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Jōmon people

From Wikipedia, the free encyclopedia
JōmonDogū pottery figure from the Late Jōmon Period, 1000–400 BC.
Prehistoric inhabitants in Japan

Diorama of Jōmon people at theSannai-Maruyama museum

TheJōmon (Japanese:縄文) were aprehistorichunter-gathererculture that inhabited theJapanese archipelago between approximately14,000 BC and 300 BC, following which they were largely assimilated by migrants from mainland East Asia of the followingYayoi culture. The Jōmon people lived as sedentary hunter-gatherers, practicing plant foraging, fishing and hunting and possibly limited farming, manufacturing stone tools andpottery, the distinctive markings on the latter giving the culture their name. Jōmon ancestry forms a minor amount of the ancestry of theYamato people (the dominant ethnic group in Japan), and a majority of the ancestry of the indigenousAinu people ofHokkaido, with the Ainu being the direct descendants of the Jōmon.

Etymology

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Jōmon (縄文,Jōmon), sometimes written asJomon (US:/ˈdʒoʊˌmɑːn/JOH-mahn,UK:/ˈdʒəʊmɒn/JOH-mon),[1] is a Japanese word directly translated as "cord-marked" or "cord pattern". The term was coined by Americanzoologist,archaeologist, andorientalistEdward S. Morse in his bookShell Mounds of Omori (1879), describing his excavation of theŌmori Shell Mound near Tokyo and subsequent discovery ofsherds ofcord-marked pottery at the site in 1877. Morse translated "straw-rope pattern" from English to Japanese asJōmon, which he would use to refer to the people living during this period ofJapanese 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 historianYamanouchi Sugao used the pottery-derived term to refer to thePaleolithic inhabitants of Japan.[5]

Jōmon is acompound word composed of twokanji: and, thepronunciation andsemantic value each being derived from their respectiveGo-on reading.

  • 縄 () – meaning "rope" or "cord", specifically "a flexible, heavy cord of tightly intertwinedhemp or otherfibers." This kanji derivesetymologically fromOld Japanese, from theProto-Japonicnapa, 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 asmoyō (模様) ormon'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 theJōmon period. These kanji appear in various related terms, creating alexical 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

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Early descriptions and depictions

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The study of the Jōmon people and their material culture has evolved significantly since theEdo period. One of the earliest recorded depictions of Jōmon artifacts dates back to Edo-periodantiquarians, who began to catalogue and produce sketches of unusual pottery fragments brought to them from shellmiddens. The eighteenth century traveler Sugae Masumi mentioned Jōmon-era remains in his writings, including his bookSumika 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 earlyMeiji 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, whenEdward S. Morse, an Americanzoologist andorientalist, excavated theŌmori Shell Mound near Tokyo. Morse coined the termJōmon (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

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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 andTorii Ryūzō conducted further investigations of shell middens, burial sites, and Jōmon settlements.NationalistKokugaku ("National Learning") scholars sought to frame Jōmon culture within Japan's historical narrative, often contrasting it with the agriculturalists of theYayoi period, whose lifestyle centered on rice cultivation was more clearlySinitic in influence.[12] During the 1920s–30s, Kojima Gizaemon andHamada Kōsaku led efforts to establish regionaltypologies of Jōmon pottery, classifying styles into chronological phases based onstratigraphy, the study of sediment layers and their effects on artifacts over time. Excavations at sites such as Kasori Shell Midden inChiba have shed light on Jōmon long-term settlement and subsistence patterns.[13]

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

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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 asSannai Maruyama (Aomori) in the 1990s, revealed that Jōmon groups lived in permanent or semi-permanent villages, contradicting earlier assumptions that they were exclusively nomadichunter-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 developmentsocial hierarchy, and the development of adivision of labor/advanced craft specialization (e.g., lacquerware, jade ornaments, figurines) despite their hunter-gather lifestyle.[16] By the new millennium, international collaboration also increased, with researchers drawing comparisons between the Jōmon and other prehistoric cultures, such as those Paleo- and Mesolithic cultures found in theAmerican Pacific Northwest andEurope.

21st-century developments

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

  • Chronological Refinements: Advances inradiocarbon dating (AMS C-14 dating) have refined the Jōmon timeline, pushing back the origins of pottery to 16,500 BCE at sites likeŌdai Yamamoto I inAomori.[17] This would corroborate the theory that Japan was among the earliest centers of pottery production in the world.
  • AncientDNA 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 toHolocene climate fluctuations by migrating between coastal and inland settlements as sea levels changed.[19]
  • Jōmon Ritual Symbolism: Research into ceremonial sites, such as theŌyu Stone Circles inAkita 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 acrossHokkaidō and northernHonshū were declaredUNESCO World Heritage sites, recognizing Jōmon culture as one of the world's longest-lasting hunter-gather traditions.[21]

Lifestyle

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

Settlements

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

Reconstruction of a Jōmon pit dwelling.

