Physics.org, Oct 5, 2016

Ancient Japan may have been far more cosmopolitan than previously thought, archaeologists said Wednesday, pointing to fresh evidence of a Persian official working in the former capital Nara more than 1,000 years ago.
Present-day Iran and Japan were known to have had direct trade links since at least the 7th century, but new testing on a piece of wood—first discovered in the 1960s—suggest broader ties, the researchers said.
Infrared imaging revealed previously unreadable characters on the wood—a standard writing surface in Japan before paper—that named a Persian official living in the country.
The official worked at an academy where government officials were trained, said Akihiro Watanabe, a researcher at the Nara National Research Institute for Cultural Properties.
The official may have been teaching mathematics, Watanabe added, pointing to ancient Iran’s expertise in the subject.
“Although earlier studies have suggested there were exchanges with Persia as early as the 7th century, this is the first time a person as far away as Persia was known to have worked in Japan (during the period),” he said.
“And this suggests Nara was a cosmopolitan city where foreigners were treated equally.”
Nara was the capital of Japan from around 710 AD to around 784 AD before it was moved to Kyoto and later present-day Tokyo. …
Read more at: http://phys.org/news/2016-10-ancient-japan-cosmopolitan-thought_1.html#bjCp

The oldest Hoabinhian site has recently been discovered in Yunnan, China. What implications does this have for the peopling of East Asia?

It has been loosely pointed out that Hoabinhian artefacts have been found in Japan (roughly corresponding to the Jomon), source: Uncovering Southeast Asia’s Past (see Chapter 33) Sandra Bowdler’s map of distribution of H. artefacts in Asia refers.

Wilhelm G. Solheim in his Archaeology and Culture in Southeast Asia: Unraveling the Nusantao cites as evidence the observations of Gerard J. Groot and P. van Stein Callenfels which find early Jomon axes (especially the finds of Kozanji shell mound) to correspond perfectly to Bacsonian axes, including polished stone tools. ‘It is now considered that the “Hoabinhian and Bacsonian are two parallel developments of the same culture”.’

Read the new May 2016 paper detailing the latest find of the earliest Hoanbinhian artifacts in Yunnan (below.)

Xueping Ji, The oldest Hoabinhian technocomplex in Asia (43.5 ka) at Xiaodong rockshelter, Yunnan Province, southwest China Quaternary International, Vol 200 2 May 2016, Pages 166–174  http://dx.doi.org/10.1016/j.quaint.2015.09.080

Abstract

The Hoabinhian is the most representative technocomplex in Southeast Asian prehistory for the later hunter–gatherer period. As a mainland technology based exclusively on seasonal tropical environments, this core-tool culture was previously defined in northern Vietnam in 1932 and characterized originally by its large, flat and long, largely unifacial cobble tools associated with tropical forest fauna. The recent discoveries and dates obtained at Xiaodong rockshelter in Yunnan Province (southwest China) allow us to discuss the origin and the homeland of this singular Asian technocomplex which spread to Southeast Asia during the end of the Late Upper Pleistocene. Here we present the first Chinese Hoabinhian lithic implements in their stratigraphic and chronological context within a rockshelter site, and we address the question of the dispersal of modern humans from South China to Southeast Asia

There are theories that Hoabinhian tool makers were mtDNA R9 or basal mtDNA N descendants (source). Nothing is really conclusive unless ancient DNA can be found confirming the identity of the Hoabinhian tool makers.

About.com characterizes the Hoabinhian culture as follows:

The Hoabinhian Period is the name given to that part of Southeast Asian prehistory from about 13,000 to 3000 BC. Archaeological evidence at sites such as Spirit Cave (Thailand) and Cai Beo(Vietnam) reveal that people lived in caves, at open air sites, or along coastal locations as hunter-gatherers and fishers. Coastal Hoabinhian sites often have large shell middens. Animal bones recovered from Hoabinhian sites include primarily wild pigs and deer. Plant remains from Spirit Cave have included almond, bamboo, and gourd. No evidence for domesticated millet or rice has been found at Hoabinhian sites to date.

Hoabinhian stone tools were made from pebbles, and include ground stone axes, grindstones and a dominant stone flake industry. Bone points and spatulas carved from animal bone are also known. In the later Hoabinhian period (argued to be about 5000 BC) sites are also found with potsherds, impressed with vines, mats, or cords.

Hoabinhian burials are generally flexed or contracted; they are often covered with hematite, a common trait of hunter-gatherers just about everywhere.

In Ancient Southeast Asia, John Norman Miksic and Goh Geok Yian write

The oldest Hoabinhian artifacts have been dated to the Pleistocene well before the domestication of plants and animals, or horticulture, is believed to have emerged: at Tham Lod (dates 32,400 – 12.100 BP uncalibrated) and Tham Khuong in Vietnam (20,000-28,000 BP, uncalibrated) 

Hoabinhian Archaeological Sites

Tögi Ndrawa (Sumatra), Spirit Cave and Banyan Valley Cave(Thailand), Cai Beo (Vietnam), Tam Hang (Laos.

….

Archaeologists discover oldest Hoabinhian site ever in China

by Matt Atherton, Dec 30, 2015

The oldest site of south-east Asian hunter-gatherer culture has been discovered in China. The site, dating back nearly 44,000 years ago, was found in the Yunnan Province at Xiaodong Rockshelter, south-west China, and is the oldest evidence of ‘Hoabinhian culture’ ever discovered.

Hoabinhian culture describes the life of hunter-gatherers in south-east Asia, and was originally believed to be a time period stretching back as far as 29,000 years ago. The new discovery, made by scientists all over the world including China, South Africa and France, suggests that the Hoabinhian age may have begun a lot earlier than thought.

“Xiaodong can be regarded as a typical early Hoabinhian site, the first such site found in China and currently the oldest in Asia as well,” said Ji Xueping, lead author of the study. “The study shows that the Lancang River valley is a possible home for the Hoabinhian culture, and a source of migration for modern humans and the transmission of their culture to south-east Asia.”

Archaeologists researching Hoabinhian sites look for areas with large axe-like tools, used for woodwork in forested areas. Some of these stone artefacts were first collected at the Xiaodong site in 2004.

Since then, further research has been carried out to try and confirm the scientific value of the site. This research was then verified and published in December 2015, in Quaternary International.

Carbon dating was used to verify the date from which the site was occupied. Four metres of vertical soil layer was dated – showing the site was inhabited between 43,500 to 24,000 years ago. The scientists speculated that the very bottom layer may be even older.

The discovery provides further insight into how hominids survived a long time ago. It shows some of their strategies for survival, as well as how – and when – they changed from sporadic settlements to agricultural communities.

Hoabinhian culture was first discovered in Vietnam nearly 100 years ago. Since then, more site discoveries in south-east Asia have been dated back between 29,000 and 5,000 years ago. This is the first of these sites to be found in China. … Read more at IB Times

…

For a discussion of what DNA might have constituted the oldest arrivals in Southeast Asia, including the Hoabinhian culture, see Hill, Catherine, Phylogeography and Ethnogenesis of Aboriginal Southeast Asians Mol Biol Evol (2006) 23 (12):2480-2491.doi: 10.1093/molbev/msl124:

Abstract

Studying the genetic history of the Orang Asli of Peninsular Malaysia can provide crucial clues to the peopling of Southeast Asia as a whole. We have analyzed mitochondrial DNA (mtDNAs) control-region and coding-region markers in 447 mtDNAs from the region, including 260 Orang Asli, representative of each of the traditional groupings, the Semang, the Senoi, and the Aboriginal Malays, allowing us to test hypotheses about their origins. All of the Orang Asli groups have undergone high levels of genetic drift, but phylogeographic traces nevertheless remain of the ancestry of their maternal lineages. The Semang have a deep ancestry within the Malay Peninsula, dating to the initial settlement from Africa >50,000 years ago. The Senoi appear to be a composite group, with approximately half of the maternal lineages tracing back to the ancestors of the Semang and about half to Indochina. This is in agreement with the suggestion that they represent the descendants of early Austroasiatic speaking agriculturalists, who brought both their language and their technology to the southern part of the peninsula ∼4,000 years ago and coalesced with the indigenous population. The Aboriginal Malays are more diverse, and although they show some connections with island Southeast Asia, as expected, they also harbor haplogroups that are either novel or rare elsewhere. Contrary to expectations, complete mtDNA genome sequences from one of these, R9b, suggest an ancestry in Indochina around the time of the Last Glacial Maximum, followed by an early-Holocene dispersal through the Malay Peninsula into island Southeast Asia.

mtDNA haplogroups M21 and R21 were suggested as ancentral in the Semang and Senoi, F1a1a a Holocene component from Indochina.

R9b and perhaps N9a are found in high frequency only in Aboriginal Malays … suggest a Pleistocene origin to the north in indochina, wiht an early Holocene dispersal southwards through the Malay Peninsula and into island Southeast Asia.  echoes … the suggestion of Van Heekeren (1072) that the Hoabinhian had originated in South China before spreading to Malaya and North Sumatra.

[What of Austronesian  expansion in the archipelago?]

… on the other hand, haplogroups N21, N22 and M7c1c suggest an equally large offshore component, dating ot the mid/late Holocene, in the ancestry of Aboriginal Malays.

Perhaps the most striking signal is the presence of F1a1a, which aside from the apparently indigenous R21 is the most common haplogroup in the Senoi[R21 diverged from the common haplogroup R ancestor ~60,000 years ago (Macaulay et al. 2005), although the putative control-region link with haplogroup R9 (at np 16304) may imply a younger common ancestor], carried by almost half of the individuals sampled. This haplogroup, which is of early to mid-Holocene age, has b een observed elsewhere at high frequences only in Indochina and probably dispersed there from South China (where it is less frequent but more diverse and where its 1-step ancestor is found) during the Holocene). This suggests that almost half of the maternal lineages of the Senoi may trace back to an origin in Indochina at some point within the last 7,000 years or so.

…

Gorman, Chester. 1969. Hoabinhian: A Pebble-Tool Complex with Early Plant Associations in Southeast Asia. Science 163(3868):671-673.

Harvick, Ben. 2006. A Methodological Study of Technological Attributes in Hoabinhian Lithic Assemblages. In Social, Cultural and Environmental Dynamics in the Highlands of Pangmapha, Mae Hong Son Province: Integrated Archaeological Research into the Region Rasmi Shoocongdej, ed. Australian National University.

Hoabinhian, Jomon, Yayoi: Early Korean States (Oxbow Monograph) by Gina Lee Barnes

“Mineral Food in the late Palaeolithic Hoabinhian Culture of Vietnam and Geophagia in Today Vietnam”, which was presented in the Symposium for Salt Production held in Tokyo Nov 2009, as a part of the paper “Further Studies on Hoabinhian” presented at the IPPA conference, Hanoi, Dec. 2009 and as a paper “Mineral Resources and Salt using in Prehistory Vietnam in comparison [comparation- sic] with Japanese Prehistory”

Facade of the State Guest House (Akasaka Palace). Built in 1909, it is one of the biggest buildings constructed during the Meiji period. Photo: Heritage of Japan

Behind every building there is a backstory of the people for whom and the purpose for which it was built. There is also the story of pioneers at the dawn of Western-style architecture in Japan. The buildings of the Meiji Era tell of a bygone era, of the incredible innovations of Industrial Revolution introduced from Europe into Japan, of the local events and developments that paralleled those in the West. Take a walk back in time to explore some of those stories.

Factories are iconic symbols of the Industrial Revolution era. During the 19th century, the worldwide demand for cloth had grown so much that merchants and nations competed fiercely to meet the supply of textiles for making clothing. Textile mills and factories, beginning with England, installed new machines to increase productivity and to cut the costs of labour.

