Ancient Jomon DNA show Jomon populations were more heterogeneous than previously thought


Choongwon Jeong et al., Deep History of East Asian Populations Revealed Through Genetic Analysis of the Ainu, Genetics 202(1) · October 2015 with 65 Reads
DOI: 10.1534/genetics.115.178673 Excerpt from the abstract:

“We find that the Ainu represent a deep branch of East Asian diversity more basal than all present-day East Asian farmers. However, we did not find a genetic connection between the Ainu and populations of the Tibetan plateau, rejecting their long-held hypothetical connection based on Y chromosome data. Unlike all other East Asian populations investigated, the Ainu have a closer genetic relationship with northeast Siberians than with central Siberians, suggesting ancient connections among populations around the Sea of Okhotsk. We also detect a recent genetic contribution of the Ainu to nearby populations, but no evidence for reciprocal recent gene flow is observed.”

This 2016 article puts the origins of the Ainu squarely with Northeast Asian populations, particularly northeast Siberians, and rejects the hypothesis (namely Hong Shi’s that follows immediately below) that there is a Y-chromosome component of the Ainu lineage that originated in Tibetan populations.

Hong Shi., Y chromosome evidence of earliest modern human settlement in East Asia and multiple origins of Tibetan and Japanese populations

We proposed that D-M174 has a southern origin and its northward expansion occurred about 60,000 years ago, predating the northward migration of other major East Asian lineages. The Neolithic expansion of Han culture and the last glacial maximum are likely the key factors leading to the current relic distribution of D-M174 in East Asia. The Tibetan and Japanese populations are the admixture of two ancient populations represented by two major East Asian specific Y chromosome lineages, the O and D haplogroups.

HLA Genetic Diversity and Linguistic Variation in East Asia (Chap. 16), Laurent Sagart et al.

Northern-southern differentiation. Geneticists are currently debating patterns of genetic differentiation between  northern and southern East Asian populations. According to one view, all East Asian populations share a unique origin in mainland Southeast Asia, with a further migration to the north (Su et al. 1999, Jin and Su 2000). Revised versions of this theory state that northern populations differ genetically from those located further south due to late genetic contributions from Central Asia (Chu et al. 1998, Karafet et al. 2001, Jin and Su 2000), but the time and magnitude of these contributions are not clear. A second view, known as the “pincer model”, more explicitly invokes two independent migrations into East Asia along a southern and a northern route, with the influence from the Central Asian gene pool being predominant in the north (Ding et al. 2000)

The study also found that “genetic profiles do not reveal a clear population
structure. Nevertheless, a finer examination shows that some alleles reach
relatively high frequencies in specific East Asian populations. ” and that the “patterns indicate that some East Asian populations deeply differ genetically from each other, and that a high level of genetic diversity characterizes this continental area. …higher than values estimated for Europe … and much higher than values for Sub-Saharan Africa.

While the HLA polymorphism reveals a complex genetic structure in East Asian, and especially Austronesian, populations, some of our findings confirm, or support, various aspects of linguistic classification. First, although Japanese, Korean and Altaic proper (Mongolic, Manchu-Tungusic and Turkic) are included by some authors into such macrophyla as Altaic and Eurasiatic, few, if any, regard Koreo-Japonic and Altaic proper as linguistically very close. Not surprisingly, we observe a major genetic differentiation between Koreo-Japonic on the one hand and Altaic-proper on the other hand.

(Hashimoto 1986). While very few linguists would argue for a genetic connection between Chinese and Altaic, the Altaic features in northern Chinese dialects clearly are of the type resulting from imperfect learning of Chinese by Altaic speakers, suggesting that Altaic speakers in northern China have been shifting to Chinese en masse in historical times: our genetic observations support Hashimoto’s altaicization hypothesis. …”

Di D, Sanchez-Mazas A Challenging views on the peopling history of East Asia: the story according to HLA markers.Am J Phys Anthropol. 2011 May;145(1):81-96. doi: 10.1002/ajpa.21470. Epub 2011 Jan 4.

Di D, Sanchez-Mazas, HLA variation reveals genetic continuity rather than population group structure in East Asia Immunogenetics. 2014 Mar;66(3):153-60. doi: 10.1007/s00251-014-0757-6. Epub 2014 Jan 22.

