South Asian admixture in Japanese people


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I noticed that many Japanese people score between 0.5% and 2% of South Asian admixture in various calculators, including Dodecad K12 and K12b and HarappaWorld K16. I thought at first that it might be a misattribution of very ancient admixture linked to Y-haplogroups C and D, but I recently saw some Japanese results from Living DNA, and that individual scored about 1.8% of South Asian too, which according to the admixture map was closest to the Balochi of southern Pakistan. He also had a surprising 1.9% of northern Near East (Caucasus/Turkey). I ran the same sample in HarappaWorld, but he got 1.89% of South Indian and 0% of Baloch.

I checked the Dodecad K12 spreadsheet for other East Asian results. The Japanese samples from the HapMap and HGDP all scored 0% of South Asian, but the Dodecad participants scored 1.5%. Individual samples I ran also scored around 1.5%. So there seems to be a discrepancy between the full genomes from the HapMap and HGDP and the commercial (23andMe, FTDNA and Living DNA) genomes. I observed the same thing with the Chinese samples. The commercial ones got 0.5% of South Asian, but those from HapMap scored 0%. The Cambodians from the HapMap had 10.5% of South Asians though, while the Thai scored even higher at 15.7%. The Dai of SW China and Vietnam scored 1.4% and the ethnic Vietnamese 3.2%.

The K12b spreadsheet showed 0% for all Japanese samples, even the commercial ones. However that's probably a mistake considering that the 4 samples I ran got between 0.2% and 1.2%, with an average of 0.7%. Cambodians scored even higher, at 15.2%, while the Burmese have 18.7%.

Based on the commercial samples analysed by the Dodecad K12 and K12b, it seems that the Japanese could possess about 1% of South Asian admixture, and that it could have come through South East Asia, as it is completely absent in East Siberia, Korea or northern China.

In my experience, HarappaWorld is a more reliable calculator than Dodecad (or most others for that matter). So I checked the HarappaWorld's average scores by population. There are two Japanese values. I believe that the first (99% NE Asian) may be an ethnic Ainu, as I have never seen such scores in regular Japanese people. The other one gives 74% NE Asian, 11% Siberian, 11% SE Asian and 1% South Indian.

Both the North and South Han Chinese lack any trace of that South Indian admixture, but the Vietnamese have 1% like the Japanese. The Khmer-Cambodians score 13% (+1% of NE Euro), which is just between Dodecad K12 and K12b. The Thai score 14% pf South Indian + 2% of Baloch, 2% of Caucasian and 1% of NE Euro.

So it does seem that the Japanese have a bit of South Asian admixture and the most likely explanation is that it came from South East Asia, although no historical migration is recorded. Once again DNA uncovers traces of prehistoric migrations about which nobody knew anything.
Actually this South Asian, might be the so called noise or not mutated parts of DNA from way back, or alleles hard to classify, . Have a look at these ancient samples some of them contain parts of almost every admixture. Times before admixtures drifted modern ways.