Tomioka Silk Mill is Japan’s oldest silk-reeling factory. Established in 1972 to mass-produce and export high-quality silk

Tomioka Silk Mill, UNESCO World Heritage site (Source)

Inside Tomioka Silk Mill: 300 machines imported from France (Source)

Ukiyoe print of the Tomioka Mill and workers at work (Source)

The Meiji oligarchy wanted the fruits of Western progress, so they sent learning missions abroad to absorb as much of the western technological innovations as possible. One such mission, led by Iwakura, Kido, and Okubo and containing forty-eight members in total, spent two years (1871-73) touring the United States and Europe, studying government institutions, courts, prison systems, schools, the import-export business, factories, shipyards, glass plants, mines, and other enterprises. [Source: Library of Congress]

The government reorganized itself and also formed a professional corps of diplomats. Consequently, many Western-style buildings were built to receive foreign experts and carry out the reforms. Many of the Meiji era buildings were designed by Dr. Katayama Tokuma, who is regarded as the father of modern architecture in Japan. Katayama studied for in many years in the UK, France and Germany and under British architect Josiah Conder.

Aerial view of the Akasaka palace. Photo: Cabinet Office

Among the more extravagant projects undertaken was the Akasaka Palace (see photo above). Styled in part after the New Palace in Vienna, Buckingham Palace and the Louvre, its basic design was based on the Versailles Palace and it remains the only neo-Baroque European style palace in Japan.

Built of stone aroundd a steel frame, the palace building is both fire-resistant and earthquake-proof Photo: Heritage of Japan

Building began in 1899 and was completed in 1909, under the overall direction of Dr. Katayama Tokuyama who was an architect who studied under British architect Josiah Conders, who advised the Japanese government on many projects. The interiors lavishly decorated with imported French mosaics, fireplaces, furniture and chandeliers, and Italian rose and white marble in the early 19th c. Empire style during the rule of Napoleon Bonaparte, Akasaka Palace is, like its Western counterparts, a stately and enduring monument of great beauty. Take a virtual tour of the palace here.

Akasaka (Togu) Palace designed by Katayama Tokuma in 1899, was built for the Crown Prince and his bride. Little used as it was deemed expensive, costly to run, instead it was used to house some government departments and the Diet Library. Recently refurbished, it now functions as the State Guest House. The garden fountain seen here features four griffin statues. (Photo credit: Heritage of Japan)

Inside are many stunning and sumptuous staterooms like this ballroom. The palace fuses Japanese motifs such as samurai armour and helmets,  Japanese drums, phoenix with western flying horses, goddesses and sphinxes in the gilded stucco reliefs.

As part of the “Japanese spirit, Western knowledge” effort, Japanese began wearing European-style army uniforms, morning coats, top hats and ball gowns. Members of the Imperial court adopted European European titles and rococo, neo-baroque, neo-classical buildings were established and concerts of classical music were being performed.

In its efforts to modernize and in adopting the cultures and systems of the West, Japan needed experts to design Western-style buildings. Josiah Conder(see photo above left. Photo: Wikimedia Commons), an architect was invited from Britain to fill the role as adviser to the Meiji government. One of Conder’s notable projects include the former Iwasaki Family House and Kyu-Iwasaki-tei Garden at Taito-ku Tokyo Japan, designed in 1896(see photo below, photo: Wikimedia Commons)

Conder taught the history and structures of Western architecture to Japanese students. His very first class of graduates included Katayama Tokuma(see photo above right, credit: Wikimedia Commons), the man who became court architect (who built the Crown Prince’s Akasaka Palace – see photos above) and who designed the Hyokeikan (see photo below).

Hyokeikan, designed by Katayama Tokuma (student of Josiah Conder) and completed in 1908, it now part of Tokyo Ueno Museum (Source: Hyokeikan website)

The Hyokeikan has a magnificent vault dome in its entranceway (Source: Hyokeikan website)

The word Diet derives from Latin and was a common name for an assembly in medieval Germany. The Meiji constitution was largely based on the form of constitutional monarchy found in nineteenth century Prussia and the new Diet was modeled partly on the German Reichstag.

19th century Japanese Parliament

In keeping with Japan’s modernization and westernization drive, German architects Wilhelm Böckmann and Hermann Ende invited to Tokyo in 1886 and 1887, respectively, drew up two plans for a Diet building which were similar to other Western legislatures of the era. Böckmann’s initial plan, for example, was a masonry structure with a dome and flanking wings, which would form the core of a large “government ring” south of the Imperial Palace. However, due to public resistance in Japan to Foreign Minister Inoue Kaoru‘s internationalist policies, the first two parliament buildings were built to a more “Japanese” design, with traditional Japanese architectural features.

Japanese Diet Hall Design by Fukuzo Watanabe (Photo: In the public domain)

Prime Minister Katsura Tarō chaired the commission, which recommended that the new building emulate an Italian Renaissance architectural style. This too received much opposition, so after a public design competition in 1918, and 118 design submissions, the current Diet building was built based on the design by the first prize winner, Watanabe Fukuzo, who produced a design similar to Ende and Böckmann’s.

Ende and Böckmann’s Diet Building was never built, but their other “government ring” designs were used for the Tokyo District Court and Ministry of Justice buildings. Returning diplomatic and study missions from the west also called for domestic reforms that were carried out. Between 1871 and 1873, a series of land and tax laws were enacted as the basis for modern fiscal policy. Private ownership was legalized, deeds were issued, and lands were assessed at fair market value with taxes paid in cash rather than in kind as in pre-Meiji days and at slightly lower rates. [Source: Library of Congress *; factsanddetails.com]

Ministry of Justice’s former Administration Building, designed by Herman Ende, Wilhelm Bockman in 1895 (Photo: Wikimedia Commons)

From the onset, the Meiji rulers embraced the concept of a market economy and adopted British and North American forms of free enterprise capitalism. The private sector– in a nation blessed with an abundance of aggressive entrepreneurs– welcomed such change.

Economic reforms included a unified modern currency based on the yen, banking, commercial and tax laws, stock exchanges, and a communications network. Establishment of a modern institutional framework conducive to an advanced capitalist economy took time but was completed by the 1890s. [Source: Library of Congress *]

Yokohama Specie Bank, 1880, which became the Bank of Tokyo’s Yokohama branch, now the Kanagawa Prefectural Museum of History and Culture (Photo: Wikimedia Commons)

As in the West, trade and the industrial revolution in Japan created a demand for a host of banking and financial services. Stocks were traded vigorously, new instruments for market speculation evolved on the back of capitalism. New buildings were erected to facilitate and conduct these financial and banking activities. Education and school institutions had to be reformed as well. Germany was the primary model for educational reform. German language and literature were taught and Western-styles schools for the elite were built.

Tokyo University built in the Uchida Gothic style  Source: Wikimedia Commons

Educational institutions and western-style university buildings such as Tokyo University (above and below) and Meiji University were established in keeping with the necessary educational reforms.

Tokyo University  Photo: Wikimedia Commons

Meiji University, Faculty of Law 1881 Photo: Meiji University

A number of Western-style brick buildings of the Meiji era have been designated as an important cultural assets and turned into museums, such as the Kyoto National Museum. Other examples may be seen below:

Craft Gallery of the National Museum of Modern Art, built by Hisashi Tamura in 1910. Designed as “The former Headquarters of the Imperial Guards.” (Photo: Craft Gallery of the National Museum of Modern Art)

Kyoto National Museum designed by Katayama Tokuma in 1895, and built to house art treasures donated by the Imperial Household Ministry as well as those owned by temples and shrines (Photo: Kyoto National Museum)

Ryounkaku (a.k.a. Asakusa Twelve Storeys), built in 1890, was Japan’s first western-style “skyscraper”, and the first to install an elevator. At 52 meters with 12 storeys, it was the tallest building in Tokyo. The building contained 46 stores selling goods from across the globe.

Ryounkaku (Asakusa Twelve Stories), 1890. (Photo: Heritage of Japan)

Japan had witnessed the improvements in transportation, communications, trade and banking made in the West, where the Industrial Revolution had taken place in the late 1700s beginning in Britain and lasting through till around 1840. Japan wanted to resist the power and hegemony of the West by emulating the West. The Japanese sought Western technology and modernized essentially to level the playing field so they would not be colonized or taken advantage of by the West.   Under the nationalistic slogan “rich country, strong military,” the Japanese government was intent on learning the secrets of the West and Western experts were brought to Japan and Japanese experts were sent abroad to learn everything they could. The government’s top-down modernization policy dictated the goal of “more production through new industry” so that giant government-operated factories for the military, such as the Koishikawa arsenal factory,  were built. The rapid development of industries in Tokyo, besides giving rise to urban problems such as noise and pollution from the smoke emissions from factory chimneys, as well as the formation of labour unions and social unrest with workers protesting their long hours, low wages and sweatshop conditions. Ultimately, that tenacious onslaught and monentum of industrial development both supported as well propelled Japan headlong into two wars: the Sino-Japanese War(1894-1895)  and the Russo-Japanese War(1904-1905).

Koishikawa Arsenal Factory  (Photo credit: Edo-Tokyo Museum; Heritage of Japan)

 Nirayama-Hansharo

In 2015, “Sites of Japan’s Meiji Industrial Revolution: Iron and Steel, Shipbuilding and Coal Mining” mainly located in the southwest of Japan were designated UNESCO World Heritage Sites.

The development of the iron and steel industry, shipbuilding and coal mining underpinned the rapid industrialization of the country from the middle of the 19th century to the early 20th century. To showcase the nation’s achievements, the country’s first National Industrial Exhibition was held on August 21, 1877 (bottom right photo: color print depicting the Opening ceremony to the first National Industrial Exhibition. Credit: National Diet Library). The national event (inspired by the 1873 Vienna International Expo) emphasized its aspect as an industrial promotion opportunity providing a meeting place for Western technologies and their Japanese counterparts, for conducting product survey and industry promotion.

Colour prints of the first National Industrial Exhibition (Photo credit: National Diet Library)

The approximately 100,000 m2 venue contained the Fine Art Building (top left photo, photo: National Diet Library), the Agricultural Production Building, the Machinery Building, the Horticultural Building, and the Animal Building. An approximately 10 m high American-style windmill (for pumping up groundwater) was constructed at the park entrance. All the exhibits collected from across Japan were categorized roughly into six groups (mining and metallurgy, manufactures, fine art, machinery, agriculture, and horticulture). They were judged based on the criteria of materials, manufacturing methods, quality, adjustment, effectiveness, value and price. Medals, certificates of merit and other honors were bestowed on excellent exhibits

Redbrick warehouses (similar to those that proliferated in Manchester during U.K’s Industrial Revolution), were constructed along with expansion of harbour facilities in the late 19th century by the Yokohama city government.  Planned by a Japanese architect and government official, Tsumaki Yorinaka, the redbrick warehouses were erected in 1911 and 1913 to serve as custom houses. When the 1923 Great Kantō earthquake struck Yokohama, the Akarenga red brick buildings suffered less damage than other buildings due to their reinforced structure with iron implanted between the bricks.

Akarenga redbrick warehouses in Yokohama were completed in the period straddling the Meiji and Taisho periods  (Source: Free domain)

Other than buildings, notable Meiji era structures included warehouses(see photo above), lighthouses and aqueducts/bridges, an early example of which is the Suirokaku Aqueduct along the Biwakososui River in Kyoto.

Suirokaku Aqueduct, Biwasosui River, Kyoto, built in 1890. Tanabe Saburo was only 22 years old when he designed and built the aqueduct.

