Overall, Japanese are closest to Tibetans and Han Chinese, but only marginally more so than to the Koreans.
The Ainu who are widely considered to be of the “old” proto-Mongoloid stock closely related to the Tibetan Buryat and Yakut peoples, and descended from the Jomon people who lived in the Tohoku area until they were later pushed northwards into Hokkaido, afterwhich they resided around the Sea of Okhotsk, mainly Hokkaido, Sakhalin, Kuril Islands and the tip of Kamchatka. However, the DNA sequences show that Ainu are actually more remotely distanced from the Jomon than is commonly believed, as they were influenced by Siberians (as with Koreans). Evidence is the haplogroup C3 (no subclade) occurs at moderately high frequencies among these populations.
The above mtDNA studies relate to maternal line gene flow, the following Y chromosome study of male-mediated gene flow shows a slightly different picture but the sharing of the common haplotypes still reveal strong affiliations of both Japanese and Koreans to the Chinese and of the Japanese to the Koreans:
Population studies of genetic markers such as HLA variation and mitochondrial DNA have been used to understand human origins, demographic and migration history. Recently, diversity on the nonrecombining portion of the Y chromosome (NRY) has been applied to the study of human history. Since NRY is passed from father to son without recombination, polymorphisms in this region are valuable for investigating male-mediated gene flow and for complementing maternally based studies of mtDNA. Haplotypes constructed from Y-chromosome markers were used to trace the paternal origins of Korean. By using 38 Y chromosome single nucleotide polymorphism markers, we analyzed the genetic structure of 195 Korean males.
The Korean males were characterized by a diverse set of 4 haplogroups (Groups IV, V, VII, X) and 14 haplotypes that were also present in Chinese.
The most frequent haplogroup in Korean was Group VII (82.6%). It was also the most frequent haplogroup in Chinese (95%) as well as in Japanese (45%). The frequencies of the haplogroups V, IV, and X were 15.4%, 1%, and 1%, respectively. The second most frequent haplogroup V in Korean was not present in Chinese, but its frequency was similar in Japanese.
Source of study: Sunghee Hong, Seong-Gene Lee, Yongsook Yoon, Kyuyoung Song /University of Ulsan College of Medicine, 388-1 Poongnap-dong, Songpa-ku, Seoul, Korea
Finally, the Y haplogroup chart below shows the relations between the various groups of Asia and their varying degrees of affinity or remoteness to each other.
MtDNA YAP haplogroups (Ainu, Honshu and Okinawan Japanese relationships seen)
Y Haplogroups of the world
Another study published in 2005 on 81 sets of Y chromosomes of six populations across Japan showed:
- The Japanese have at least two very deep pre-Yayoi ancestral Y chromosome lineages (D-P37.1 and C-M8) that descend from Paleolithic founders who had diverged from the mainland and that were then isolated from those populations on the mainland for a very long time. Scientists thought these D lineages to mean the Jomon populations in Japan once upon a time the same ancestors as Tibetans from central Asia who are found with the highest frequency of continental D lineages is found in central Asia. Scientists hypothesized that the area between Tibet and the Altai Mountains in northwestern China is the most likely geographic source of Paleolithic Japanese founding Y chromosomes. ( Historical records suggest that Tibetan populations were derived from ancient tribes of northwestern China that subsequently moved to the south and mixed with the southern natives in the last 3,000 years.) A
separate recent mtDNA study on the Haplogroup M12 – the mitochondrial component of Japanese genes, the counterpart of Y chromosome D lineage – also confirmed the direct connections of Japanese haplotypes with Tibet. This rare haplogroup is possessed only by mainland Japanese, Koreans, and Tibetans, with the highest frequency and diversity in Tibet. These Paleolithic ancestors were thought to have migrated into Japan sometime around 20,000 years ago.
Interestingly, the Y chromosome study also suggested that there could be one other Japanese Paleolithic founding that found its way to the Japanese archipelago, these early ancestors carried the Y-STR haplogroup, C-M8, a Y-chromosome haplotype that is related to Indian and central Asian C chromosomes. This set of C-M8 Y chromosomes were thought to be carried into Japan sometime around just before 12,000 years ago.
The same study also concluded that Jomon genes have survived till today showing up at high frequencies in Japanese populations today (34.7%) The scientists having charted the Haplogroup D chromosome-carrying populations who were found to exist at frequencies distributed in an inverted U-shaped pattern across the archipelago, with the highest frequencies occurring in the southern Ryukyuans (Okinawa) and the northern Ainu (Hokkaido). The results suggested to scientists that not only the distinct genetic contribution of Paleolithic ancestors but that they had intermarried (admixed) with the later income Yayoi migrant populations who were of a separate and different haplotype O lineage.
In a nutshell, what we can evince and conclude from all the DNA data that has been presented is that the Japanese people are a people with mixed diverse origins, formed from many waves of migrations from various locations in the remote past as well as in the more recent past.