Genetic differences between Northeast Asian (NEA) and Southeast Asian (SEA) populations have been observed in numerous studies. At the among-population level, despite a clear north-south differentiation observed for many genetic markers, debates were led between abrupt differences and a continuous pattern. At the within-population level, whether NEA or SEA populations have higher genetic diversity is also highly controversial. In this study, we analyzed a large set of HLA data from East Asia in order to map the genetic variation among and within populations in this continent and to clarify the distribution pattern of HLA lineages and alleles. We observed a genetic differentiation between NEA and SEA populations following a continuous pattern from north to south, and we show a significant and continuous decrease of HLA diversity by the same direction. This continuity is shaped by clinal distributions of many HLA lineages and alleles with increasing or decreasing frequencies along the latitude. These results bring new evidence in favor of the “overlapping model” proposed previously for East Asian peopling history, whereby modern humans migrated eastward from western Eurasia via two independent routes along each side of the Himalayas and, later, overlapped in East Asia across open land areas. Our study strongly suggests that intensive gene flow between NEA and SEA populations occurred and shaped the latitude-related continuous pattern of genetic variation and the peculiar HLA lineage and allele distributions observed in this continent. Probably for a very long period, the exact duration of these events remains to be estimated.


The peopling of East Asia by the first modern humans is strongly debated from a genetic point of view. A north-south genetic differentiation observed in this geographic area suggests different hypotheses on the origin of Northern East Asian (NEA) and Southern East Asian (SEA) populations. In this study, the highly polymorphic HLA markers were used to investigate East Asian genetic diversity. Our database covers a total of about 127,000 individuals belonging to 84 distinct Asian populations tested for HLA-A, -B, -C, -DPB1, and/or -DRB1 alleles. Many Chinese populations are represented, which have been sampled in the last 30 years but rarely taken into account in international research due to their data published in Chinese. By using different statistical methods, we found a significant correlation between genetics and geography and relevant genetic clines in East Asia. Additionally, HLA alleles appear to be unevenly distributed: some alleles observed in NEA populations are widespread at the global level, while some alleles observed in SEA populations are virtually unique in Asia. The HLA genetic variation in East Asia is also characterized by a decrease of diversity from north to south, although a reverse pattern appears when one only focuses on alleles restricted to Asia. These results reflect a more complex migration history than that illustrated by the “southern-origin” hypothesis, as genetic contribution of ancient human migrations through a northern route has probably been quite substantial. We thus suggest a new overlapping model where northward and southward opposite migrations occurring at different periods overlapped


N. Adachi, K. Shinoda, K. Umetsu, Y. Dodo, Mitochondrial DNA analysis of the Jomon and Epi-Jomon individuals in Hokkaido, Japan. American Journal of Physical Anthropology doi: 10.1002/ajpa.20923

“From the morphological point of view, prehistoric populations in Hokkaido are considered to have been least influenced by Yayoi immigrants. Therefore, genetic study of these people can be expected to provide important information on the genealogy of the early settlers of the Japanese archipelago. In the present study, we examined the genealogy of the seventy-six Jomon and Epi-Jomon skeletons excavated in Hokkaido, Japan by mitochondrial DNA analysis. To identify their genealogy securely, we analyzed the coding region of mtDNA by using amplified product-length polymorphisms (Umetsu et al., 2001, 2005) and direct sequencing. We also sequenced the segments of two hypervariable regions of mtDNA, and assigned the mtDNA under study to relevant haplogroups using the known mtDNA databases.

Haplogroups D4, G1, M7a, and N9b were observed in the individuals, and N9b was by far the most predominant. The requencies of the haplogroups were quite different from any modern populations including Ainu and Okinawans. Haplogroup N9b is hitherto observed almost only in Japanese populations; therefore, this haplogroup might be the (pre-) Jomon contribution to the modern Japanese mtDNA pool.”