Eight lighthouses were built according to western specifications during the Meiji era. The lighthouse seen in the photo below is one of eight built during the Meiji period.

Oldest Western-style lighthouse, in Shinagawa, Tokyo Bay waterfront, built by French engineer Francois L. Verny in 1870. (photo credit: Flicker Creative Commons, Daniel Rubio)

Below are a few sample closeup photos of tattooed faces of the Jomon mostly of clay figurines (called dogu) or of pottery relief:

Relief face in a clay pot from Yamanashi prefecture(Minami-Alps city) 3,000BC)

Dogu head from Saga prefecture, 3,300BC

Tattooed face of a dogu from Tokyo (Tama New Town), 3000BC

Dogu from Iwate prefecture, 1300BC

Dogu from Yamanashi prefecture, 3000BC

A sketch of a dogu from Kanaaraizawa site, Ibaragi prefecture

Bearded dogu from Goto site, Tochigi prefecture

tattooed dogu face from Gunma prefecture

Dogu from Yamanashi prefecture (minami-Alps city), 3000BC

Dogu with heavily tattooed eyes and lips from Akita prefecture, Final Jomon

National Treasure dogu figurine from Aomori prefecture, Final Jomon

Dogu from Akita prefecture, Final Jomon

Clay mask from Akita prefecture (Late Jomon Asao site)

Another clay mask showing ornate tattoo markings from Iwate prefecture (Shidanai site), Final Jomon

Dogu from Chiba Prefecture (Late Jomon period)

A rare figurine with ornate face markings and large headgear, from Ishikawa prefecture, Late Jomon period

Dogu from Ibaragi prefecture, Final Jomon

Dogu from Nagano prefecture, Middle Jomon period

“Mimizuku dogu” from Chiba prefecture, Final Jomon period

“Mimizuku dogu” from Saitama prefecture

Dogu from Kanagawa prefecture, Late Jomon period

Dogu from Kanagawa prefecture, Middle Jomon period

Dogu from the Ikawazu Shellmidden site in Aichi Prefecture (Late Jomon period)

Clay mask from the Sanganchi Shellmidden site in Fukushima prefecture (Final Jomon period)

Dogu from Miyagi prefecture (Late Jomon period)

Dogu from Niigata prefecture (Nagaoka city) 3000BC

The most common type of tattoo appears to a simple double line running in a curve or straight line from the eye across the cheek to the side of the face. Other figurines feature crow’s feet lines from the corner of each eye (pictured below).

Dogu from Akita prefecture, 600BC

Eyes and lips may also have completely been surrounded by scarification or needle punctures creating the famous goggle-eyed and thick-lipped look of many figurines.

A closeup of these clay dogu of body parts – lips give an idea of how highly tattooed lips may have been

Eyelids may have been tattooed as well.

The eyelids appear to have dotted lined tattoos, both upper and lower ones. Clay mask from Aomori prefecture (period unknown)

Why did the Jomon tattoo their faces?

Local fishing folk believe that tattoos are done for protection against predators like shark. This practice may have been handed down from Jomon times.

Some of the tattoos such as the double lines from eye across cheek appear to have been fairly stable features, lasting from around 3,300 BC through the final phase of the Jomon period in the Kanto region. They may have been rites of passage or cultural traits intended to have been cultural/tribe identifiers.

Ainu women were known (until fairly recent times) to have tattooed their lips. According to Ainu tradition, they attributed tattooing to a gift from the “Ancestral Mother” of the Ainu Okikurumi (Turesh) Machi, the younger sister of the creator god, Okikurumi. And (like with the Inuit people)the tattoos were a prerequisite for Ainu women to getting married (source: Lars Krutak). Other Ainus have attributed a healing or protective function to tattoos that are believed to repel evil spirits(source: Lars Krutak). As the Ainu have been established to be genetically partially of Jomon stock, we can postulate that the practice may have been part of the goddess culture of the Jomon people as well (other cultures like Inuit, Eskimo Imooyok (see photo below) and Maoris women also tattooed their lips. Facial tattoos are especially sacred for the Maoris, a moko on the face is the ultimate statement of one’s identity as a Māori, and the head is believed to be the most sacred part of the body).

Later periods also showed up more ornamental and varied types of tattoos, where perhaps they became fashion or artistic adornments as well.

Jomon tattoos were unlikely to have had warpaint uses, i.e. they were probably not intended to scare off their enemies. Internecine warfare was unknown until the arrival of the Yayoi immigrants

Sources and References

縄文の力 THE POWER OF JOMON (別冊太陽 日本のこころ Author: 小林 達雄 ISBN9784582922127

土偶・コスモス(Published by MIHO MUSEUM) ISBN9784904702376

列島の考古学　縄文時代 (by 能登) ISBN9784309714424

縄文人の道具 古代史復元 (3) Author: 達雄, 小林) ISBN4061864238

縄文のわざと道具 縄文時代1 (日本のあけぼの)Author: 小林 達雄 ISBN4620603023

Tattoo History: The Tattooed Ainu Women of Japan by Minerva

Tattooing among Japan’s Ainu people by Lars Krutak

Ta moko: The significance of Maori tattoos 

Between the Lines:
Tracing the controversial history and recent revival of Inuit facial tattoos Sep 20, Ashleigh Gaul

‘This is so powerful:’ Kitikmeot women revive traditional Inuit tattoos CBC News,May 3, 2016

An thoughtful piece about why the Murakami pirates were so successful, their innovations, and how they turned islands into vibrant local trading economies…

via The Exact Opposite Idea of the Pirate Cliché

Musashi-Mitake-jinja

The Musashi-Mitake-jinja Shrine is believed to have been founded in 90 BC by Emperor Sujin, which makes it one of the oldest in Japan. However, the shrine also records that Priest Gyōki built a hall on this site and enshrined the Zaō Gongen statue in it in 736. The mountain, close to Tokyo, has been known as a sacred mountain and an object of worship since ancient times.

Musashi country (Musashi no kuni) painted by Ryusai Yukinobu Source: Great- Edo database

Hinting of the antiquity of the mountains’ ritual practices, the Hinode (Sunrise) Festival is the annual spring festival of Musashi-mitake Jinja Shrine. It is the most important of this shrine’s festivals.

The name of this festival comes from a ceremony held when reaching the peak of the mountain by Buddhist mountain priests, which is thought to be the origin of the 2000-year-old festival, which was supposedly held together with the sunrise on February 8 according to the old lunisolar calendar. These days the festival is held on May 8. (See photo of sunrise on Mt Mitake here.)  Despite the Shinto jinja’s presence being thought of as Shinto, we can see how the syncretism of faiths, of Shinto and Buddhism practices, was at work and was the norm from early times.

The Festival on May 7 includes a present-day solemn Shinto procession starts from the plaza in front of the cable car station on the mountain’s summit and winds through the Mitake village. Mainly focused on a mikoshi (a palanquin-styled portable shrine), this procession also includes Shinto priests, men dressed in white, armored warriors, and children.

After passing through the village, the procession goes up 300 stone steps to the main shrine at the summit of Mt. Mitake (929 meters high). While the initial procession ends at the location of the sacred palanquin with the receipt of symbols of the deities accompanied by gagaku (traditional Japanese court music) performed at twilight and the faint light of the lamps. At the end, participants are entertained by a kagura (Shinto music-and-dance) performance at the end.

Mountain ascetics, numerous shugenja visited the mountain especially after the Kamakura Period (1185–1333), when mountain religions proliferated. Mountain ascetics secluded themselves in the mountain to perform purification rites, cleansing themselves ritually under the nearby waterfalls (Nanayo-taki and Ayashiro-no-taki).

From the 17th century, commoners began to visit the shrine, and to accommodate all the pilgrim visitors to Mt. Mitake to pray at Mitake-jinja Shrine, the path to the mountain shrine became dotted with Shukubo temples lodgings. Many of those Shukubo lodges remain open today especially to kendo martial arts practitioners and others here to practise mountain austerities and meditation.

As to the origin of the Japanese solar cult religions, author Jacques H. Kamstra – in his 1967 book, “Encounter Or Syncretism: The Initial Growth of Japanese Buddhism” has made strong connections between hi-kami and hinode matsuri practices and the northern Asian continental solar cults possibly via Korean immigrants.

Like most mystical mountains, this one comes with its own set of folklore and legends. But among the folklore, wolves are beloved heroes and not the big bad wolves of modern fairytales. And they are seen in several forms on this mountain, as guardians of the small Inari shrine here, and as venerable guardian Shirookami deity of the Musashi-Mitake jinja, and the sacred messenger that led the legendary imperial ancestor, Yamato Takeru to safety.

Strangely, the baddie in the folklore here is a stag which is honoured elsewhere as a messenger of the gods at Kashima shrine in the east and in Nara’s imperial sheine. According to legend, wolves led Prince Yamato Takeru back to safety after a mountain demon disguised as a stag, led him astray on the slopes of Mount Mitake. Not surprisingly, the prince declared the wolves divine, and that is how they became sacred guardians of the Mitake mountain peak. (One wonders if the stag vs wolf opposition is merely a depiction of totemic animal symbols representing euphemistically an ancient tribalistic rivalry between political factions’ rulers.)

Statue of Hatakeyama Shigetada

The statue of the Kamakura period warlord-Shigetada Hatakeyama on horseback adds an air of samurai splendour to the already colourful shrines. The shrine’s treasure house is also famous for the Akaito Odoshi Yoroi (red-thread-armour) offering (now designated a national treasure) dedicated by Hatakeyama Shigetada in 1191.

Shrine visitors are set to increase in the zodiac Year of the Dog as in 2018. Lots of votive emas of the wolf-dog will be offered up.

Votive ema of wolf

You can view the rest of the photos of my walk on Mt Mitake at Field trip: Following the trail of Mt Mitake’s mountain pilgrims

Finally, if you are planning a trip yourself, you can find information on access to the mountain, by clicking on this page and this page.

Hu Li et al.,2009, Refined Geographic Distribution of the Oriental ALDH2*504Lys (nee 487Lys) Variant

Summary
Mitochondrial aldehyde dehydrogenase (ALDH2) is one of the most important enzymes in human alcohol metabolism. The oriental ALDH2*504Lys variant functions as a dominant negative greatly reducing activity in heterozygotes and abolishing activity in homozygotes. This allele is associated with serious disorders such as alcohol liver disease, late onset Alzheimer disease, colorectal cancer, and esophageal cancer, and is best known for protection against alcoholism. Many hundreds of papers in various languages have been published on this variant, providing allele frequency data for many different populations. To develop a highly refined global geographic distribution of ALDH2*504Lys, we have collected new data on 4,091 individuals from 86 population samples and assembled published data on a total of 80,691 individuals from 366 population samples. The allele is essentially absent in all parts of the world except East Asia. The ALDH2*504Lys allele has its highest frequency in Southeast China, and occurs in most areas of China, Japan, Korea, Mongolia, and Indochina with frequencies gradually declining radially from Southeast China. As the indigenous populations in South China have much lower frequencies than the southern Han migrants from Central China, we conclude that ALDH2*504Lys was carried by Han Chinese as they spread throughout East Asia. Esophageal cancer, with its highest incidence in East Asia, may be associated with ALDH2*504Lys because of a toxic effect of increased acetaldehyde in the tissue where ingested ethanol has its highest concentration. While the distributions of esophageal cancer and ALDH2*504Lys do not precisely correlate, that does not disprove the hypothesis. In general the study of fine scale geographic distributions of ALDH2*504Lys and diseases may help in understanding the multiple relationships among genes, diseases, environments, and cultures.

