From the 15th century, waves of Japanese settlers began crowding out Ainu communities on Honshu island and pushing them northwards. The settlers also brought infectious diseases that caused Ainu populations to fall. Ainu land was redistributed to Japanese farmers.
In 1899, the Japanese government passed an act which labelled the Ainu “former Aborigines”, ostensibly declaring that the Ainu had been integrated into the Japanese population – the act, together with the various assimilation policies had the drastic effect of eroding Ainu identity and traditions. The Meiji government’s 1899 assimilation policies resulted in the ban of the Ainu language and Ainu children being given Japanese names and put into Japanese schools. As a result of these policies, many Ainu people suffered discrimination and became ashamed of their language and culture. The act continued for a hundred years.
The 1899 act was finally officially reversed on June 6th, 2008, when the Japanese government passed a resolution adopt a resolution that, for the first time, formally recognised the Ainu as “an indigenous people who have their own language, religion and culture”.
Today only small numbers of Ainu remain, and they constitute one of Japan’s most marginalised groups. The Ainu are thought to number around 25,000 (official sources) while unofficially, they are believed to number around 200,000 or more since many Ainu still do not disclose their roots out of fear of discrimination.
Origins: Where did the Ainu come from?
Historically, they spoke the Ainu language and have traditionally been considered the descendents of the Jomon or post-Jomon people of Japan. In their Yukar Upopo (Ainu Legends) is told, “The Ainu lived in this place a hundred thousand years before the Children of the Sun came”.
Groundbreaking genetic mapping studies by Cavalli-Sforza have shown a sharp gradient in gene frequencies centered in the area around the Sea of Japan, suggesting that the area was a center of expansion for the ancestral Jomon-Ainu populations (thought to have occurred during the Jomon period although the studies cannot fix clear dates). This expansion of populations is thought to be the third most important genetic movement in Eurasia (after the “Great expansion” from the African continent, to Arabia and adjacent parts of the Middle East, as well as to the northern regions of Eurasia, (particularly Siberia from regions to the south).
According to genetic tests, the Ainu people belong mainly to Y-DNA haplogroup D2 (a haplogroup that is found uniquely in and frequently throughout Japan including Okinawa with its closest relations being Tibetans and Andaman Islanders in the Indian Ocean). On the paternal side, the vast majority (87.5%) of the Ainu were, according to a 2004 study to be of Asian-specific YAP+ lineages (Y-haplogroups D-M55* and D-M125), that were only distributed in the Japanese Archipelago. The Ainu exhibited no other Y-haplogroups (i.e. none of the common East Asian C-M8, O-M175*, and O-M122* haplogroups) and shared no other Y-DNA in common in mainland Japanese and Okinawans.
According to a 2005 study, haplogroup D originated in Eurasia OR in sub-Saharan Africa, but reached higher frequency outside of Africa and during the human migration out of Africa, and that its emergence coincided with the spread of domestication and emergence of cities from the Middle East. Below is the representation of the evolutionary trail and distribution of the haplogroup D chromosome from the same 2005 study:
According to a study led by Hammer, one of the most useful and widely studied Y-linked polymorphisms is known as the “Y Alu polymorphic” (YAP) element (Hammer 1994). This polymorphism has resulted from the single and stable insertion of a member of the repetitive Alu family at a specific site (locus DYS287) on the long arm of the human Y chromosome during the past 29,000-334,000 years.
