidō]] and [[Aomori]]. It is also believed that mainland Japanese primarily derive their Jōmon ancestry from western Jōmon populations.<ref name=":31" /><ref name=":30">{{Cite web |title=日本人のルーツ「縄文人」とは？ |url=https://app.zene360.com/free/anc/jomon/article/shinoda/ |access-date=6 May 2025 |website=app.zene360.com}}</ref><ref>{{Cite web |title=縄文人と渡来人の混血史から日本列島人の地域的多様性の起源を探る |url=https://www.s.u-tokyo.ac.jp/ja/info/8252/ |access-date=6 May 2025 |website=東京大学 大学院理学系研究科・理学部 |language=ja}}</ref>
-Low levels of Jōmon ancestry have been identified among Koreans (approximately 1–5%), as well as in some Northeast Asian and coastal East Asian populations. For example, Taiwanese aborigines like [[Amis people|Ami]] and [[Atayal people|Atayal]], along with [[Kra–Dai-speaking peoples|Kra-Dai]] populations, have some genetic affinities with the Jōmon.<ref name=":30" /><ref name=":24" /><ref name="Wang2021-Guangxi">{{cite journal |last1=Wang |first1=Tianyi |last2=Wang |first2=Wei |last3=Xie |first3=Guangmao |last4=Li |first4=Zhen |last5=Fan |first5=Xuechun |year=2021 |title=Human population history at the crossroads of East and Southeast Asia since 11,000 years ago |journal=Cell |publisher=Elsevier BV |volume=184 |issue=14 |pages=3829–3841.e21 |doi=10.1016/j.cell.2021.05.018 |pmid=34171307 |doi-access=free}}</ref> However, the affinities between Jōmon and groups like Taiwanese aborigines and coastal Siberians is more likely due to their ancestors belonging to the same metapopulation that colonized Eastern Asia from south to north. That said, there is strong evidence of intermixing between Siberians and Ainu.<ref name=":24" />
+Low levels of Jōmon ancestry are found in present Koreans (approximately 1–5%), as well as in some Northeast Asian and coastal East Asian populations. For example, Taiwanese aborigines like [[Amis people|Ami]] and [[Atayal people|Atayal]], along with [[Kra–Dai-speaking peoples|Kra-Dai]] populations, have some genetic affinities with the Jōmon.<ref name=":30" /><ref name=":24" /><ref name="Wang2021-Guangxi">{{cite journal |last1=Wang |first1=Tianyi |last2=Wang |first2=Wei |last3=Xie |first3=Guangmao |last4=Li |first4=Zhen |last5=Fan |first5=Xuechun |year=2021 |title=Human population history at the crossroads of East and Southeast Asia since 11,000 years ago |journal=Cell |publisher=Elsevier BV |volume=184 |issue=14 |pages=3829–3841.e21 |doi=10.1016/j.cell.2021.05.018 |pmid=34171307 |doi-access=free}}</ref> However, the affinities between Jōmon and groups like Taiwanese aborigines and coastal Siberians is more likely due to their ancestors belonging to the same metapopulation that colonized Eastern Asia from south to north. That said, there is strong evidence of intermixing between Siberians and Ainu.<ref name=":24" />
 == In popular culture ==