Central China Origin of ALDH2*504Lys
The frequency decline from Southeast China to West and North China is quite smooth. The allele frequencies decrease to less than 20% in Southwest and Central China, and to less than 10% in Manchuria, Mongolia, Xinjiang, and Tibet within the broader region of East Asia. In Central Asia and Siberia, beyond the pronounced genetic influence of Han Chinese, the ALDH2*504Lys allele is rare. The allele is also detected in some Iranian populations, which may be explained by diffusion along the Silk Road. We conclude that the spread of ALDH2*504Lys to the north and west was concomitant with the expansion of Han Chinese and diffusion of the allele into surrounding populations.
Although the ALDH2*504Lys allele frequency reaches a peak in Southeastern Chinese populations, we cannot draw the conclusion that this allele originated there. The population history shows clearly that Hakka and Minnam Chinese presently in Southeast China are descendants of migrants from Central China (Wen et al., 2004). The indigenous populations in South China, such as Hmong-Mien populations (Hmong and She) from the Yangtze River area, and Daic populations (Kam, Laka, Mulam, and Maonan) from the Pearl River area, exhibit much lower frequency of ALDH2*504Lys. ALDH2*504Lys is almost absent in the aboriginal populations of Hainan and Taiwan, the two largest islands in South China. Therefore, it is unlikely that the Southeast Chinese obtained the ALDH2*504Lys allele from the indigenous populations. Unlike the gradually decreasing frequency to the north and west, the allele frequency drops sharply to the south. The allele exists at low frequency in Peninsular Southeast Asia, and is rare in the Southeast Asian islands. If this allele originated in the Southeast Chinese populations after they arrived in the present region, the quick expansion of the allele to the north and west cannot be explained. Therefore, we conclude that the ALDH2*504Lys allele was most probably carried south by the Han Chinese migrants from Central China, rather than originating in the indigenous populations in the region where it now has the highest frequencies.
Understanding why the present Central China populations exhibit much lower ALDH2*504Lys than the Southeast China populations is crucial in the study of the history of this allele. Both the decrease in Central China and the increase in Southeast China should be accounted for. In the history of China, many Altaic populations moved from the North China to Central China after wars in the 4th, 12th, and 13th centuries which also resulted in the migration of some Chinese populations from Central China to South China. These Altaic populations later merged with the Central Chinese populations after their kingdoms or dynasties ended. The most famous examples are Sienbers (Xianbei, founders of Former Yan Kingdom, Later Yan Kingdom, Western Qin Kingdom, Southern Liang Kingdom and Southern Yan Kingdom of Sixteen Kingdoms Period, and Northern Dynasties), Huns (founders of Han-Zhao Kingdom and Northern Liang Kingdom of Sixteen Kingdoms Period), Khitans (founders of Liao Dynasty), and Jurchens (founders of Jin Dynasty). Those Altaic migrants may have included very few or no individuals carrying the ALDH2*504Lys allele because present Altaic populations have a low frequency of the allele. The merging of these Altaic populations could have decreased the proportion of ALDH2*504Lys in the Central Chinese populations. On the other hand, some as yet unknown protective effects of ALDH2*504Lys against diseases might also have contributed to the increased frequency of this allele in Southern Chinese. Since migrations to South China resulted from wars, the refugees may have been subjected to considerable stress and a selective advantage could have had great impact. We can speculate that the ALDH2*504Lys heterozygotes had an advantage because they tended to drink less alcohol or had some other advantage (Chen et al., 1999). The recent appreciation of other metabolic/pharmacologic roles for ALDH2 (Li et al., 2006; Larson et al., 2007; Chen et al., 2008) suggest that if selective factors are responsible for the high ALDH2*2 frequency in East Asia, their nature may be unrelated to the current association with esophageal cancer or ethanol metabolism. Alternative hypotheses of increased resistance to some disease organisms (Enoch and Goldman, 1990;Yokoyama et al., 2001; Oota et al., 2004; Yokoyama & Omori, 2005; Yang et al., 2007; Li et al., 2008) would also explain a clear advantage to heterozygotes. However, statistically positive selection on ALDH2*504Lys cannot be detected using the extended haplotype test (Sabeti et al., 2007) as very low levels of recombination exist in the genomic region of ALDH2 locus (Oota et al., 2004). Other methods suggest positive selection on ALDH2*504Lys (Long et al., 2006).
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Geographic Association with Esophageal Cancer Incidence
Whatever positive selection may have increased the frequency of ALDH2*504Lys, serious diseases such as esophageal cancer or ischemia could act to decrease the ALDH2*504Lys allele frequency among the populations since studies report that heavy alcohol drinkers who are heterozygotes for ALDH2*504Lys have higher risk for esophageal cancer (Yokoyama & Omori, 2005; Yang et al., 2007; Li et al., 2008). In addition, ALDH2 activation was shown to reduce ischemic damage to the heart, suggesting that patients with reduced ALDH2 activity may suffer increased damage during cardiac ischemic events or coronary bypass surgery (Chen et al., 2008). The typical age of onset for esophageal cancer in the high incidence area can be earlier than 30 (He et al., 2006). We compared the geographic distribution of esophageal cancer incidence with the ALDH2*504Lys allele and carrier frequency distributions. We collected the male esophageal cancer incidence data of 355 populations from the literature, covering most countries in the world (Table S2). Central and Southeast China were examined in detail. Figure 3 illustrates the world distribution of esophageal cancer incidence and the details in East Asia. The extremely high incidences only appear in East Asia and some populations in Central Asia where the frequency of ALDH2*504Lys carriers is also high. However, comparison of Figure 2 and Figure 3 shows that the distributions are far from identical. However, the high cancer incidence areas mostly fall into the high frequency area of the derived allele carriers. The acetaldehyde accumulation resulting from ALDH2*504Lys in those who drink alcohol is certainly not the only risk factor for esophageal cancer. As noted above, ALDH2 also has other metabolic functions that could be independently influencing the distribution of ALDH2 variants (Li et al., 2006; Larson et al., 2007). Some environmental factors such as soil and vegetation characteristics and life styles may also be associated with the esophageal cancer risk (Wu et al., 2007; Fan et al., 2008; Moradi, 2008).

In Central Chinese populations, the heritability of esophageal cancer is estimated at around 49% (Han et al., 1994; Li et al., 1998). East Asian migrants in America also have a much higher esophageal cancer incidence than European Americans and African Americans (Parkin et al., 1997), indicating the pronounced heritability of esophageal cancer. Therefore, the incidence of esophageal cancer is affected by multiple factors that interact with the ALDH2*504Lys allele frequency in a complex way. That complexity could explain the differences between the distributions of esophageal cancer and the ALDH2*504Lys allele carriers in East Asia.
In most areas of South China and Southeast Asia, the incidence of esophageal cancer is much lower than that observed in Central China, indicating that there are fewer environmental risk factors and lower susceptibility of esophageal cancer in South China. However, there is still a high incidence area in Southeast China, which might be associated with the highest allele frequency of ALDH2*504Lys in exactly the same geographic area. In contrast to the high incidence of esophageal cancer in Southeast China being the consequence of the high ALDH2*504Lys frequency, it is possible that the high incidence of esophageal cancer in Central China is working to decrease the ALDH2*504Lys frequency while cultural pressure to consume ethanol increases as the impact of *504Lys decreases. The answer depends on which factors increasing risk are most important in which area and how they interact.
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Conclusion
In conclusion, we hypothesize that the oriental ALDH2*504Lys variant might have originated in the ancient Han Chinese population in Central China and spread to most areas of East Asia with the expansion of Han Chinese and their genetic influences on neighboring populations over the past few thousand years. Some diseases such as esophageal cancer show a complex relationship with the frequency of ALDH2*504Lys. Where the ALDH2*504Lys frequency is high for whatever reason, as in Southeast China, there is a clear increased risk of esophageal cancer in heterozygotes that results in higher esophageal cancer incidences in some subregions. In other areas of China there is also an increased risk of esophageal cancer in heterozygotes (Yang et al., 2007; Wu et al., 2001; Chen, 2005; Yang, 2005; Xiao, 2007) but the lower frequency of ALDH2*504Lys is not sufficient to explain the high incidence of esophageal cancer. More genetic epidemiological investigations in China are required to reveal any possible reciprocal relationship between esophageal cancer and the ALDH2*504Lys allele and identify the other risk factors that appear to be present.

ALDH2, ADH1B, AND ADH1C GENOTYPES IN ASIANS: A LITERATURE REVIEW   Non-pDF version

2004 The evolution and population genetics of the ALDH2 locus: Random genetic drift, selection, and low levels of recombination

Effects of Worldwide Population Subdivision on ALDH2 Linkage Disequilibrium

Full article pdf
Yayoi Source of ALDH2 https://upload.wikimedia.org/wikipedia/commons/8/8b/ALDH2_rs671_genotype_frequency.png

Origins of Japanese lecture by Saitou https://ocw.u-tokyo.ac.jp/lecture_files/gf_14/4/notes/en/04saito_eng.pdf

2017 Takeuchi et al., The fine-scale genetic structure and evolution of the Japanese population

See also Tracing Jomon and Yayoi ancestries in Japan using ALDH2 and JCV virus genotypes

Source: Ancient Eurasian DNA sequencing is revealing links with modern humans

Many voices and new models disproving the Southern Dispersal route model (following the coast of India) have been steadily coming onstream for a while, but it has been difficult to dislodge the consensus model for more than a decade ever since it emerged, and the mountain of media and literature that followed the original model (see Vincent Macaulay; et al. (13 May 2005), “Single, Rapid Coastal Settlement of Asia Revealed by Analysis of Complete Mitochondrial Genomes; Vol. 308. no. 5724”, Science Magazine, 308 (5724), pp. 1034–36, doi:10.1126/science.1109792, PMID 15890885”. These newer models suggest a pincer model including a route that goes either goes north or south of the Himalayas, before arriving at the coasts of South East Asia and northeast Asia.

Below we survey some of the literature representing the dissonance with the Southern dispersal hypothesis, the most recent of which being:

Nicolas Zwyns Et al., The Northern Route for Human dispersal in Central and Northeast Asia: New evidence from the site of Tolbor-16, Mongolia
Scientific Reports, volume 9, Article number: 11759 (2019)

Abstract

The fossil record suggests that at least two major human dispersals occurred across the Eurasian steppe during the Late Pleistocene. Neanderthals and Modern Humans moved eastward into Central Asia, a region intermittently occupied by the enigmatic Denisovans. Genetic data indicates that the Denisovans interbred with Neanderthals near the Altai Mountains (South Siberia) but where and when they met H. sapiens is yet to be determined. Here we present archaeological evidence that document the timing and environmental context of a third long-distance population movement in Central Asia, during a temperate climatic event around 45,000 years ago. The early occurrence of the Initial Upper Palaeolithic, a techno-complex whose sudden appearance coincides with the first occurrence of H. sapiens in the Eurasian steppes, establishes an essential archaeological link between the Siberian Altai and Northwestern China. Such connection between regions provides empirical ground to discuss contacts between local and exogenous populations in Central and Northeast Asia during the Late Pleistocene.