The Korekawa site, inHachinohe,Aomori Prefecture, is unique because it has three subsites, each from a different Jōmon timeframe:Ichioji Site (一王寺遺跡) (Early to Middle Jōmon period),Hotta Site (堀田遺跡) (Middle Jōmon period), andNakai Site (中居遺跡) (Final Jōmon period). They are near each other on a terrace by the Niida River. Ichioji is the largest of the three subsites, while Nakai is the smallest but has yielded the most artifacts.[26][27][28]

The excavation ofSannai 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, andstone 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 soakingJapanese horse chestnuts.

Reconstructed Jōmon pit dwelling interior at theŌgushi Site.

As mentioned, Jōmon people typically resided inpit dwellings, semi-subterranean buildings built by digging a shallow hole in the ground, constructing aroof extending upwards from each side, and placing ahearth 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 ofbark orthatch and may have been covered with soil to provide an extra layer ofinsulation.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[29] comparable to contemporaneous Meso- and Neolithicstructures found inEurope andthe Americas.

Tools

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Like other Paleolithic cultures, Jōmon sites display widespread evidence of the use and production ofstone tools. Jōmon tools were most commonly fashioned fromchipped stone, made ofsiliceous shale. However, tools made from other types of stone, wood, and rarer materials such asobsidian andjade have also been discovered in Jōmon-period sites.[30]

Early Jōmon-period stone tools excavated from the Oimatsuyama site, on display at theSaga Prefectural Museum.

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 usedbitumen as anadhesive to bind the stone point with its wooden shaft.

However, some stone implements appear to have been made without the normal chipping process. This includesground stoneaxes, made fromgranodiorite,greenstone, orblueschist, abrasion cutting stone tools,whetstones,grindstones with or without grooves,hammer stones,saddle querns, and stoneweights.

Bone tools from theZoku-Jōmon Period, on display at theHokkaido Museum.

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 toweave baskets.

Hunting

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The Jōmon people were incredibly skilled, likelyopportunistichunters capable oftracking, catching, and killing a wide variety of both large and smallgame endemic to their environment. These includedflying 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, andducks. Hunting techniques included the use ofprojectile weapons like bows and spears,pitfall traps, andhunting dogs.[29]

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 largelycarnivorous diet. However, in theSannai Maruyama site, flying squirrels and hares are the dominant sources of meat most likely as a result of environmental factors.

Fishing

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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 adeptfishermen and mariners. Some of the marine species found at Jōmon sites includeyellowtail amberjack,right-eyed flounder, various types ofsharks,mackerel,herring,flounder,scorpion fishes,globefish,greenling,Pacific sea bream, andPacific cod. The Jōmon also gatheredshellfish, includingJapanese oysters, Ezoabalones,clams,crabs,octopuses,squid,mantis shrimp, and other types of crustaceans.[29]

The Jōmon fished usingharpoons,spears,lines, andnets. 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 usingfish hooks fashioned fromantler or bone. Jōmonfish hooks generally fall into two categories: single-ended hooks and coupled/combined hooks. The main difference between the two was that coupled fish hooks were barbed while single-ended hooks were not. However, both types had notches to tie the line. Stone weights were attached to nets to act assinkers.

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 Jōmonwatercraft usedsails orpaddles as their primary means ofpropulsion.[31]

Plant foraging and domestication

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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 asfuel andbuilding material. Other types of flora regularly consumed by the Jōmon includewalnuts,Japanese horse chestnuts,adzuki beans,Udo,silver vines,elderberries,wild grapes,mulberries,raspberries, andyams.Roots,tubers such as yams, and other subterranean forage was dug up usingdigging sticks.[29] 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 plantdomestication.[32]

Food processing

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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 theSannai Maruyama Site, archaeologists discovered a reservoir, filled and emptied by a spring, that may have been used to process nuts through soaking.[29] The Jōmon might have also been able to distillalcohol using elderberries.

Cooking

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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.[29]

Trade networks

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The Jōmon maintained extensive trade networks that extended several hundred kilometers across the Japanese archipelago. Key trade items includedobsidian,gemstones such asjade,amber,asphalt, red pigments, and various types of stone materials used to produce polished stone axes includinggranodiorite,greenstone, andblueschist.[33] For example,Moroiso-style pottery, which is just south of Tokyo, in theKansai region, has been found as far south as the Satogi site inOkayama Prefecture and as far north as the Taigi andTashirojima sites inMiyagi Prefecture,[34][35] both about 500 kilometers (310 miles) from Moroiso.[36]

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, theSannai Maruyama site, a major trading hub, was particularly known for its jade artifacts. Its inhabitants also engaged in the exchange of finished obsidian tools raw obsidian sourced, in some cases, from as far away asHokkaido andNagano. These tools, made of high-quality obsidian, have been found over 700 kilometers from their origin points.