Mitochondrial DNA analysis of Jomon skeletons from the Funadomari site, Hokkaido, and its implication for the origins of Native American

Ancient DNA recovered from 16 Jomon skeletons excavated from Funadomari site, Hokkaido, Japan was analyzed to elucidate the genealogy of the early settlers of the Japanese archipelago. Both the control and coding regions of their mitochondrial DNA were analyzed in detail, and we could securely assign 14 mtDNAs to relevant haplogroups. Haplogroups D1a, M7a, and N9b were observed in these individuals, and N9b was by far the most predominant. The fact that haplogroups N9b and M7a were observed in Hokkaido Jomons bore out the hypothesis that these haplogroups are the (pre-) Jomon contribution to the modern Japanese mtDNA pool. Moreover, the fact that Hokkaido Jomons shared haplogroup D1 with Native Americans validates the hypothesized genetic affinity of the Jomon people to Native Americans, providing direct evidence for the genetic relationships between these populations. However, probably due to the small sample size or close consanguinity among the members of the site, the frequencies of the haplogroups in Funadomari skeletons were quite different from any modern populations, including Hokkaido Ainu, who have been regarded as the direct descendant of the Hokkaido Jomon people. It appears that the genetic study of ancient populations in northern part of Japan brings important information to the understanding of human migration in northeast Asia and America.

Miroslava Derenko, et al.,  Origin and Post-Glacial Dispersal of Mitochondrial DNA Haplogroups C and D in Northern Asia

Kanzawa H., et al., Ancient mitochondrial DNA sequences of Jomon teeth samples from Sanganji, Tohoku district, Japan Anthropological Science

Bannai M. et al., Analysis of HLA genes and haplotypes in Ainu (from Hokkaido, northern Japan) supports the premise that they descent from Upper Paleolithic populations of East Asia  Tissue Antigens, Volume 55, Number 2, 1 February 2000, pp. 128-139(12)

Scheinfeldt Laura, Population Genomic Analysis of ALMS1 in Humans Reveals a Surprisingly Complex Evolutionary History

“…four of the ALMS1nsSNPs … (rs3813227, rs6546838, rs2056486, and rs10193972) were genotyped, and we used two additional genotyped SNPs (rs3820700 and rs1052161) to distinguish between Haplogroups D1 and D2. The worldwide distribution of ALMS1 haplogroups (fig. 4) reveals a particularly interesting pattern where Haplogroup D is nearly fixed in East Asian samples (98.9%), but is at considerably lower frequency in the American samples (43.0%). Similarly, the frequency of Haplogroup D1 in the American samples is extremely low (0.8%) compared with East Asian samples (24.6%). Conversely, Haplogroup A is common in the Americas (57.03%) but nearly absent in East Asia (0.01%). This geographic distribution is peculiar given that Asia was the likely source population of the Americas (Karafet et al. 1997; Mulligan et al. 2004; Goebel et al. 2008;Volodko et al. 2008). The simplest explanation for these data is that Haplogroups A and D were both present in Asia before the founding of the Americas, but Haplogroup D dramatically increased in frequency in East Asia sometime after the colonization of the Americas 15–20 kya (Karafet et al. 1997; Mulligan et al. 2004; Goebel et al. 2008; Volodko et al. 2008).”

Fig. 4

Fig. 4

Distribution of ALMS1 haplogroups in 52 populations. Haplogroup frequencies are indicated with pie charts. Haplogroups A, D1, and D2 are shown in magenta, green, and blue, respectively.

Adachi N., Mitochondrial DNA analysis of the human skeleton of the initial Jomon phase excavated at the Yugura cave site, Nagano, Japan See pdf full text

Abstract: In the present study, we performed a detailed mitochondrial DNA (mtDNA) analysis of a skeleton of the initial Jomon era unearthed from the Yugura cave site in Nagano, Japan, which was dated to 7920–7795 calBP by direct 14C dating. mtDNA of the Yugura skeleton was designated to haplogroup D4b2, which is widely observed in present-day East Asians, including the Japanese, but is absent in Hokkaido Jomon people. This finding indicates that the basal population of Japan was heterogeneous with respect to their mtDNA lineage. This is the first report on the genotype of the people from the initial phase of the Jomon period.


“Haplogroup  D4bb is widely observed among East Asian populations including Japanese populations (e.g. Yao et al., 2002; Umetsu et al, 2005; Lee et al., Nohira et al,m 2010). ALthough the timing, origin and route of migration of this haplogroup to the Japanese archipelago is still unknown, D4b mt DNA were already present in the center of the Japanese archipelago during the initial phase of the Jomon era.