Introduction

Although models for H. sapiens’ early dispersals out of Africa emphasize a southern route to Asia1,2,3,4,5, Neanderthal and Modern Human (MH) fossils in Siberia6,7,8,9 suggest that at least two other dispersals took place across the Eurasian steppe north of the Asian high mountains. Given the size of the area considered, human fossils are few but recent studies have suggested that a major change in the regional archaeological record could be indicative of a large-scale human dispersal event. Known as the Initial Upper Palaeolithic (IUP), it refers to the sudden appearance in contiguous regions of a specific blade technology sometimes associated with bone tools and ornaments10,11,12,13,14,15,16,17. How old these assemblages are, and how long the phenomenon lasts are still controversial questions, and little is known about the timing and environmental context of these population movements. Here we present new data following excavations of an archaeological site located in a low altitude pass, the Ikh-Tolborin-Gol, which connects Siberia with northern Mongolia. Our results document the early occurrence of the Upper Paleolithic in Mongolia and provide a chronological reference for population movement across Northeast Asia during the Late Pleistocene. …

To summarize, the data at hand suggests that H. sapiens are more likely to be the makers of the IUP. The sudden appearance of this technology in Mongolia takes place in GI12, a temperate phase contemporaneous with the expansion of H. sapiens, in Western and Northern Siberia. Other scenarios cannot be rejected but they are less parsimonious, and they simply lack convincing alternatives regarding the archaeology of H. sapiens populations. Either way, the population movements illustrated by the dispersal of the IUP occur in a general context of climatic instability associated with MIS3 in Mongolia, and more generally in Central and Northeast Asia⁶⁶. Such variations in the higher latitude of the Eurasian steppe imply different challenges (eg. continental climate, aridity) than those met along the southern route into the Indian subcontinent⁶⁷. An inland route to Asia borne out by the archaeological and fossil record is, however, not exclusive of other dispersal models (e.g. Southern or ‘coastal’ Route) while it remains consistent with the available genetic data. The genome of an aboriginal Australian shows that deeply rooted populations have a shared ancestry coming from at least two early H. sapiens dispersals out of Africa into Asia⁶⁸. Meanwhile, extant populations from continental East-Asia⁶⁹ and in Melanesia^70,71show evidence of gene flow from Denisovan individuals from at least two gene flow events⁶⁵. The timing might still be uncertain, but the dates presented here for the dispersal of IUP are consistent with the age estimates for an early H. sapiens – Denisovan encounter, distinct from the other gene flow events that would take place much later in Southeast Asia (or Melanesia)⁶⁵. After subsequent mutations, the genes passed along from Denisovans around 45 ka may have been decisive for the survival of our species in extreme environments (Tibetan populations’ adaptation to hypoxia of high altitude)^72,73. Finally, it is notable that East-Asian and Melanesian populations do also show evidence of gene flow coming from Neanderthal individuals⁶⁵. Granted that the Pleistocene population dynamics were probably complex, a model integrating dispersals of several taxa, such as Neanderthal and H. sapiens across the continent is a parsimonious complement to a strict coastal migration scenario^{74, 42}.

Conclusions

The results obtained at T16 indicate that the IUP techno-complex occurs in Western front of East Asia as early as 45 ka. Contemporaneous with skeletal evidence of H. sapiens, the IUP in Tolbor establishes an essential archaeological link between Siberia and Northern China. Together with evidence from these adjacent regions, the material found in AH6 suggest that a widespread behavioral shift took place along the Eurasian steppe belt during a period of climatic instability.

Corollary scenarios that extend the northern route scenario theories are now more plausible ones — see various authors‘ writings on the northeast Asian/East Eurasian origins of Tibetan/Nepali/Sherpa populations, and  George Van Driem(The Eastern Himalayan corridor in prehistory” whose model (see maps immediately above)for a Trans-Himalayan Ice Age Refugia”route, and Larruga et al., of the following 2017 paper:

– Carriers of Mitochondrial DNA macrohaplogroup R colonized Eurasia and Australasia from a Southeast Asia core area:

Coeval independently dispersals around 50 kya of the West Asia haplogroup U and the Wallacea haplogroup P, points to a halfway core area in southeast Asia as the most probable centre of expansion of macrohaplogroup R, what fits in the phylogeographic pattern of its ancestor, macrohaplogroup N, for which a northern route and a southeast Asian origin has been already proposed.

– Viral markers model migration showing hitherto unknown northern routes

Proposed routes of migration carrying JCV genotypes to the New World. It is assumed that the initial dispersal of JCV from Africa coincides with ‘Out of Africa 2’, but JCV phylogeny does not provide any independent estimate of the dates. Dispersal of some genotypes with the earlier ‘Out of Africa 1’ migration is still a theoretical possibility. Later migrations carried distinctive genotypes to island southeast Asia and Oceania. The Americas, however, have the northeast Asian genotype, type 2A. Post-Columbian migrations from Europe (types 1 and 4) and forced migrations from Africa (types 3 and 6) to North and South America complete the picture. It should be noted, however, that no studies of JCV in African populations in Brazil have yet been reported.

– Chaubey et al., had in 2012 proposed that AA speakers in India today are derived from dispersals from southeast Asia, followed by extensive sex-specific admixture with local Indian populations, disproving the timing of dispersal from a westerly and Indian coastal source. Source: Population genetic structure in India Austroasiatic speakers: The role of landscape barriers and sex-specific admixture

— This paper(excerpted below) supersedes an earlier paper showing a counterclockwise dispersal of the N Mtdna macrohaplogroup from southern East Asia, and is more consonant with the large density of N across Eurasia: Carriers of Mitochondrial DNA Macrohaplogroup N Lineages Reached Australia around 50,000 Years Ago following a Northern Asian Route

Fig 1. Geographic dispersal routes of (A) AMH out of Africa migration, and (B) secondary worldwide human expansions, deduced from the age and geographic localization of L3 and N(xR) mtDNA haplogroups including Lineages O and S from Australia. Climatic marine isotope stages (MIS) and most probable places of genetic admixture with Neanderthals and Denisovans are depicted.

Basic N haplogroup trees (excepting N1kt, N2, N3, X and A) showing coalescence ages and sample geographic origin.

Practically all humans out-of-Africa belong to mtDNA macrohaplogroups N or M, both sister branches of L3 African clade. N shows a global Eurasian distribution but most of its lineages everywhere are members of the R subclade. Only in Aboriginal Australians N(xR) lineages reach frequencies over 50% [5,79], and in some regions of East and Central Asia, haplogroups N9 and A can, respectively, exceed 10% [30,39,58,68,80]. In the rest of its geographic range, the presence of N(xR) lineages is residual and represent small younger expansions driven by the later spread of human groups, mainly harboring R derivatives in Western Asia and R and M derivatives in South and East Asia. …

N5 could not be an Indian autochthonous clade based on phylogenetic reconstruction, as it shares transition 1719 with its sister clade N1 that is a haplogroup of undoubted West Asian origin [34], and it has been also found in the Caucasus, Pakistan, Iran and Nepal [26,69–71]. Third, other N lineages detected in India as I, W, X2, or N9a, Y2 and A4, are derived branches of the basal clades N1, N2, X, or N9 and A, of western and eastern Asian origins respectively. Thus, the presence of N lineages in India is better explained as the product of late migration from northwestern and northeastern areas. Even though haplogroup N5 is accepted as an autochthonous Indian lineage, its coalescence age (35.7 ± 8.2) is significantly younger (p < 0.0055) than that of the Australian S lineage (46.8 ± 5.5). This scenario strongly contrasts with the huge presence of autochthonous M [40,72] and R [31,59,60,73] lineages with deep coalescence ages in India. It could be alleged that primary autochthonous N lineages existed in India but became extinct due to genetic drift, but this hypothesis is in contradiction with the fast population growth detected in prehistoric southern Asia [74]. In summary, it seems that the first colonizers of Australia, carrying mtDNA haplogroup N(xR) lineages, could use a route not involving India as a stage. …

Our phylogenetic and phylogeographic analysis of macrohaplogroup N in Eurasia supports the existence of an additional northern route out of Africa, not involving the Arabian Peninsula or the Indian subcontinent as previously envisaged [17]. This long journey ended in Australia when it was still a part of the Sahul, most probably at the last glacial stage MIS-4 (Fig 1A). On the top of the common L3* trunk, macrohaplogroup N accumulated a stem of five mutations without any known bifurcation. From this fact, it can be deduced that, after the out-of-Africa, the bearers of this lineage seem to have had demographic difficulties and remained as a stagnate population for a long time. So, the first stages of the proposed haplogroup N northern route would be speculative and have to find indirect support on other genetic, archaeological and anthropologic evidences. … as this study demonstrates, an additional Levant northern route is more congruent with available multidisciplinary data. In addition, combined genetic, archaeological and bioclimatic evidence suggest that, although the early anatomically modern human was born in Africa, the nursery of the modern humans that colonized Eurasia, Oceania and the New World might be first at the south Siberia northwest China core and later in Southeast Asia.

— Candidates for Hoa binhian (early dispersals in Asia) are found in Yunnan, SW China (thought to be bearers of Mtdna R9) which may indicate that the previously-supposed southern early people populating SEA may have had a more northerly origin than thought.

— Excerpts from the Abstract and body of the paper by Sheila Misora et al., Continuity of the microblade technology in the Indian Subcontinent since 45ka: Implications for the dispersal of modern humans

Based on our older ages for microblade technology in the Indian Subcontinent, and the arguments presented above, we present the following model for modern human dispersal (as illustrated in Figure 2):

• 1. During MIS 6 widely dispersed hominin populations with a common ancestor in Homoerectus had differentiated into distinct populations with modern humans and possibly other archaics in Africa, Neanderthals in Europe, Denisovans in temperate Eastern Eurasia and archaic Indians in the Indian Subcontinent and Sundaland (Figure 2.1).

• 2. During the Interglacial climate of MIS 5, modern humans expanded into Eurasia at the expense of both Neanderthals and Denisovans and reached SE Asia. Due to competition with Indian archaics, modern humans were unable to disperse into the Indian Subcontinent and modern humans reached SE Asia at this time via a northerly route through the Middle East, Central and Eastern Eurasia and Southern China. During this time admixture with both Neanderthals and Denisovans is likely to have occurred in the modern humans reaching SE Asia (Figure 2.2) … Sharp cultural boundaries between the Indian Subcontinent and adjacent areas are not in conformity with a rapid dispersal through India to SE Asia from Africa. Archaeological sites in Arabia and Africa dating to MIS 5 show some distinctive technological features, such as Nubian cores and bifacial projectiles which are absent from any assemblage in the Indian Subcontinent, making it unlikely that modern humans dispersed into the Indian Subcontinent at this time. On the other hand microblade technology or blade technology is attested to at archaeological sites dating to around 60 ka in Africa which have a closer resemblance to the Indian microblade technology. Core and flake assemblages are associated with modern humans in SE Asia and may date back to MIS 5 times. We suggest that the later entry of modern humans into the Indian Subcontinent compared to adjacent regions is because Indian Archaics could easily compete with modern humans during climate conditions favorable to both. …

– A number of research papers in recent years have been coming onstream, concluding that the findings of variations of Altai Denisovan, Neanderthal genetic introgressions into Asian genes suggest complex migration scenarios that do not corroborate the Southern dispersal route hypothesis(see Tracing the peopling of the world through genomics). Since Neanderthal and Denisovan fossils are located in northerly or central zones, it goes that encounters had to have taken place further north than along the southern Indian Ocean coastal route.  Along with the emergence of a great many ancient DNA with some of the oldest dates seen in northern parts of Eurasia, such as Ust’ Ishim or Mal’ta beret fossils, a model that includes a northern route now seems a lot more plausible. Incidentally, these new scenarios are closer to the findings and proposed migration model of virus markers — compare the map immediately below…

A recent two-migration path or pincer model Source: Utility of polyomavirus in tracing human migrations dating to prehistoric times

Pavesi found:

Type 2 includes several variants, with subtype 2A mainly in the Japanese population and native Americans (excluding Inuits), 2B in Eurasians, 2D in Indians, and 2E in Australians and western Pacific populations (Fernandez-Cobo et al., 2002; Yanagihara et al., 2002; Zheng et al., 2003; Miranda et al., 2004; Takasaka et al., 2004). Subtype 7A was found to be characteristic of southern China and South-East Asia (Saruwatari et al., 2002), while subtype 7B of northern China, Mongolia and Japan (Sugimoto et al., 2002b; Zheng et al., 2004a). A third subtype (7C), spread throughout northern and southern China, has recently been character- ized by Cui et al. (2004). Finally, type 8 was found in Papua New Guinea and the Pacific Islands (Jobes et al., 2001; Yanagihara et al., 2002).
The ubiquitous distribution of JCV, combined with a transmission mechanism largely within families or popula- tions (Kunitake et al., 1995; Kato et al., 1997; Suzuki et al., 2002; Zheng et al., 2004b), make it an attractive candidate for reconstructing human migrations dating to prehistoric times. The close relationship of JCV found in native Americans with that in North-East Asia is consistent with the migration of Amerindian ancestors from Asia across the Bering land bridge (Agostini et al., 1997a). Doubts regarding the reliability of JCV as a marker of human evolution (Wooding, 2001) have recently been dispelled by a whole-genome phylogenetic analysis focused on the distinction between slow- and fast-evolving sites (Pavesi, 2003). By this approach, it was proposed that the associa- tion of JCV with humans originated in Africa, since type 6 was found to be the putative ancestral genotype. It was also demonstrated how type 6 gave rise to two independent evolutionary lineages: one including types 1 and 4, the other including types 2, 3, 7 and 8 (Pavesi, 2003).