Evidence of trade between the Jōmon ofHokkaido andHonshu, as well as between those living on theKyushu andRyukyu Islands, would further suggest that the Jōmon were skilled navigators and seafarers capable of long-distance maritime travel.[29] According to a 2006 study, it is also possible that the Jōmon traded withsouthern Chinese andSoutheast Asians viaFujian.[37]

Culture

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See also:Jōmon period

Elements of Jōmon culture are believed to be preserved in various aspects of modern Japanese culture. These include early forms of spiritual beliefs that precededShinto, 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.[38]

Other examples of Jōmon influence in present Japanese culture, especially inKyūshū, include the worship ofAme-no-Uzume (アメノウズメ) inMiyazaki Prefecture,Ta no Kami-sa (田の神さぁ) in theAso region ofKumamoto Prefecture, and theMishaguji (ミシャグジ) belief system.[39][40][41]

Pottery

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kaen-style pottery (火焔型土器)
Main article:Jōmon 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 thekaen-style pottery (火焔型土器, kaen-gata doki) from the Middle Jōmon period, noted for its elaborate patterns and dynamic forms.[42]

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.[43]

Lacquerware

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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.[29]

Clothing

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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 needles of bone and antler.[29]

Jewelry and accessories

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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.[44]

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.[45]

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.[44]

Magatama

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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.[46]

Magatama continued to be widely used not only during the Jōmon period but also throughout theYayoi andKofun 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, theYasakani no Magatama (八尺瓊勾玉), is considered a symbol of the Japanese monarchy.[47]

These artifacts were most commonly made fromjade (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.[46]

Religion

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Main article:Ko-Shintō

It is suggested that the religion of the Jōmon people was similar to earlyShinto, specificallyKo-Shintō. It was largely based onanimism, and possiblyshamanism. Other similar religions are theRyukyuan andAinu religions.[48] Certain strange stone implements in various shapes are thought to have been used astalisman.[29]

Rituals and festivals

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Accessories and jewelry are thought to have been worn more during special occasions such as festivals, burials, and rituals than in everyday life.[29]

Central ritual sites outside settlements and belonging to multiple villages have started to appear during the LateJōmon 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 clayfigurines 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 areearthenware 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 inceremonial 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.[29] The Jōmon also crafted stone batons or rods and swords[43] 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.

InSannai 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.[29]

Burials

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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.

InSannai 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.[29]

Languages

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It is not known what language or languages were spoken in Japan during the Jōmon period. Suggested languages are: theAinu language,Japonic languages,Austronesian languages, or unknown and todayextinct languages.[49][50] 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 theJapanese archipelago.[51]

Alexander Vovin (1993) argues that theAinu languages originated in centralHonshu, and were later pushed northwards intoHokkaido, where the early Ainu-speakers merged with local groups, forming the historical Ainu ethnicity. Bilingualism between Ainu and Japanese was common inTohoku until the 10th century.[52][53] According to Vovin (2021) there is also some evidence for the presence ofAustronesian languages close to the Japanese archipelago, which may have contributed some loanwords to early Japanese.[53]

Somelinguists suggest that the Japonic languages may have been already present within the Japanese archipelago and coastal Korea, before theYayoi 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.[54]

Origins

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See also:Genetic history of East Asians § Diversification and substructure,Genetic history of East Asians § Jōmon people, andGenetic and anthropometric studies on Japanese people

The Jōmon people represent the descendants of thePaleolithic 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".[55][56][57][58]

Genetics

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Phylogenetic position of the Jōmon lineage among otherEast 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 AsianTianyuan andHoabinhian lineages, but before Ancient East Asians split intoAncient Northern East Asians andAncient Southern East Asians.[59][60][56][61] Like other East Asian populations, the ancestors of the Jōmon people are suggested to have originated from Southeast Asia and expanded northwards to East Asia via both an interior and a coastal route. They represent one of the "earliest waves of migration".[56][62][63][64] Although the Jōmon lineage can be modeled as a mixture of "basal Asian" (Hoabinhian/Onge-related) ancestries and derived East Asian-related ancestries, especially those related to Ancient Southern East Asians[65][18][66][67][56][68][69][70] or ancient populations from northern coastal China,[71][72] who contributed to East Asian ancestry of East Asians,East Siberians andNative Americans after the Last Glacial Maximum, other studies argue for an unadmixed lineage which split after those "basal Asian" lineages diverged from present-day East Asians. Subsequent studies found that Hoabinhians are an unlikely source for deeper ancestry in the Jōmon. Instead, a yet unidentified deep East Asian source is suggested.[73][56][68][70]