The frequency of Y chromosomes carrying the YAP element (YAP+) varies greatly among human populations from different geographic locations: Global surveys have shown that sub-Saharan African populations have the highest overall frequency of YAP chromosomes, followed by populations from northern Africa, Asia, Europe, the New World, and Oceania. However, an intriguing finding by Hammer (1997) that the ancestral YAP haplotype is the Asian haplotype 3 from which other haplotypes 4 and 5 evolved and derived, suggesting the possibility that YAP haplotype 3 originated in Asia and migrated to Africa. This hypothesis is supported by the finding of high frequencies of haplotype 3 in some Asian populations (i.e., -50% in Tibet) and by the observation of higher levels of diversity (based on the number and frequency of alleles at the DYS1 9 microsatellite locus) associated with Asian versus African haplotype 3 chromosomes. Chandrasekhar et al. 2007, have also argued for the Asian origin of the YAP+ on the basis of evidence from the presence of the YAP insertion in Northeast Indian tribes and Andaman Islanders with haplogroup D that suggests that some of the M168 chromosomes gave rise to the YAP insertion and M174 mutation in South Asia. Others such as Underhill and Bravi stand by an African origin for YAP+. The prevalence of the YAP+ allele in central Asian populations was alternatively suggested by some (Altheide and Hammer 1997; Jin and Su 2000; Karafet et al. 2001) to point to a genetic contribution to the east Asian populations from the northwest, probably from central Asia.
In Japan, the frequency of the YAP element ranges from 33% in Shizuoka to 56% in Okinawa, with an intermediate frequency of 39% in Aomori. The frequency is significantly higher in Okinawa than in Shizuoka (Fisher’s exact test, P = .0284), but the Okinawa frequency is not significantly different from the Aomori frequency (P= .2196). However, the frequency in Okinawa is significantly higher than in the combination of the two Honshu prefectures (P = .0256). 87.5% of the Ainu were, according to a 2004 study to be of Asian-specific YAP+ lineages. By contrast, YAP was absent from Korean male samples. This result is consistent with previous surveys that showed the YAP element to be polymorphic in Japan but absent in other Asian and Oceanic populations. In terms of antiquity as well as the relationship of the different YAP+ lineages, another interesting conclusion was made by the Hammer analysis: “All pairwise F., values were calculated on the basis of YAP allele frequencies in Japan and Taiwan, as well as in 13 other populations (Hammer 1994; Spurdle et al. 1994b). The neighbor-joining method was used to generate a clustering diagram (fig. 2). All Asian and Oceanic populations, except the Japanese, form a single group that is closely allied with the European populations. The greatest genetic distance is the one that separates these Eurasian populations from the Japanese and African populations. The Okinawan and Honshu populations are separated; the former population clusters in the middle of the African groups, and the latter population clusters between the African and Eurasian samples.”
In other tests of two out of a sample of sixteen – i.e. 12.5% of Ainu men were found to belong to Haplogroup C3, which is the most common Y-chromosome haplogroup among the indigenous populations of the Russian Far East and Mongolia. A separate test (a sample of four Ainu men) found that one in four Ainu men belonged to haplogroup C3.
The presence of the C3 haplogroup is believed to reflect the genetic influence of the nomadic Nivkhs people of northern Sakhalin Island, with whom the Ainu have long-standing cultural interactions.
M7 has been detected so far in China, Vietnam, the West Siberian Mansi, Mongols and island Southeast Asia, apart from from the Korean peninsula and Japanese islands where the subclades expanded. Haplogroup M7a has been found in Southeast Asia-Taiwan, but mainly among Japanese and Ryukyuans. Haplogroup M7 is seen as characteristically distributed in East Asia while M7a is regarded as its daughter group specific for (pre-Jomon to Jomon) Japanese populations (while M7b2 is specific for Korean populations). The 2002 study puts the estimated settlement times for M7a, M7b and M7c at between 6,000 and 18,000 years … although it suggests that the M7a and M7b pioneer settlers may have entered even earlier ~ 30,000 years at a time when the Yellow Sea had fallen dry and was more like a large lake , but that the populations became bottle-necked toward the Last Glacial Maximum (LGM). Beyond the ancestral M7, it has been noted that M7 nested subclades are not shuffled between the Koreans and Japanese, so the M7a, M7b and M7c starlike clades are thought to represent the post LGM resettlement process, with M7a in the area of the southern Japanese Sea. This settlement event would have been contemporary with the spread of microblades, e.g. of the Suyanggae-type and before the onset of the Jomon culture.