Source: Pavesi, 2005 Utility of polyomavirus in tracing human migrations dating to prehistoric times The Journal of general virology 2005 DOI:10.1099/vir.0.80650-

…See also the pincer models or central Asian route viz. 2012 Alvie’s et al., model below:

Alves I, Šrámková Hanulová A, Foll M, Excoffier L (2012) Genomic Data Reveal a Complex Making of Humans. PLoS Genet 8(7): e1002837. https://doi.org/10.1371/journal.pgen.1002837

See excerpts from the abstract and relevant portions of the paper below

We underline the need to properly model differential admixture in various populations to correctly reconstruct past demography. We also stress the importance of taking into account the spatial dimension of human evolution, which proceeded by a series of range expansions that could have promoted both the introgression of archaic genes and background selection.

Interbreeding between Modern and Archaic Humans

In line with previous studies [10]–[12]which suggested that some aspects of human genomic diversity were incompatible with a complete replacement of archaic hominins, evidence for admixture between humans and Neanderthals emerged from the first analysis of a complete Neanderthal genome [13]. Indeed, the presence of a significant excess of Neanderthal-derived alleles in Eurasian populations as compared to Africans has been interpreted as resulting from an admixture episode between the ancestors of Eurasians and Neanderthals somewhere in the Middle East [13](Figure 1A). Even though the existence of a very ancient population subdivision in Africa from which both Neanderthals and Eurasians would have emerged could lead to similar patterns [14], the maintenance of such a subdivision over tens of thousands of generations seems unlikely. The sequencing of another archaic hominin from the Denisova cave in the Altaï mountains in Siberia has further revealed that Papua New Guineans showed signs of introgression from this archaic human [15]. Further studies of 33 populations from Southeast Asia and Oceania [16]showed that Denisovan admixture was actually present in other Oceanians, Melanesians, Polynesians, and east Indonesians but was virtually absent in mainland east Asians (but see [17]for evidence of possible Denisovan introgression on the Asian continent). Overall, these genomic analyses of admixture suggest that 1%–3% of the genome of all Eurasians and native Amerindians is of Neanderthal origin [15], and that Papua New Guineans and Australians have another 3.5% of their genome of Denisovan origin [16]. The out-of-Africa model of human evolution, which posited a complete replacement of archaic by modern humans in Eurasia, thus needs to be modified to include a limited assimilation of archaic genes, but the fact that most of the genetic variation observed in extant non-African populations comes from Africa remains true.

…The fact that Denisovan admixture had been first evidenced in Papua New Guineans suggested that admixture had occurred as a single pulse in Southeast Asia, after the separation of the ancestors of Oceanians and other Asians [15], [16](Figure 1A). The analysis of an Australian genome has confirmed the presence of Denisovan admixture in Australians [24]and suggested that admixture occurred during a first early wave of colonization towards Oceania, either in Southeast Asia or earlier in Eurasia (Figure 1B). A reanalysis of a large human SNP database and its comparison with Denisovan-derived alleles has suggested the presence of Denisovan admixture in East Asians, albeit at lower levels than in Oceanians [17], which could have occurred at a different place than for Oceanians, somewhere in East Asia (Figure 1C). Contrastingly, Currat and Excoffier [25]introduced a spatially explicit model of interbreeding between Neanderthals and Eurasians that could occur over the whole Neanderthal range (Figure 1D). They obtained similarly low levels (1%–3%) of Neanderthal introgression in both Europe and China if interspecific exchanges were locally extremely limited (only 200–400 interbreeding events over the >6,000 years of co-existence between the two species). An extension of this scenario to Denisovan admixture would imply that modern humans could have hybridized along all migration routes overlapping with the range(s) of archaic humans (Figure 1D). The fact that the largest levels of Denisovan introgression are found in Oceanians raises the question of a potential discontinuity in the Denisovan range (Figure 1A, 1B) or of a genetic differentiation of archaic hominins living in different ecosystems (Figure 1D). Alternatively, modern humans could have admixed with other hominins [26], and/or inferred hominin introgression could result from the sharing of some derived sites between Neanderthals, Denisovans, and unidentified archaic hominins. A scenario involving an unsampled Eurasian archaic hominin has received support from a recent study [27]showing the presence of a highly divergent (>3 Mya) haplotype of the innate immune gene OAS1. This deep lineage is found at high frequencies in Oceania (and at lower frequencies up to Pakistan). This DNA segment is more closely related (0.6 Mya divergence) to the Denisova sequence than to the Neanderthal sequence, which is itself closer to the human reference sequence. It has been speculated [27]that this fragment had introgressed from a more archaic hominin than Denisovans, who could have been themselves introgressed earlier….

Our understanding of the exact sequence and location of admixture events would highly benefit from a more precise knowledge of the nature and the distribution of Neanderthal segments in our genome. Unfortunately, current estimations of introgression levels are based on a statistic measuring a genome-wide difference in the proportion of archaic-derived alleles between two human populations [13], [14], so that the genomic distribution of introgressed segments is still unknown. However, in addition to the OAS1segment mentioned above [27], several authors have recently argued they had identified candidate regions harboring archaic haplotypes [13], [28], [29]. These regions usually show highly divergent haplotypes with very little evidence for recombination [30]. A dozen genomic regions where Eurasians have haplotypes much more divergent than Africans and a high proportion of derived Neanderthal alleles have been proposed as candidates for Neanderthal introgression [13]. More recently, an X-linked haplotype (B006) in an intron of the dystrophin (dys44) gene, almost absent from Africa but with 9% average frequency outside Africa, has been proposed to be of Neanderthal origin [29]. It is close to the ancestral X haplotype, shares 2/3 of derived alleles with Neanderthals, and has little associated diversity, suggesting a recent origin in humans. Another study has also suggested that several immune-related HLA class I alleles in humans could be of Denisovan origin and that they helped Eurasian populations build their immunity [28]. Whereas the hypothesis of an adaptive introgression is highly seductive, its support is relatively thin. “Denisovan” HLA class I alleles are currently not confined to Oceania but are found widespread in Asia. Moreover, the strongest argued case of Denisovan allelic ancestry (HLA-B*73) is actually not found at all in the Denisovan genome and is presently distributed in western Asia, well in the former Neanderthal range. One should therefore be extremely cautious not to assume that each very divergent haplotype found in humans is necessarily of archaic origin, as cases of incomplete lineage sorting are not rare between higher primates [31], especially in the HLA system where trans-specific polymorphism is facilitated by balancing selection [32]. However, if some introgressed genes were really advantageous, they should have spread and fixed in the human population, but as discussed below there is no widespread signature of strong selective sweeps in Eurasia.

…it is likely that differential admixture should affect population genetic affinities under more complex models of population differentiation. The proper interpretation of human genetic affinities should thus probably be re-evaluated in the light of these results. In particular, the divergence between Africans and Oceanians (showing up to 5% archaic admixture [16]) could be more recent than previously reported (62–75 Kya [24]). It remains unclear whether the method used by Rasmussen et al. [24]to date this divergence is also sensitive to differential introgression, but, if that was the case, the colonization wave to Oceania thought to well predate that towards East Asia [24]could have occurred at roughly the same time once differential admixture had been taken into account.

The paper’s author Clarkson suggests that those early dates of a Middle-Stone-Age-like people are consonant with the previous hypotheses of an early Eurasian split with Papuans (i.e. Abor. Australians’ ancestor) as well as of the incorporation of Neanderthal genes into their lineages. See Chris Clarkson, Richard G. Roberts, Zenobia Jacobs, Ben Manwick, Richard Fullagar, Lee J. Arnold & Qian Hua(2018): Reply to Clarkson et al., (2017), ‘Human occupation of Northern Australia by 65,000 years ago’, Australian Archaeology, DOI:10.1080/03122417.2018.1402884

On the question of whether there was an early arrival in the Japanese archipelago from the north, the controversy is a long-standing one. On the one hand, archaeology has shown the arrival of a northern set of lithics – microblades accompanied by burins (which has only a northern Eurasian transmission route) and virus markers and archaic genes suggest a northern migration route, on the other hand, these thin signals of a northern route taken during glacial times, the evidence of such perilous journeys likely buried in the permafrost, and the voices supporting it are often drowned out by the plethora of denser data on later migration entries from the south. This 2017 paper elucidates the uphill task of proving the early northern route that scientists face:

“How Do the DNA Studies Tell Us about the Routes of Human Entry into Japan?

A more recently proven “lost culture”, the arrival of the Okhotsk culture from the north whose Siberian Amur region genetic components are significantly admixed with the Ainu, and whose genetic signals can be seen even in northeast Japan — is still relatively unknown today, despite having had a major influence on introducing barley agriculture, bear ceremonies and whaling culture to the northeast parts of Japan. See Barley dispersal patterns mirror the settlement of a forgotten culture from the north 

Finally, if you take into account all of the above recent literature, the above dispersal scenarios are easier to reconcile with recent admixture models and analyses of genetic affinities between both ancient DNA and MtDNA of modern Asians…

… see the analyses of both McColl et al.’s 2018 Ancient genomics reveals four prehistoric migration waves into Southeast Asia as well as Kanzawa-Kiriyama’s 2019 paper, Late Jomon male and female genome sequences from the Funadomari site in Hokkaido, Japan

Fig. 1: High-resolution spectra of mtDNA haplogroups in the Japanese population.

From: Genetic and phenotypic landscape of the mitochondrial genome in the Japanese population  (Open Access pub. under Creative Commons license)

c Stacked bar plots of the frequencies of the macrohaplogroups within the geographical regions in Japan and subpopulations from 1KG. The geographical regions in Japan are defined as Hokkaido, Tohoku, Kanto-Koshinetsu, Chubu-Hokuriku, Kinki, Kyushu, and Okinawa from northeast to southwest areas of Japan, as described elsewhere42.