Overall, Jōmon ancestry consistently forms a clade with Ancient Northern and Southern East Asians. They diverged from Ancient East Asians around the same time as theLonglin specimen from Guangxi, China although other studies show an earlier divergence date for the latter. The Jōmon likewise diverged from Ancient East Asians much later than the Xingyi_EN lineage from Yunnan, China. According to Wang et al. (2025), the ancestors of Ancient East Asians were a mixture of Tianyuan-related and Xingyi_EN-related lineages.[74][56][69] The Jōmon also exhibit a high degree of genetic homogeneity,[73][75][76][77] which is attributed to "strong bottleneck and small effective population size".[75]

Beyond theirgenetic affinities with other East Eurasian lineages, the Jōmon display weak but marginally relevant genetic affinity with theYana Rhinoceros Horn Site specimen, associated withAncient North Eurasians (or Ancient North Siberians). This indicatesgene flow between Ancient North Siberians and the ancestral Jōmon prior to the Jōmon's isolation from other East Eurasians. This gene flow is also associated with the introduction ofmicroblade technology to Northern Japan.[73][78] According to Bennett et al. (2024), the Basal Asian-like ancestors of the Jōmon may have interacted with groups that entered Siberia through a northern migration route, thus explaining the observed affinities between the Jōmon and Ancient North Siberians.[68] Other studies found no evidence for direct ANE-related gene flow into the Jōmon. However, the possibility of small non-East Eurasian input is not completely ruled out.[79][80][81][82][78][83]

According to Yang et al. (2025), the Jōmon have the lowest amount ofDenisovan ancestry among East Asians, suggesting partial descent from an East Asian lineage with no or low Denisovan ancestry. Neither Hoabinhian nor West Eurasian admixture can explain the low Denisovan ancestry in the Jōmon, as Hoabinhians carry higher amounts of Denisovan ancestry than the Jōmon do (around the same amounts as present-day East Asians), and no West Eurasian admixture is detected among the Jōmon.[70]

There is also evidence of genetic affinities between the Jōmon and lowland coastal East Asians.[84][85][86][87] These affinities imply later contact episodes between the Jōmon and other East Eurasian populations[37][84][86][88][89][87][70][90] but the direction of gene flow is unclear.[91][70] Alternatively, they reflect shared ancestry.[91][92][70] Other studies show little to no gene flow from continental Asians (e.g. Austronesians) into the Jōmon,[93][77] including Ryukyuan Jōmon.[94][95][96][97] Overall, the Jōmon are not closely related to most Asian populations besides modern Japanese andUlchi.[98]

Jōmon and Continental Asian contributions to modern Japanese

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 theEDAR 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 developingliver spots as a result of excessive sun exposure.[62][99][100]

Genetic data further indicates that the Jōmon peoples were genetically predisposed for higher triglyceride andblood 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.[62] 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 theBody 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.[101]

Haplogroups

[edit]

It is thought that the haplogroupsD-M55 (D1a2a) andC1a1 were frequent among the historical Jōmon period people of Japan. One 3,800-year-old Jōmon man excavated fromRebun Island was found to belong to Haplogroup D1a2b1(D-CTS 220).[102] Today, haplogroup D-M55 is found in about 35%[103] and haplogroup C1a1 in about 6% of modernJapanese people. D-M55 is found regularly only in Japanese (Ainu,Ryukyuans, andYamato) and Koreans (albeit with much lower frequency).[104] D-M55 also has been observed inMicronesia 5.1%,Timor 0.2%, China 0–0.4%, this is explained by recent admixture, dating back to theJapanese empire (1868–1945) occupation of those regions.[104] 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 inNing'an andHan Chinese inLinghai,Guancheng Hui District,Haigang District, andDinghai District).[105] A 2021 study estimated that the frequency of the D-M55 clade increased during the late Jōmon period.[106] The divergence between the D1a2-M55 and the D1a-F6251 subclades (the latter of which is common inTibetans, otherTibeto-Burmese groups, andAltaians, and has a moderate distribution in the rest of East Asia, Southeast Asia, and Central Asia) may have occurred near theTibetan Plateau.[103] A 2024 study suggests that the Jōmon, highland Tibetans and Andamanese Onge share similar Paleolithic ancestral components due to the high frequencies of haplogroup D in these groups.