A 2010 Russian Derenko study clarified that D4 has an age of 24–28 kya and is further subdivided into fifteen principal subclades (D4a–D4j, D4k’o’p’, D4l–D4n, D4q), which range from ~6 to ~28 kya. These D4 subclades have a very distinctive geographic distribution, which is highly informative about the demographic history of the northern Asia. The study showed that all the subclades are found in eastern Asia and that they had already expanded before the LGM, with their oldest lineages being present in the eastern Asia. In particular, most of the eastern Asian subclades of haplogroup D show coalescence ages of between 15 and 42 kya, thus suggesting that some of them were already present here before the LGM.
Relationship to other populations
While Y-chromosome haplogroup markers D2 and mtDNA D4 and M7a (and M7a1) indicate that Ainu are related to other Japanese populations in the rest of Japan, the various mtDNA studies indicate that Ainu men took wives from a variety of locations throughout Central Asia, Siberia and the Russian Far East.
It has also been noted that the Ainu of today are not pure descendants of the Jomon, but rather from the Jomon-Yayoi mixture of the Satsumon/Emishi people. The Emishi were Jomon descendants with Yayoi assimilated cultural traits. It is believed from place names in Tohoku that the Emishi spoke the Ainu language as well. As the Yayoi people pushed north, it is thought that the Emishi people advanced on Hokkaido, infusing the Jomon culture in Hokkaido with an agrarian society and with metal-using traits from the Yayoi culture. Citing Gary Crawford, Paula Nielsen writes in “Origins of the Ainu People of Northern Japan” that “the Satsumon culture recently discovered in Hokkaido was descended from the Tohoku Emishi of northeastern Honshu who migrated to Hokkaido, bringing a fused culture of the Middle Yayoi, along with the ancient physical traits of the Jomon”.
Of note, is that although the Ainu of Japan have traditionally considered descendents of the Jomon or post-Jomon Satsumon people (indicated by the D or D2 gene marker), they have been found to carry the Y-chromosome DNA haplogroup C3 showing a paternal lineage from North Asia including Sakhalin, while mitochondrial DNA gene marker (Y-haplogroup C-M217*) shows similar maternal inputs — they are gene characteristics also shared by the Nivkhi in northern Sakhalin, and Koryaks in the Kamchatka Peninsula. Hence, the Ainu can be said to be related to the Nivkhi and the Koryaks. However, since the Nivkhi do not carry haplogroup D which has a dominant presence in the Ainu, the migration is seen to have occurred unidirectionally, from the North into Hokkaido. This appears to be confirmed by the research of the Saitou laboratory at the National Institute of Genetics, which concluded that the Ainu of Hokkaido (as well as ancient Jomon) showed the closest genetic affinity to native Okinawans.
Based on non-metric cranial traits studies, the Ainu people occupy an intermediate position between Jomon and Northeast Asians (the Okhotsk) on the one hand, and between and to a lesser extent the recent Hokkaido Ainu.
The Ainu are also considered to occupy an intermediate position between Jomon and Northeast Asians on the one hand, and between Jomon and the Native Americans on the other. Thus studies on the variations among the three Ainu series from Sakhalin Island, the northeast Hokkaido coast, and central/south Hokkaido shown in the study, conclude that there has been admixture between the ancestors of recent Ainu and northern groups such as the Okhotsk people in the post-Jomon periods.
Current molecular genetic evidence suggest that the initial founders of the Americas emerged from an ancestral population of less than 5,000 individuals that evolved in isolation, likely in Beringia, from where they dispersed south after approximately 17 kya. Recent findings about the peopling of northern Asia reconstructed by archaeologists suggest that modern humans (haplogroups C and D) colonized the southern part of Siberia around 40 thousand years ago (kya, pre-LGM) and the far northern parts of Siberia and ancient Beringia, by approximately 30 kya. Haplogroup D4, the most represented of D clades, is subdivided into fifteen principal subclades (D4a–D4j, D4k’o’p’, D4l–D4n, D4q), which range from ~6 to ~28 kya when using the sequence variation of the entire genome and from ~3 to ~42 kya but all subclades are found in eastern Asia, with the eastern Asian lineages the oldest among them. The expansion of haplogroup D4 settlers took place in northern Asia post LGM. Of the subclades shared with eastern Asians, D4b1a is thought to represent a separate Upper Paleolithic migration initiated northward from the Altai-Sayan region of southern Siberia around 11-20 kya. D4b1a falls into two branches, one of which, D4b1a2, is largely restricted to northern Asia and its major subclade, D4b1a2a, resulted from the earliest split from the Yukaghir mtDNA within D4b1a2.