Below is an excerpt of the open access 2020 paper:

Yamamoto, K., Sakaue, S., Matsuda, K. et al. Genetic and phenotypic landscape of the mitochondrial genome in the Japanese population. Commun Biol 3, 104 (2020). https://doi.org/10.1038/s42003-020-0812-9 PDF

Abtstract

The genetic landscape of mitochondrial DNA (mtDNA) has been elusive. By analyzing mtDNA using the whole genome sequence (WGS) of Japanese individuals (n = 1928), we identified 2023 mtDNA variants and high-resolution haplogroups. Frequency spectra of the haplogroups were population-specific and were heterogeneous among geographic regions within Japan. Application of machine learning methods could finely classify the subjects corresponding to the high-digit mtDNA sub-haplogroups. mtDNA had distinct genetic structures from that of nuclear DNA (nDNA), characterized by no distance-dependent linkage disequilibrium decay, sparse tagging of common variants, and the existence of common haplotypes spanning the entire mtDNA. We did not detect any evidence of mtDNA–nDNA (or mtDNA copy number–nDNA) genotype associations. Together with WGS-based mtDNA variant imputation, we conducted a phenome-wide association study of 147,437 Japanese individuals with 99 clinical phenotypes. We observed pleiotropy of mtDNA genetic risk on the five late-onset human complex traits including creatine kinase (P = 1.7 × 10−12).

… Here we provide a comprehensive analysis that characterizes the genetic and phenotypic landscape of mitochondria in the Japanese population. (i) We constructed a high-resolution mtDNA variant list and haplotype classifications in the Japanese population based on deep WGS of ~2000 individuals. (ii) We conducted unsupervised clustering of the mtDNA variant patterns and assessed their correspondence with defined haplogroups by using a set of machine learning (ML) methods. (iii) We quantitatively assessed positional distributions and LD structure of the mtDNA variants by parallelly comparing with those of nDNA. (iv) We performed genome-wide scans to investigate the mtDNA–nDNA and mtCN–nDNA genotype associations. (v) Finally, we conducted mitochondrial genomewide genotype imputation of genome-wide association study (GWAS) data of more than 140,000 Japanese individuals, by using the population-specific WGS reference data. We then conducted a PheWAS [Phenome-wide association study] of 99 complex human disease and quantitative traits.

RESULTS

High-resolution mtDNA variant and haplogroup lists in the Japanese population

We re-analyzed the previously reported WGS data of the Japanese population (n = 1928)18. We realigned the WGS reads on the human reference genome GRCh37, which includes the revised Cambridge Reference Sequence (rCRS, NC_012920.1) as the human reference mitochondrial genome. The rCRS has been widely used in mitochondrial genome analyses including Japanese individuals. We only used the reads uniquely mapped on the mitochondrial region to avoid the contamination of nuclear copies of the mitochondrial genome (nuMTs)19. In this study, we focused on the analyses of homoplasmy. Then, we identified 2023 variant sites, of which 63 sites were multiallelic (the mean depth = 1488; Supplementary Data 1). Of these, 516 variants (25.5%) were newly identified in our WGS data. Minor allele frequency (MAF) spectra indicated that the majority of the identified variants were rare in Japanese; rare variants (MAF < 0.5%), low-frequency variants (0.5% ≤ MAF < 5%), and common variants (MAF ≥ 5%) accounted for 79.3%, 16.4%, and 4.3%, respectively (Supplementary Fig. 1). We observed clear concordances of the alternative allele frequencies with those in the previously reported two Japanese databases (1507 and 1025 variants with 3.5 KJPN [n = 3552] and Giib-JST mtSNP [n = 672], respectively; Supplementary Fig. 2)7,20,21. As previously reported22,23, mutational spectrum indicated a high transition to transversion (Ti/Tv) ratio of 16.44 (Supplementary Fig. 3).

Next, each individual was classified into the mtDNA haplogroup based on a variant list detected by the WGS using HaploGrep (v2.1.14)24. Haplogroups are classifications of the mtDNA haplotypes defined according to a set of the specific mtDNA variants. As mtDNA is a haploid genome, the detected variants could be directly used for haplogroup classification without phasing. Nomenclature of each haplogroup is hierarchically defined based on the number of the letters (from one to nine), which was divided into sub-haplogroups (e.g, “D4b” as three letters). The number of the haplogroups monotonically increased from the macrohaplogroup (n = 11 at one letter) to the sub-haplogroups with larger number of letters (n = 310 at nine letters; Supplementary Data 2). Increments in the number of the haplogroups became limited from seven to nine letters (Fig. 1a, b).

The frequency distribution of each haplogroup was obtained according to geographical regions in Japan (as defined by BioBank Japan Project: Hokkaido, Tohoku, Kanto-Koshinetsu, Chubu-Hokuriku, Kinki, Kyushu, and Okinawa from northeast to southwest areas of Japan; Supplementary Fig. 4)18 and all the populations from the 1000 Genomes Project Phase 3 (1KG, n = 2504; Fig. 1c)25. In the Japanese population, macrohaplogroups A, B, D, M, and N had more than 1% of frequencies across all the regions. In the regions from Hokkaido to Kyushu, macrohaplogroup D was most prevalent (>28%), followed by M and B. In contrast, the different spectrum was observed in Okinawa (the islandic region at the most southwest area in Japan), where M and B were more prevalent (37.5% and 25%, respectively) than D (18.8%). Furthermore, although the D4a and D4b haplogroups were prevalent from Hokkaido to Kyushu, the D4c haplogroup was prevalent in Okinawa (Supplementary Fig. 5). Although the haplogroup spectra in 1KG East Asians (EAS) were relatively similar to those in Japanese, R was more enriched in 1KG EAS, and D, G, and M were more frequent in Japanese. 1KG populations other than EAS showed distinct haplogroup patterns from the Japanese population. M, A, H, and L were most prevalent in 1KG South Asians, Americans, Europeans, and Africans (AFR), respectively. Especially, 1KG AFR showed the least diversity within macrohaplogroups, of which African-specific macrohaplogroup of L accounted for >90% of frequencies.

Fig. 1: High-resolution spectra of mtDNA haplogroups in the Japanese population

c Stacked bar plots of the frequencies of the macrohaplogroups within the geographical regions in Japan and subpopulations from 1KG. The geographical regions in Japan are defined as Hokkaido, Tohoku, Kanto-Koshinetsu, Chubu-Hokuriku, Kinki, Kyushu, and Okinawa from northeast to southwest areas of Japan, as described elsewhere42.

Fig. 1: High-resolution spectra of mtDNA haplogroups in the Japanese population.

From: Genetic and phenotypic landscape of the mitochondrial genome in the Japanese population

Unsupervised ML approaches deconvoluted mtDNA classification patterns. To evaluate how the defined haplogroups reflect the mtDNA diversity within a population, we conducted unsupervised clustering of the subjects based on the mtDNA variants and evaluated the concordances with haplogroup assignments. We adopted three unsupervised ML classification approaches of phylogenetic approach, principal component analysis (PCA), and uniform manifold approximation and projection for dimensionality reduction (UMAP). We first constructed the phylogenetic tree of the WGS individuals, which was illustrated as an unrooted tree type (Fig. 2a). The tree branch was mainly divided into the major two lineages at the root base, which were known as the “M” and “N” clusters. Each major lineage was further divided into sub-lineages corresponding to the sub-haplogroups. Next, we applied the linear dimensionality reduction technique of PCA and examined up to the 20 PCs. The explained variances were 12.6% for the top 20 PCs. As the two-dimensional plot of the PC1 and PC2 was difficult to fully capture the cluster classifications (Supplementary Fig. 6), we adopted the three-dimensional plot consisting of the top three PCs (Fig.2b). The major M and N clusters were also illustrated as distinct groups in the PCA plot. In contrast to the M cluster, the N cluster was further divided into sub-haplogroups, such as A5a, B4a, B4b, B4c, B5*, F1a, F1b, N9a, and N9b.

Fig. 2 Unsupervised ML-based sample classification of the Japanese mtDNA variant data. All the three unsupervised ML method classifications were performed on the WGS variant data of the Japanese population (n = 1928). a The unrooted phylogenetic tree using maximum-parsimony method. b The 3D plot of the top three components of PCA. c The plot of the two components of UMAP. Each color and marker represents haplogroups. Distinction between the M and N haplogroup clusters is displayed with dotted lines in each panel.

Fig 2

Fig 2 UMAP

UMAP is a recently developed nonlinear dimensionality reduction algorithm, which has a merit in preserving the topology of the local and global structure26. Although UMAP has been previously applied to high-dimensional biological data such as single-cell RNA sequencing27, here we applied it to the genomic data of the mtDNA variants. An application of UMAP could classify the subjects into >20 clusters, which was concordant with the pre-defined sub-haplogroups with three letters (Fig.2c). UMAP could differentiate the sub-haplogroups belonging to the same macrohaplogroup in more detail (e.g., D4a, D4b1, D4b2,D4c, D4e, and D4g belonging to D). On the other hand, we did not find the clear delineation between the M and N clusters, which was observed in the phylogenetic approach and PCA. Several sub-haplogroups with small sample sizes were clustered closely with other macrohaplogroups (e.g., M7c clustered with D macrohaplogroup). These observations could be the potential limitations of UMAP. As each ML classification method hadunique advantages to classify mtDNA variations, we would propose a value of applying multiple ML methods to comprehensively visualize haplogroup diversity within a population.Distinct characteristics of mtDNA variant structure from nDNA. Due to lack of recombination and higher mutation rate, LD structure and tag variant distribution in mtDNA are considered to be distinct from those in nDNA, whereas the details have been unclear especially in non-Europeans. Thus, we conducted a comprehensive assessment of these features in Japanese by using the WGS data. In addition to calculate the haplotype correlations (r2) between common mtDNA variant pairs (MAF≥5%,n=80), we estimated those obtained from the randomly selected autosomal phased haplotypes with adjustment on variant positional differences (±8.3 kbp). Fractions of the variant pairs with high correlations were relatively smaller in mtDNA than in nDNA (2.4% and 20.2% of the variant pairs with r2≥0.9 in mtDNA and nDNA, respectively; Fig.3a).When we checked distance-dependent decay of LD, we observed clear LD decay in the nDNA variant pairs according to physical distances between the variant pairs, which would reflect LD blocks (R=−0.092,P=1.0 × 10−7, as highlighted with red; Fig.3b). However, mtDNA variant showed no distance-dependent LD decay (R=0.022,P=0.21). Although there existed controversial discussions16,28, our results did not support the hypothesis of potential recombination events in mtDNA. Lack of recombination and relatively weak LD in mtDNA should propose that the common mtDNA variants are sparsely tagged bythe surrounding single-nucleotide polymorphisms (SNPs) when compared with nDNA. The numbers of the tag variants per common variant were smaller in mtDNA than in nDNA, even when the variant distances were adjusted (Fig.3c). As many as 13.8% of the common mtDNA variants did not have any tag variants with r2≥0.5, whereas only 5.0% in nDNA. Systematic visualization of pairwise LD patterns revealed that mtDNA variants did not constitute LD blocks among neighboring variants (Fig.3d). On the other hand, we observed multiple common haplotypes spanning the entire mtDNA (n=8), which might have been the consequence of lack of recombination and no distance-dependent LD decay. Interestingly, mtDNA variants without any tag variants were mostly identified in the D-loop region, one of the non-coding but functional regions in mtDNA. By using WGS data, we highlighted the characteristics of the mtDNA variants28, which were (i) no distance-dependent LD decay (i.e., absence of LD blocks) and (ii) sparse tagging of the common variants, in non-European population. In addition, we could newly detect existence of the common haplotypes spanning the entire mtDNA. No evidence of mtDNA–nDNA genotype association. Mitochondrial function is regulated not only by the genes encoded in mtDNA but also by those in nDNA. As these two typesof genes confer synergistic biological functions6, co-evolutionof the genetic variants embedded within them5, namely “mtDNA–nDNA genotype association”, has been suggested17. Thus, we tested the hypothesis that there might exist preferential transmission between nDNA and mtDNA at a genotype level. To explore footprints of the mtDNA–nDNA genotype association,we conducted a genome-wide scan to assess genotype distribution dependence between mtDNA and nDNA variants using the WGS data. We investigated 86 common mtDNA (MAF≥5%) and the genome-wide 7,124,343 nDNA variants (MAF≥1%), but there was no significant mtDNA–nDNA genotype association when multiple comparisons were considered (P=5.0 × 10−8/86=5.8 × 10−10; Fig.4a). Even when we focused on the variants located within ±10 kbp of the previously defined nDNA mito-chondrial genes (n=1105)29, we still did not detect a significant association. In addition, we investigated the associations by using the imputed GWAS data (n=141,552; see details in the next section). We analyzed the association between the 8 mtDNA(MAF≥5%) and the 7,402,102 nDNA variants (Rsq≥0.7 and MAF≥1%), but no significant signals were detected (P=5.0 ×10−8/8=6.3 × 10−9). We neither observed the enrichment of the association signals in the mitochondrial-related gene variants in nDNA (Fig.4b).