TheMtDNA haplogroup diversity of the Jōmon people is characterized by the presence of haplogroups M7a and N9b.[107][108][109] 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.[110][111]N9b is frequently found among the Hokkaido Jōmon whileM7a is found frequently among the Honshu Jōmon.[112] However N9b is found only at very low percentage among the Honshu Jōmon.[112] 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".[113] Haplogroup M7a now has its highest frequency inOkinawa.[114]

Using theFossa 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.[113] 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.[115] According to a 2025 study, haplogroup M7 diverged into M7a and M7b'c, which further split into M7b and M7c, with the latter two being common in Southern East Asia.[116]

Morphological characteristics

[edit]
Male skull of the late Jōmon period (replica). Excavated at Miyano Kaizuka (Iwate Prefecture). Exhibition in National Museum of Nature and Science.[117]

Although there is regional variance among different Jōmon remains, they displayed an overall coherent morphology. Historically, the Jōmon people were classified as "South Mongoloid" or "Proto-Mongoloid"; displaying specific affinities with Native Americans and to an extent,Negrito samples.[118][119][120][121]

They broadly resemble groups such as "[...] Southeast Asians, Upper Paleolithic Asians, or Northeastern Asians, as well as present-day indigenous populations of the Ainu of Hokkaido and Ryukyu Islanders", as well asCro-Magnon populations.[68][122] Certain Jōmon features indicate long-term adaptation to a hunter-gatherer lifestyle[123][124] and to an extent, colder climates.[125][126][127] Close morphological similarities also exist between the Jōmon people and the ~33,000 to 23,000 years oldLiujiang man fromGuangxi, China and theMinatogawa Man fromOkinawa.[128][129]

The Jōmon additionally display affinities with putativeAustralo-Papuan groups, specifically prehistoric populations from Southern East Asia, such as the Hoabinhian hunter-gatherers, and Northern China, such as the Upper PaleolithicZhoukoudian remains. They possessed traits such as 'dolichocephalic calvaria, large zygomatic bones, remarkably prominent glabellae and superciliary arches, concave nasal roots, and low and wide faces',[130][131][132] yet were genetically closer or ancestral to later East Asians despite phenotypic discontinuities. These Paleolithic variations were lost in modern Eastern Asian populations due to long-term demographic replacement.[133][134][135]

Forensic reconstruction from a Jōmon skull, displayed at Niigata Prefectural Museum of History

Dental morphology suggests that the Jōmon hadSundadont dental structure, which is more common among modern Southeast Asians and indigenous Taiwanese. Sundadonty 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.[136]

Chatters, citing anthropologist C. Loring Brace, classified Jōmon and Polynesians as a single craniofacial "Jōmon -Pacific" cluster.[137] Chatters, citing Powell, noted 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".[138][139]

Kondo et al. analyzed the regional morphological andcraniometric 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 thecranial 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 environmental effects.[140]

According to a 2023 study, there were no significant differences in craniofacial or facial shapes within the Jōmon. However, Southern and Western Jōmon often have more globular neurocraniums when viewed in the sagittal plane compared to Northeastern Honshu Jōmon, who often have high and large frontal regions, along with low, more compressed and angled occipital regions. This reflects a shift towards agricultural lifestyles among Southern and Western Jōmon whilst older forager lifestyles were upheld by Northeastern Honshu Jōmon. Jōmon from Southern and Western Japan and inland central Honshu also differ from Jōmon from coastal central Honshu, Northeastern Honshu and Hokkaido in terms of their temporalis muscle region, reflecting differential influences of plant-based and marine-based diets respectively. The former Jōmon group are described as having "an anteroposteriorly shorter, superoinferiorly taller temporalis region with a mediolaterally narrower temporal fossa".[141] A 2025 study shows no significant inter-phase or geographical differences among different Jōmon specimens. However, variations within phases and geographical regions are more salient.[142]

Craniofacial features of the Jōmon people were significantly retained by the Ainu and Okinawans/Ryukyuans.[143] The Ainu have 2 genes "associated with facial structure in Europeans" but still possessed hair and teeth morphology found in East Asians.[144] In regards to facial flatness, the Ainu were intermediate betweenCaucasoids andMongoloids[145] but another study states that they were well within the Mongoloid range.[146] Ainu also exhibit strong influence from Northeast Asian populations.[147][96] Meanwhile, Okinawans/Ryukyuans have a "well-defined and less flat upper face", which is characterized by a prominentglabella andnasal root.[143] Among contemporary Japanese subpopulations, Southern Japanese exhibit strong similarities with Jōmon and Ainu groups, as well as Yayoi groups, and are relatively less impacted by Northeast Asian groups.[96] Other Japanese subpopulations show intermediate affinities with the Jōmon, especially the Hokkaido Ainu, except for Kinki populations, who show the most morphological disparities. Morphological affinities with the Hokkaido Ainu are moderately strong for contemporary Tohoku populations.[148]

ATL retrovirus

[edit]

A gene common in Jōmon people is a retrovirus ofATL (human T lymphotropic virus, HTVL-I). This virus was discovered as a cause ofadult T cell leukemia (ATL), and research was advanced by Yorio Hinuma ofKyoto University Virus Research Institute.[149]