Prehistoric anthropological significance…

With regard to the early Jomon samples, the Hokkaido Jomon individuals contained haplogroups M7a(Kita-KoganeNo.7) and D4h2 (Kita-Kogane no. 9; Irie No. 12) (Adachi et al., 2011). Inferring from the HVS1 sequence motif (16223-16291-16362). anther early Jomon mtDNA sample (Urawa 1: Horai et al., 1989) can be assigned to haplogroup E1a1a. [origin of E alleged to be exclusively indigenous to ISEA see A Mitochondrial Stratography for ISEA]. The addition of haplogroup D4b detected in the Yugara skeleton indicates that at least four haplogroups were likely resent by the early stage of the Jomon period.

Interestingly, in the late Upper Paleolithic period, microblade cultures that were mainly  distributed in the western part of Japan (e.g. the Yadegawa industry) spread to central Japan in conjunction with northern-style microblade culture (Oda, 2003; Ambiru, 2010; Inada, 2010; Tsusumi, 2010, 2011). In addition the lithic source area study indicated that there might have been a long-distance trade of raw materials in the upper Paleolithic period (Suzuki, 1973a, b; Ono, 2007; Amibiru, 2010; Tsusumi, 2011).

These archaeological findings indicate that there might have been a wide range of human interactions accompanying the exchange of material cultures prior to the Jomon era. Therefore it is possible that the heterogeneity of the early Jomon people  might have arisen from that of the Upper Paleolithic people. Moreover the presence of the E1a1a in Urawa 1 may hint that wide-scale human interaction was still observed in the Jomon era, since this haplogroup seems to date to the early Holocene (7200 years, 95% CI: 4600-9800 years) and to originate in Southeast Asia.)  [Note: New study alleges origin of E is exclusively indigenous to ISEA see A Mitochondrial Stratography for ISEA].

Tajima A., et al., Genetic origins of the Ainu inferred from combined DNA analyses of maternal and paternal lineages J Hum Genet. 2004;49(4):187-93. Epub 2004 Mar 2.

The Ainu, a minority ethnic group from the northernmost island of Japan, was investigated for DNA polymorphisms both from maternal (mitochondrial DNA) and paternal (Y chromosome) lineages extensively. Other Asian populations inhabiting North, East, and Southeast Asia were also examined for detailed phylogeographic analyses at the mtDNA sequence type as well as Y-haplogroup levels. The maternal and paternal gene pools of the Ainu contained 25 mtDNA sequence types and three Y-haplogroups, respectively. Eleven of the 25 mtDNA sequence types were unique to the Ainu and accounted for over 50% of the population, whereas 14 were widely distributed among other Asian populations. Of the 14 shared types, the most frequently shared type was found in common among the Ainu, Nivkhi in northern Sakhalin, and Koryaks in the Kamchatka Peninsula. Moreover, analysis of genetic distances calculated from the mtDNA data revealed that the Ainu seemed to be related to both the Nivkhi and other Japanese populations (such as mainland Japanese and Okinawans) at the population level. On the paternal side, the vast majority (87.5%) of the Ainu exhibited the Asian-specific YAP+ lineages (Y-haplogroups D-M55* and D-M125), which were distributed only in the Japanese Archipelago in this analysis. On the other hand, the Ainu exhibited no other Y-haplogroups (C-M8, O-M175*, and O-M122*) common in mainland Japanese and Okinawans. It is noteworthy that the rest of the Ainu gene pool was occupied by the paternal lineage (Y-haplogroup C-M217*) from North Asia including Sakhalin. Thus, the present findings suggest that the Ainu retain a certain degree of their own genetic uniqueness, while having higher genetic affinities with other regional populations in Japan and the Nivkhi among Asian populations

Of the 16 haplotypes found, 6 were unique to the Okhotsk people, whereas the other 10 were shared by northeastern Asian people that are currently distributed around Sakhalin and downstream of the Amur River. The phylogenetic relationships inferred from mtDNA sequences showed that the Okhotsk people were more closely related to the Nivkhi and Ulchi people among populations of northeastern Asia. In addition, the Okhotsk people had a relatively closer genetic affinity with the Ainu people of Hokkaido, and were likely intermediates of gene flow from the northeastern Asian people to the Ainu people. These findings support the hypothesis that the Okhotsk culture joined the Satsumon culture (direct descendants of the Jomon people) resulting in the Ainu culture, as suggested by previous archaeological and anthropological studies.