DISCUSSION

UMAP is a recently developed nonlinear dimensionality reduction algorithm, which has a merit in preserving the topology of the local and global structure26. Although UMAP has been previously applied to high-dimensional biological data such as single-cell RNA sequencing27, here we applied it to the genomic data of the mtDNA variants. An application of UMAP could classify the subjects into >20 clusters, which was concordant with the pre-defined sub-haplogroups with three letters (Fig. 2c). UMAP could differentiate the sub-haplogroups belonging to the same macrohaplogroup in more detail (e.g., D4a, D4b1, D4b2, D4c, D4e, and D4g belonging to D). On the other hand, we did not find the clear delineation between the M and N clusters, which was observed in the phylogenetic approach and PCA. Several sub-haplogroups with small sample sizes were clustered closely with other macrohaplogroups (e.g., M7c clustered with D macrohaplogroup). These observations could be the potential limitations of UMAP. As each ML classification method had unique advantages to classify mtDNA variations, we would propose a value of applying multiple ML methods to comprehensively visualize haplogroup diversity within a population.

Distinct characteristics of mtDNA variant structure from nDNA
Due to lack of recombination and higher mutation rate, LD structure and tag variant distribution in mtDNA are considered to be distinct from those in nDNA, whereas the details have been unclear especially in non-Europeans. Thus, we conducted a comprehensive assessment of these features in Japanese by using the WGS data. In addition to calculate the haplotype correlations (r2) between common mtDNA variant pairs (MAF ≥ 5%, n = 80), we estimated those obtained from the randomly selected autosomal phased haplotypes with adjustment on variant positional differences (±8.3 kbp). Fractions of the variant pairs with high correlations were relatively smaller in mtDNA than in nDNA (2.4% and 20.2% of the variant pairs with r2 ≥ 0.9 in mtDNA and nDNA, respectively; Fig. 3a). …

Our study demonstrated a successful imputation of the mtDNA variants by using the large-scale WGS as a reference panel. …

In conclusion, through the large-scale WGS and PheWAS of mtDNA, our study could comprehensively elucidate the genetic and phenotypic landscapes of mtDNA in the Japanese population.

Preparatory drawing (hanshita-e) for an illustrated book, mounted on card. Sea monster assailing a ship. Ink on paper.
© The Trustees of the British Museum

Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)

103 recently uncovered drawings by the Japanese painter and printmaker Katsushika Hokusai were added to the British Museum’s collection. The works, which resurfaced for the first time since 1948 in Paris last year, were created in 1829 for an unpublished book titled Great Picture Book of Everything(Banbutsu ehon taizen zu 万物絵本大全図 )

The small-scale works were previously owned by Art Nouveau jeweler Henri Vever, and the museum said in a release that they had been held in a private collection in France before their reemergence in 2019 at Piasa auction house in Paris. AFP reports details about the discovery, see excerpts below:

British Museum acquires ‘lost’ drawings of Japan’s Hokusai

London (AFP)

The British Museum said Thursday it had acquired 103 “lost” drawings from the 19th century of Japanese artist Hokusai, whose internationally renowned work includes the iconic “The Great Wave”.

The black-and-white drawings were composed in 1829, when Hokusai was 70, as illustrations for an unpublished book. They resurfaced in Paris in 2019 after they were last publicly recorded at an auction in 1948.

Their subjects range from the religious and historical to the mythological, and include previously unknown features of Hokusai’s oeuvre such as a musing on the origins of human culture in ancient China, the London museum said in a statement.

“These works are a major new re-discovery, expanding considerably our knowledge of the artist’s activities at a key period in his life and work,” honorary research fellow Tim Clark said.

“All 103 pieces are treated with the customary fantasy, invention and brush skill found in Hokusai’s late works and it is wonderful that they can finally be enjoyed by the many lovers of his art worldwide,” he said.

The drawings are available to view online and will feature in a future, free exhibition, the museum said.

Read the rest of the article here… and also more at Artnews’

British Museum Acquires 103 Recently Resurfaced, Rarely Seen Hokusai Drawings

Image of a maize weevil impression from the surface of a pottery fragment.
CREDIT: Prof. Hiroki Obata

Researchers from Kumamoto University have studied nationwide maize weevil impressions from 10,000 year-old pottery,  from the southern Japanese island of Tanegashima,  to pottery fragments from the Sannai-Maruyama site in northern Aomori., to Tatesaki archaeological site in Hokkaido.

The study comparing the differential in the size of  nationwide samples of weevil impressions in the west from the 20 per cent larger ones in the northeast revealed that pots in the west stored acorns while pots in northeastern climes stored chestnuts.

As chestnuts are not native to Hokkaido,  the presence of the maize weevils is evidence that the Jomon people of Tohoku  from south of Hokkkaido, carried supplies including chestnuts infested by weevils, over the Tsugaru Strait by ship.

***

See excerpts from the study below:

Hiroki Obata et al, Discovery of the Jomon era maize weevils in Hokkaido, Japan and its mean, Journal of Archaeological Science: Reports (2018). DOI: 10.1016/j.jasrep.2018.10.037 Dec 19, 2018

Ancient Japanese pottery includes an estimated 500 maize weevils
by Kumamoto University.

Researchers have discovered an ancient Japanese pottery vessel from the late Jomon period (4500-3300 BP) with an estimated 500 maize weevils incorporated into its design. The vessel was discovered in February 2016 from ruins in Hokkaido, Japan. This extremely rare discovery provides clues on the cultivation and distribution of chestnuts, food in the Jomon era, and the spirituality of ancient Japanese people.

Maize weevils are beetles of the Dryophthorinae subfamily, and are destructive pests of stored rice and grains. By 2003, Jomon-period pottery and pottery fragments containing foreign-body impressions had been collected by various researchers from multiple archeological sites around Japan. Surveys of these impressions exposed hundreds of seed and insect traces on and in the pottery. Over the years, researchers found that maize weevils constituted over 90 percent of all recorded insect impressions.

In 2010, Professor Obata’s research group from Kumamoto University (KU) in Japan found maize weevil impressions in 10,000 year-old pottery that had been recovered from the southern Japanese island of Tanegashima. They showed that maize weevils, which were thought to have come from the Korean Peninsula, had damaged stored food, such as acorns and chestnuts, long before rice cultivation began in the area.

In 2012, the KU research group found maize weevils impressions in pottery fragments from the Sannai-Maruyama site in the northern Japanese prefecture of Aomori. The fact that weevils inhabited an area with a cold winter is an indicator for the distribution food by humans and a warm indoor environment that persisted throughout winter. It is presumed that weevil infestation of stored food was well underway in the Jomon period.

Interestingly, when comparing the body size of 337 maize weevil impressions found nationwide, the team discovered that the body length of maize weevils from eastern Japan was about 20 percent longer than that of western Japan. It is presumed that this body-length discrepancy is due to the different nutritional values between the types of foods they infested—the sweet chestnuts of eastern Japan vs the acorns of western Japan.

Chestnuts are not native to Hokkaido and previous studies surmised that people carried them to the northern Japanese island. The discovery of weevils at the Tatesaki archaeological site in Hokkaido is evidence that the Jomon people of Tohoku (south of Hokkaido) carried supplies, including chestnuts infested by weevils, over the Tsugaru Strait by ship.

See more photos and read more about the research here.

References and further readings:

Hiroki Obata et al, Discovery of the Jomon era maize weevils in Hokkaido, Japan and its mean, Journal of Archaeological Science: Reports (2018). DOI: 10.1016/j.jasrep.2018.10.037 Dec 19, 2018

Ancient Japanese pottery includes an estimated 500 maize weevils -The rare discovery of a vessel with a high number of weevils provides clues to life in ancient Japan (Kumamoto University website) The images above are used in compliance with the image use restrictions from this webpage. See more photos and read more about the research here.

An exhibit featured this week at Tama Center’s Jomon Village Archaeological Center reveals that the Jomon people collected shellfish mostly during the spring to summer seasons.

Exhibit at Tama Center’s Jomon Village Archaeological Center

After eating the shellfish, the empty shells would be deposited in a dumping site in a location away from the village as can be seen in the left foreground of the replica village below.

Scientists have studied the shells found in the shell mound and determined that they were gathered mostly during the spring to summer period.

Shellfish of Nishigahara She’ll Mound collected by season

How were they able to do this? They were able to do so by studying the growth line of the outer shell layers.

Here is a cross-section of the Nishigahara shellfish mound, which is essentially the remains of a large kitchen dump of the Late to Final Jomon period.

All rights reserved. Text and photos of exhibits by Heritage of Japan.

First things first…

I have begun a series on the Jomon Village Historic Garden of the Tama Hills (which I have visited probably over 10 times!). Archaeologists have excavated 770 out of the 964 sites from the Tama Hills (aka the Tama New Town to locals). A “Jomon village” based on settlement traces was recreated, with archaeological exhibits from 40 years of diggings on display at the adjacent Exhibition Hall run by the Tokyo Metropolitan Archaeological Center.

People began living in this area around 32,000 years ago, towards the end of the Ice Age when the climate was colder and more like Hokkaido’s, and when people hunted game such as Giant Elk and Naumann elephants, salmon from the rivers and large animals that lived in the coniferous forests. (They left behind stone tools and burnt stones from their fires, but I will post in another episode about the Upper Palaeolithic traces and remains, because the focus of this post is the Jomon people from the Maedakochi site).

The Maedakochi site (see photo at the top of the page) is currently the central exhibit being featured at the Exhibition Hall of the Jomon Village.

The discovery of the Maedakochi site is an important one as it is one of the earliest sites of the Jomon people belonging to the Incipient Jomon Period radiocarbon dated to 15,500 years ago. Being at the transition phase between the Upper Paleolithic and the Neolithic Jomon Period, the excavation of the site reveals important clues to neolithic lifestyles, such as why early pottery was invented and what the ceramic pots contained and were used for. Numerous salmon teeth and bones were found at the site too. Much recent literature has emerged based on analysis of the archaeological evidence from this site, indicating that the Jomon neolithic package likely was part of an entire Aquatic Neolithic complex extending to Sakhalin Island and to the Russian Far East Amur region. To know more, read the rest at The earliest Jomon developed and used pottery for fishing salmon and molluscs 15,500 years ago

Click here to see video https://www.bbc.com/reel/embed/p07lq60x

All kind of megalithic pyramids have awed the ancient local populace for generations. Japan’s ancient Kofun tombs remain relatively unknown or unvisited locations by tourists. This BBC video documentary clip gives a rare English view into the labour-intensive creations of the early centuries of the First Millennium.