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 manyAfricans,Native Americans,Tibetans,Siberians, Burmese people,Indigenous people of New Guinea, Polynesians, etc. Looking at distribution in Japan, it is seen particularly frequently in southernKyushu,Nagasaki Prefecture,Okinawa and among theAinu. And it is seen at medium frequency in the southern part ofShikoku, southern part of theKii Peninsula, the Pacific side of theTōhoku region (Sanriku) andOki 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.[150][149]

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).[151]

Based on the above, Hinuma concluded that the high frequency area of this virus indicates that high density remains of Jōmon people.[150]

Contributions to other populations

[edit]

Historical groups

[edit]

Full genome analyses ofOkhotsk culture remains onSakhalin show their descent from three major ancestral sources, notablyAncient 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.[152] Jōmon ancestry is detected in other Far East Siberian individuals such as the 7,000-year-old Letuchaya Mysh individual and an outlier from the Middle Neolithic Boisman population (c. 29.7% ± 9.8%).[153]

Genetic analyses on ancient remains from the southernKorean Peninsula during theThree Kingdoms period reveal elevated Jōmon ancestry at c. 37%, whileYayoi remains in Japan were found to carry nearly equal amounts of Jōmon ancestry (35–60%) andAncient Northeast Asian-like ancestry (40–65%). These results suggest the presence of the Jōmon people and their culture or a Jōmon-like population on the Korean peninsula and their significant contribution to the formation of earlyJaponic-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 NeolithicWest Liao River farmers from northeast China.[73][154]

The Yokchido individual from ancient Korea is estimated to have 95–100% Jōmon-related ancestry[76][155][156] and shows the closest genetic affinities with the Late Jōmon individual from Shikoku.[157] Several ancient Northeast Asian individuals from inland East Asia (Yumin) and theDevil's Gate Cave (NEO240) can also be modeled as mixtures of deep lineages that are ancestral to the Jōmon and Tianyuan respectively, despite NEO240 being more related to the Jōmon.[70]

Modern groups

[edit]
The Ainu are among the modern groups displaying the highest amounts of Jōmon-derived ancestry.

TheAinu have the highest proportion of Jōmon ancestry among modern populations, estimated at up to 70%, followed by theRyukyuan/Okinawan people at around 30%, and mainland Japanese at approximately 10–20%. Overall, Jōmon ancestry peaks in the northernmost and southernmost parts of Japan (Hokkaido and Okinawa, respectively), followed byTohoku andKanto. Residents ofTōhoku,Kantō, andKyūshū show closer genetic affinities withRyukyuans. Genetic relatedness between the Ainu and mainland Japanese is particularly strong in westernHokkaidō andAomori. It is also believed that mainland Japanese primarily derive their Jōmon ancestry from western Jōmon populations. Conversely, Jōmon ancestry is the lowest inKinki andShikoku, where Yayoi ancestry is more dominant.[148][158][159][160] Yamamoto et al. 2024 found a wide range of Jōmon ancestry within different Japanese subgroups, ranging from 10–32%.[101] According to a 2025 study, mainland Japanese derive ~20% of their ancestry from Jōmon peoples and are especially close to Early and Middle Jōmon specimens from Kumamoto and Tokyo respectively.[77]

In modern Koreans, Jōmon ancestry is present at about 5%.[161] Jōmon-related ancestry is also present in several Siberian (particularly in theUlchi at 7% andNivkh at 10%) and Southeast Asian groups.[162][93][70][163]

In popular culture

[edit]

Aspects of the Jōmon culture and pottery were used in the video gameThe Legend of Zelda: Breath of the Wild. The art director of Nintendo Takizawa Satoru said that the Jōmon culture was the inspiration for the "Sheikah Slates, shrines and other ancient objects" in the game.[164]

A recreated Jōmon village in the form of an experience park (Sarashina no Sato), which offers different activities, can be visited inChikuma, Nagano.[165]

See also

[edit]