T732095Oase1 F999936C-V199 M561778 M225927 M325047KO1, I-L68F999935K-M526 F999914R
Romania, Central Balkans40kya Kostenki37kya Vestonice, Czech 24KyaEl Miron Spain18 kya Hungarian, Tiszaszőlős-Domaháza7.7 kya Ust'-Ishim, Siberia45kya Mal'ta24kya
Run time4.52 Run time18.02 Run time Run time6.76 Run time9.43 Run time21.09 Run time8
S-Indian26.35 S-Indian13.18 S-Indian14.06 S-Indian5.3 S-Indian- S-Indian26.72 S-Indian10.13
Baloch6.99 Baloch12.49 Baloch1.68 Baloch- Baloch- Baloch8.4 Baloch24.09
Caucasian2.19 Caucasian- Caucasian- Caucasian- Caucasian- Caucasian- Caucasian-
NE-Euro16.81 NE-Euro29.02 NE-Euro41.3 NE-Euro54.59 NE-Euro80.37 NE-Euro6.51 NE-Euro40.14
SE-Asian14.75 SE-Asian4.28 SE-Asian0.8 SE-Asian5.79 SE-Asian- SE-Asian12.11 SE-Asian-
Siberian0.22 Siberian1.75 Siberian3.98 Siberian0.82 Siberian- Siberian2.05 Siberian-
NE-Asian1.21 NE-Asian- NE-Asian- NE-Asian- NE-Asian- NE-Asian3.84 NE-Asian-
Papuan9.3 Papuan5.16 Papuan4.65 Papuan2.84 Papuan0.53 Papuan10.9 Papuan0.7
American- American3.32 American3.75 American1.27 American- American1.13 American17.71
Beringian- Beringian1.43 Beringian- Beringian- Beringian- Beringian2.7 Beringian6.74
Mediterranean7.61 Mediterranean18.76 Mediterranean23.93 Mediterranean28.84 Mediterranean18.59 Mediterranean8.14 Mediterranean-
SW-Asian2.94 SW-Asian5.89 SW-Asian2.99 SW-Asian- SW-Asian- SW-Asian4.65 SW-Asian-
San5.62 San1.24 San1.27 San0.12 San- San2.44 San0.3
E-African3.02 E-African1.82 E-African0.42 E-African- E-African- E-African7.27 E-African-
Pygmy- Pygmy0.92 Pygmy- Pygmy- Pygmy- Pygmy1.74 Pygmy0.19
W-African2.99 W-African0.73 W-African1.18 W-African0.42 W-African0.5 W-African1.39 W-African-
It's possible some Indians reached Japan, especially during the spread of Buddhism to Eastwards. Most SE Asians have 10-20% South Asian admixture so some absorbed minorities (Thai, Philippono) would also increase Indian like admixture.
It's possible some Indians reached Japan, especially during the spread of Buddhism to Eastwards. Most SE Asians have 10-20% South Asian admixture so some absorbed minorities (Thai, Philippono) would also increase Indian like admixture.
Yes, it is possible, but I think it is more likely that these are genetic artifacts from way back.
Did Indians or Cambodians reached Oase1 40kya? We have to keep in mind that these admixtures were composed on modern people.
I can't confirm myself this informaiton, but I think it'd be interesting to put this up for discussion: according to a Japanese guy whom I talked with about the formation of the Japanese people, the Jomon people who preceded the Yayoi (Japanese "proper" people) weren't the ancestors of the still surviving Ainu people, but a 3rd ethnicity that occupied Japan and was totally admixed and absorbed by the Yayoi, forming a mixed ethnicity which eventually also encroached on the Ainu and assimilated part of them. Those Jomon, still according to that Japanese guy, were found to have skull features closer to Austronesian people in Southeast Asia than to Siberian ones (perhaps he meant Southern China and the archipelagos near to it).

If that's really true and an indication of a Southeast Asian origin for at least a part of the Jomon people, then this could solve the mystery of this tiny South Asian component in modern Japanese: the Southeast Asian people who migrated northeastward brought a minor South Asian admixture. Y-DNA O-P31 is most common in Southeast Asia and, far away, in Japan/Korea. Also, some linguists still propose (very controversially, though) that there are connections between Japanese and Austronesian languages, though I wouldn't buy it too much.
Ishigaki Island is one of the westernmost islands in Japan. Due to its geographical location, it is considered to have played a significant role in the migration route from Southern Asia to the Japanese archipelagos. Recently, human remains were excavated from Shiraho-Saonetabaru Cave, constituting the first physical evidence of human occupation on Ishigaki Island. In order to investigate the genetic makeup of the ancient Ishigaki people and to assess their genetic relationship with other Asian populations at a molecular level, we analysed the single nucleotide polymorphisms of the coding region of mtDNA that defines the haplogroups of these individuals. Because of the poor quality of the DNA extracted from the ancient material, it was not possible to analyse all samples. Among the 10 samples considered in this study, ancient DNA data was successfully extracted from five individuals. MtDNA haplogroups show geographic specificity within Asia; the existence of haplogroup B4e and M7a in this population hints at their linkage with Southeast Asia and the Late Pleistocene Ryukyu Islands.

Though small in number, the distribution of mtDNA haplogroups in this period provides insights into regional population history. Haplogroups B4 and R are the most prevalent in Southeast Asia, especially in the coastal region (Trejaut et al. 2005), indicating that this haplogroup may have been introduced to Japan from Southeast Asia. Interestingly, haplogroup B was also found in ancient Chinese samples (Fu et al. 2012). It seems that the ancestral population of coastal East Asia and Island Southeast Asia was enriched by the founder lineages of haplogroup B4, and the Ryukyu Islands may be one of the northernmost regions where this population arrived in the Palaeolithic period. This finding indicates that the southeast influx into the ancient Ryukyu population affected their genetic makeup and that the ancestors of the Aboriginal Taiwanese or Asian coastal region populations might be the main source of this haplogroup in the Ryukyu Islands.

Japan's southernmost island is called Okinawa or Ryukyu and the genetic study (Shinoda and Adachi 2017) identified the existence of mtDNA haplogroup B4e in ancient Ryukyu samples, which may have been introduced to Japan from Southeast Asia. B4e is common among populations native to Southeast Asia and this can be taken as the genetic evidence of ancient Polynesian migration to the Ryukyu Islands in the Palaeolithic period.
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