D2 (the D4 subcluster with coalescence ages of 11.1±4.3 kya), is thought to have its most likely homeland in the Baikal region of southern Siberia, from where it expanded in the Holocene northward to northeastern Asia and further to northern America. Other remaining northern Asian-specific clusters of haplogroup D are deemed significantly younger with the age estimates not exceeding 5–8 kya.
The Paleolithic Siberian population expansions are also thought to be responsible for a migration to the Americas and that North America may have had ancestral relatives of the Jomon and Ainu among its early settlers. The best-known evidence that may support this theory is probably Kennewick Man.
The Ainu are thought to be connected to ancestry that might be in common with those of Native Americans – one connection lies in the detection of the common presence of Haplogroup X in both populations. Haplogroup X is traceable to ancient remains of Altaians in the Gobi desert, as well as to the Altai populations today, but ultimately to the Basque populations. Although it is not at the moment, known how the Haplogroup X arrived in the Ainu ancestral lines, nor to Native American populations in ancient times, a 1998 study concluded that Native American founders may have had Caucasian ancestry. For more on this see DNA analyses and inferred genetic origins of the Ainu.
On the other hand, a study on the HLA gene (alleles and haplotypes) frequencies on North, Meso, South American AmeriIndians showed that AmerIndians have little relatedness with Asians, according to genealogy studies except that North-Americans only share one haplotype (A*24-B*40-DRB1*1401-DQB1*0503) with Taiwanese and Japanese in low frequencies.
The final clarification may have come from a study showing that all type 2A JC Virus strains from North and South Americans are closely related to strains in present-day Japan. The strains of JC virus present in Navajo in New Mexico (speakers of an Athapaskan language in the Na-Dene language phylum) were found to be of a prototype type 2A strain of a northeast Asian genotype found in Japan. The partial VP1 gene sequences of the JC virus from the Salish people in Montana (speakers of a language in the Salishan group in the Amerind family) and from the Guarani Indians of Argentina (speakers of the Tupi-Guarani language and Equatorial branch of the Amerind family) were however shown to be closely related to several strains variants of strains found in Japan.
To find out more about the Ainu people, watch these video presentations “Ainu: Spirit of a Northern People” by the Arctic Studies Center and “Ainu: the first peoples of Japan“, a documentary film by Rhawan Joseph, Ph. D
Morphological affinities between Jomon and Ainu: reassessment based on nonmetric cranial traits”: Shigematsu, Masahito; et al. Anthropological Science Vol. 112: 161-172 (2004) doi:10.1537/ase.00092.
“Origins and genetic features of the Okhotsk people, revealed by ancient mitochondrial DNA analysis”. Sato, Takehiro; et al. (2007). Journal of Human Genetics 52 (7): 618–627. doi:10.1007/s10038-007-0164-z
The History and Geography of Human Genes p253, Cavalli-Sforza ISBN 0-691-08750-4
Jomon genes: using DNA, researchers probe the genetic origins of modern Japanese – Science News, Feb 15, 1997 by John Travis
The Boone Collection – Image Gallery: Ainu Artifacts. Retrieved on 2008-05-08
Genetic origins of the Ainu inferred from combined DNA analyses of maternal and paternal lineages Source: Journal of Human Genetics, Volume 49, Number 4, April 2004 , pp. 187-193(7)
“NOVA Online – Island of the Spirits – Origins of the Ainu” by Gary Crawford
“Origins of the Ainu People of Northern Japan“, Suite 101, Jan 9, 2010 by Paula I. Nielson
‘Diet officially declares Ainu indigenous’, Japan Times, 7 June, 2008 Ito, M, Am J Hum Genet. 1995 April; 56(4): 951–962.