References

[edit]
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  58. ^Cooke, Niall P.; Murray, Madeleine; Cassidy, Lara M.; et al. (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.
  59. ^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.
  60. ^Cooke, Niall P.; Mattiangeli, Valeria; Cassidy, Lara M.; et al. (17 September 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.
  61. ^Kim, Jonghyun; Mizuno, Fuzuki; Matsushita, Takayuki; et al. (2024)."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.
  62. ^abcWatanabe, 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.
  63. ^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) 20231262.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.
  64. ^Yamamoto, Kenichi; Namba, Shinichi; Sonehara, Kyuto; et al. (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.
  65. ^McColl, Hugh; Racimo, Fernando; Vinner, Lasse; et al. (6 July 2018). "The prehistoric peopling of Southeast Asia".Science.361 (6397):88–92.Bibcode:2018Sci...361...88M.doi:10.1126/science.aat3628.hdl:10072/383365.PMID 29976827.
  66. ^Huang, Xiufeng; Xia, Zi-Yang; Bin, Xiaoyun; et al. (2020). "Genomic Insights into the Demographic History of Southern Chinese".bioRxiv 10.1101/2020.11.08.373225.
  67. ^Wang, Chuan-Chao; Yeh, Hui-Yuan; Popov, Alexander N.; et al. (18 March 2021)."Genomic insights into the formation of human populations in East Asia".Nature.591 (7850):413–419.Bibcode:2021Natur.591..413W.doi:10.1038/s41586-021-03336-2.PMC 7993749.PMID 33618348.
  68. ^abcdBennett, 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]
  69. ^abWang, Tianyi; Yang, Melinda A.; Zhu, Zhonghua; et al. (29 May 2025)."Prehistoric genomes from Yunnan reveal ancestry related to Tibetans and Austroasiatic speakers".Science.388 (6750) eadq9792.Bibcode:2025Sci...388q9792W.doi:10.1126/science.adq9792.PMID 40440384.The 8,800-year-old individual (91) Jomon8.8k and 2,800-year-old Ikawazu individual from the Jōmon period of Japan possesses a deeply diverged East Asian ancestry defined as Jōmon ancestry(10). Unlike Longlin, the ancient individuals from Japan and ancient northern and southern East Asians consistently form a clade with each other relative to Xingyi_EN, i.e. f4(Mbuti, nEA/sEA, 28Xingyi_EN, Jomon8.8k/Ikawazu)>0 (2.7<Z<11.3), f4(Mbuti, Jomon8.8k/Ikawazu, Xingyi_EN, nEA/sEA)>0 (5.5<Z<12.8), and f4(Mbuti, Xingyi_EN, Jomon8.8k/Ikawazu, nEA/sEA)~0 (0<Z<3.3, Data S2c). These results show that Xingyi_EN diverged prior to the separation of Jōmon and East Asian ancestries, consistent with our finding that Xingyi_EN has a deeply diverged Basal Asian ancestry as old as that found in groups carrying Tianyuan and Hòabìnhian ancestries.
  70. ^abcdefghYang, Jiaqi; Iasi, Leonardo N.M.; Fu, Qiaomei; et al. (October 2025). "An early East Asian lineage with unexpectedly low Denisovan ancestry".Current Biology.35 (20): 4898–4908.e4.doi:10.1016/j.cub.2025.08.051.PMID 41118724.
  71. ^He, Guanglin; Wang, Mengge; Zou, Xing; et al. (2021)."Peopling History of the Tibetan Plateau and Multiple Waves of Admixture of Tibetans Inferred From Both Ancient and Modern Genome-Wide Data".Frontiers in Genetics.12 725243.doi:10.3389/fgene.2021.725243.PMC 8506211.PMID 34650596.
  72. ^Li, Yu-Chun; Gao, Zong-Liang; Liu, Kai-Jun; et al. (May 2023). "Mitogenome evidence shows two radiation events and dispersals of matrilineal ancestry from northern coastal China to the Americas and Japan".Cell Reports.42 (5) 112413.doi:10.1016/j.celrep.2023.112413.PMID 37164007.
  73. ^abcdCooke, Niall P.; Mattiangeli, Valeria; Cassidy, Lara M.; et al. (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).
  74. ^Wang, Tianyi; Wang, Wei; Xie, Guangmao; et al. (July 2021)."Human population history at the crossroads of East and Southeast Asia since 11,000 years ago".Cell.184 (14): 3829–3841.e21.Bibcode:2021Cell..184.3829W.doi:10.1016/j.cell.2021.05.018.PMID 34171307.
  75. ^abCooke, Niall P.; Murray, Madeleine; Cassidy, Lara M.; et al. (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.
  76. ^abIshiya, 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".bioRxiv 10.1101/2024.08.09.606917.
  77. ^abcKato, Masahiko; Mizuno, Fuzuki; Taniguchi, Yasuhiro; et al. (2025). "High-Coverage Jomon Genomes Provide Insights into Population Structure and Genetic Traits of Ancient Japanese Hunter-Gatherers".bioRxiv 10.64898/2025.12.14.694187.
  78. ^abOsada, 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.
  79. ^Kanzawa-Kiriyama, Hideaki; Kryukov, Kirill; Jinam, Timothy A; et al. (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.We also examined whether the uniqueness of the Sanganji Jomon in East Eurasia was the result of gene flow from non-East Eurasians, but the evidence for this was not suggested. This indicates that the ancestor of the Sanganji Jomon had been genetically isolated from continental populations after their divergence. However, our results do not deny a possibility of small fraction of gene flow between the Jomon people and the non-East Eurasians, which might not be detected in the current study because of the small amount of the determined Jomon genome sequences.