To investigate the genetic characteristics of the ancient populations of Hokkaido, northern Japan, polymorphisms of the ABO blood group gene were analyzed for 17 Jomon/Epi-Jomon specimens and 15 Okhotsk specimens using amplified product-length polymorphism and restriction fragment length polymorphism analyses. Five ABO alleles were identified from the Jomon/ Epi-Jomon and Okhotsk people. Allele frequencies of the Jomon/Epi-Jomon and Okhotsk people were compared with those of the modern Asian, European and Oceanic populations. The genetic relationships inferred from principal component analyses indicated that both Jomon/Epi-Jomon and Okhotsk people are included in the same group as modern Asian populations. However, the genetic characteristics of these ancient populations in Hokkaido were significantly different from each other, which is in agreement with the conclusions from mitochondrial DNA and ABCC11 gene analyses that were previously reported.


Takeshi Nishiyama, et al., Detailed Analysis of Japanese Population Substructure with a Focus on the Southwest Islands of Japan PLoS One. 2012; 7(4): e35000.  2012 April 3. doi: 10.1371/journal.pone.0035000

Masashi Tanaka, Ken-ichi Shinoda, Mitochondrial Genome Variation in Eastern Asia and the Peopling of Japan  Genome Res. 2004 October; 14(10a): 1832–1850. doi: 10.1101/gr.2286304

There are two principal branches of mtDNA Haplogroup D (found quite frequently in Central Asia, where it makes up the second most common mtDNA clade (after H)), D4 and D5’6. D1 is a basal branch of D4.

D4 (3010, 8414, 14668): The subclade D4 is the most frequently occurring mtDNA haplogroup among modern populations of northern East Asia, such as Japanese, Okinawans, Koreans, and Mongolic- or Tungusic-speaking populations of northern China. D4 is also the most common haplogroup among the Buryats and Khamnigans of the Buryat Republic, the Kalmyks of the Kalmyk Republic, and the Telenghits and Kazakhs of the Altai Republic. D4 is also widespread and diverse in the Americas.

D5’6 (16189): Mainly in East Asia and Southeast Asia, especially among Chinese people

[For comparison: D2, which occurs with high frequency in some arctic and subarctic populations (especially Aleuts), is a subclade of D4e1 parallel to D4e1a and D4e1c, so it properly should be termed D4e1b. / D3, which has been found mainly in some Siberian populations and in Inuit of Canada and Greenland, is a branch of D4b1c.]

D4 haplogroups and subclades signals found in Japan:

Japanese(0.412) D4(xD4b)=75, D5(xD5a)=10, D5a=1, D4b=1  Maruyama 2003

Northern Kyushu(0.414)  D4b=26, D4(xD4a, D4b, D4e, D4g, D4j)=24, D4a=19, D4e=16, D5=10, D4g(xD4g1)=8, D4j=3 Umetsu 2005

Japanese Tokai (0.411)  D4b=34, D4a=26, D4(xD4a, D4b, D4e, D4g, D4j)=24, D5=14, D4e=13, D4j=3, D4g(xD4g1)=2 Umetsu 2005

Japanese Hokkaido (0.415) D4a=24, D4b=21, D4(xD4a, D4b, D4e, D4g, D4j)=21, D4e=11, D5=10, D4g=2, D4j=1 Asari 2007

Tohoku (0.399) D4a=31, D4b=30, D4(xD4a, D4b, D4e, D4g, D4j)=29, D4e=17, D4g(xD4g1)=11, D5=10, D4j=4, D4g1=2 Umetsu 2005

Japanese Tokyo (0.356) D4=39, D5=3 Zheng 2011

Japanese Miyazaki (0.300) D4(xD4a,D4b1,D4b2b)=16, D4a=5, D4b2b=3, D5a(xD5a2)=3, D4b1=1, D5(xD5a)=1, D5a2=1Uchiyama 2007

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