Y chromosomal DNA variation and the peopling of Japan. M F Hammer and S Horai Am J Hum Genet. 1995 April; 56(4): 951–962 PMC1801189
Evidence for a Possible Asian Origin of YAP+ Y Chromosomes. Am. J. Hum. Genet. 61:462-466, 1997, Tasha K. Altheide and Michael F. Hammer
Chandrasekar A, Saheb SY, Gangopadyaya P, et al. (2007). “YAP insertion signature in South Asia“. Ann. Hum. Biol. 34 (5): 582–6. Doi:10.1080/03014460701556262. PMID 17786594.
Underhill et al (2000). “The phylogeography of Y chromosome binary haplotypes and the origins of modern human populations“. Ann. Hum. Genet. 65 (Pt 1): 43–62.
Claudio M. Bravi et al., Tracing the origin and geographic distribution of an ancestral form of the modern human Y chromosome, Revista Chilena de Historia Natural, 74: 139-149; 2001
Ongoing Adaptive Evolution of ASPM, a Brain Size Determinant in Homo sapiens, Nitzan Mekel-Bobrov, et al., Science 9 September 2005: 309 (5741), 1720-1722. [DOI:10.1126/science.1116815]
Sjöberg, Katarina V. (1993). The Return of the Ainu: Cultural Mobilization and the Practice of Ethnicity in Japan. Studies in Anthropology and History. 9. Chur: Harwood Academic Publ.. ISBN 3718654016. OCLC 27684176.
Hammer, Michael F.; et al. (2006). “Dual origins of the Japanese: Common ground for hunter-gatherer and farmer Y chromosomes”. Journal of Human Genetics 51 (1): 47–58. doi:10.1007/s10038-005-0322-0.
The Peopling of the Americas: A Complex Issue AmeriIndian, Na-Dene, Aleut and Eskimo first inhabitants International Journal of Modern Anthropology, Int. J. Mod. Anthrop. 3 (2010) Available online at http://www.ata.org.tn
mtDNA haplogroup X: an ancient link between Europe/Western Asia? American Journal of Human Genetics, 1998 ISSN: 0002-9297
The Emerging Limbs and Twigs of the mtDNA Tree, Mol Biol Evol (2002) 19 (10): 1737-1751
Origin and Post-Glacial Dispersal of Mitochondrial DNA Haplogroups C and D in Northern Asia Derenko M, Malyarchuk B, Grzybowski T, Denisova G, Rogalla U, et al. 2010 Origin and Post-Glacial Dispersal of Mitochondrial DNA Haplogroups C and D in Northern Asia. PLoS ONE 5(12): e15214. doi:10.1371/journal.pone.0015214
Strains of JC virus in Amerind-speakers of North America (Salish) and South America (Guarani), Na-Dene-speakers of New Mexico (Navajo), and modern Japanese suggest links through an ancestral Asian population. Am J Phys Anthropol. 2002 Jun;118(2):154-68.
Archaeology in the Kuril Islands: Advances in the Study of Human Paleogeography and Northwest Pacific Prehistory, Ben Fitzhug et al., Arctic Anthropology, Vol 39, nos 1-2 pp 69-94, 2002 The article examines the human occupation patterns in the Kuril Islands and touches upon the relationship between the Okhotsk, Satsumon and Ainu in the chain of islands.
Abstract: “Within this vast region, scattered Late Pleistocene technological assemblages that include leaf-shaped bifaces and stemmed projectile points found in coastal or peri-coastal sites from Japan and Kamchatka to western North America, and much of South America may support the idea that a coastal migration contributed to the peopling of the Americas.”
Hong Shi, et al., Y chromosome evidence of earliest modern human settlement in East Asia and multiple origins of Tibetan and Japanese populations BMC Biology 2008, 6:45 doi:10.1186/1741-7007-6-45
“Genetic, Linguistic and Archaeological Perspectives on Human Diversity in Southeast Asia“, Recent Advances in Human Biology Vol. 8 by Li Jin Mark Seielstad, Chunjie Xiao p. 50