  80. ^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.doi:10.1537/ase.190415.Next, we assessed the possibility of gene flow between non-East Asians and the ancestor of Funadomari Jomons to explain the deep divergence. f4 (African, non-East Asian; East Asian, F23) showed that no modern populations, except for Sardinian, Relli, and Aboriginal Australian, who had small positive f4 values (but without statistical significance), supported the gene flow. The 24000 year old MA1 also did not support the gene flow.
  81. ^de Boer, Elisabeth; Yang, Melinda A.; Kawagoe, Aileen; et al. (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.
  82. ^Gakuhari, Takashi; Nakagome, Shigeki; Rasmussen, Simon; et al. (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.
  83. ^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 date, the conclusion remains unchanged. However, not all Jomon genome sequences analyzed so far have undergone the type of southern versus northern route-focused analysis presented in Gakuhari et al. (2020). Conducting further analysis on this issue remains a task for the future.
  84. ^abJeong, Choongwon; Nakagome, Shikegi; Di Rienzo, Anna (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.
  85. ^Kanzawa-Kiriyama, Hideaki; Kryukov, Kirill; Jinam, Timothy A; et al. (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.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.
  86. ^abYang, Melinda A.; Fan, Xuechun; Sun, Bo; et al. (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.
  87. ^abBennett, 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.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.
  88. ^de Boer, Elisabeth; Yang, Melinda A.; Kawagoe, Aileen; et al. (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.
  89. ^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 10.1101/2021.06.19.449013.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.
  90. ^Sato, Takehiro; Kubo, Daisuke; Hirasawa, Yu; et al. (2025)."Genome of an early Okhotsk individual reveals ancient admixture between Jomon and Kamchatka lineages".Scientific Reports.15 (37520): 37520.Bibcode:2025NatSR..1537520S.doi:10.1038/s41598-025-21522-4.PMC 12559309.PMID 41145628.
  91. ^abGakuhari, 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): 437.doi:10.1038/s42003-020-01162-2.PMC 7447786.PMID 32843717.
  92. ^Wang, Chuan-Chao; Yeh, Hui-Yuan; Popov, Alexander N.; et al. (2020). "The Genomic Formation of Human Populations in East Asia".bioRxiv 10.1101/2020.03.25.004606.The Taiwan Hanben are well modelled as deriving about 14% of their ancestry from a lineage remotely related to Onge and the rest of their ancestry from a lineage that also contributed to Jomon and Boisman on the Tianyuan side, a scenario that would explain the observed affinity among Jomon, Boisman and Taiwan Hanben.
  93. ^abGakuhari, Takashi; Nakagome, Shigeki; Rasmussen, Simon; et al. (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.Our admixture graph in Fig.S10 supports a model whereby the Ami originated from the admixture between the Jomon and the other lineage who had both Shamanka- and Chokhopani-related ancestries, with a relatively low fitting score (Z=2.9). This fitting was improved if we assumed no admixture in this second source population (Z=2.5 in Supplementary Figure 13), which implies very little impact of the Austronesian migration on the genetic makeup of Jomon.
  94. ^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.Bibcode:2010AJPA..142..211M.doi:10.1002/ajpa.21212.PMID 20091849.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.
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  99. ^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.doi:10.1537/ase.190415.
  100. ^Gakuhari, Takashi; Nakagome, Shigeki; Rasmussen, Simon; et al. (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).
  101. ^abYamamoto, Kenichi; Namba, Shinichi; Sonehara, Kyuto; et al. (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.ISSN 2041-1723.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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  135. ^Matsumura, Hirofumi; Xie, Guangmao; Nguyen, Lan Cuong; et al. (2021)."Female craniometrics support the 'two-layer model' of human dispersal in Eastern Eurasia".Scientific Reports.11 (20830): 20830.Bibcode:2021NatSR..1120830M.doi:10.1038/s41598-021-00295-6.PMC 8531373.PMID 34675295.
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  153. ^Wang, Ke; Yu, He; Radzevičiūtė, Rita; et al. (February 2023). "Middle Holocene Siberian genomes reveal highly connected gene pools throughout North Asia".Current Biology.33 (3): 423–433.e5.Bibcode:2023CBio...33E.423W.doi:10.1016/j.cub.2022.11.062.PMID 36638796.
  154. ^Wang, Rui; Wang, Chuan-Chao (August 2022)."Human genetics: The dual origin of Three Kingdoms period Koreans".Current Biology.32 (15):R844–R847.Bibcode:2022CBio...32.R844W.doi:10.1016/j.cub.2022.06.044.PMID 35944486.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.
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