Different Jōmon maternal lineages N9b, M7a and G in the japanese archipelago

The Jōmon name is associated with a specific culture that entered Japan 12,000 years ago but it is used to describe all earlier inhabitants of the Japanese archipelago prior to the Yayoi migrations, although it is now evident that they were quite different themselves. The Jōmon mtdna haplogroups mainly included N9b and M7a, which showed an opposite cline from Hokkaido to Ryukyu for N9b and from Ryukyu to Hokkaido for M7a. This was already observable in the Tōhoku region where N9b starts to decrease and M7a starts to increase. Also, mtdna G exhibits remarkable frequency and diversity in eastern Japan and northeast Asia.

M7a has been found in Jōmon samples from all Japanese archipelago. M7a1 was most frequently found in western Jōmon and Ryukyuans and also Koreans while M7a2 in Tōhoku Jōmon and Udege with 19.6%. It coalesced around 25,000 years ago and came from Taiwan around 20,000 years ago via a southern route as opposed to the Kyushu and Hokkaido route that virtually every other haplogroup in Japan used to come. It is most likely connected with the dispersal of Japonic languages. M7a1 is likely connected with the western Japanese and Ryukyuan dialects and M7a2 is connected with the eastern Japanese and Hachijō dialects. Modern samples from the Gifu-Aichi region which linguistically belongs to the eastern dialects are also positive for M7a2 which supports this connection. Additionally, all south Korean M7a belongs to M7a1 and probably moved there during the middle Jōmon period.

N9b has been found in Jōmon samples from Hokkaido to the Ryukyu islands with a frequency from 57,5% in Hokkaido in 16,5% in Okinawa and probably corresponds to the historical Ainu people. It has a coalescence age of 4,000-14,800 years. Unlike M7a and G it doesn't come from mtdna haplogroup M but from mtdna haplogroup N which is common in west Eurasia, but also east Eurasia and Australia. Within the northern Jōmon it is broken down in many branches N9b1, N9b2 etc. During the latest centuries, the Ainu received maternal geneflow from the Nivkhs in the form of mtdna Y with a frequency of 33-43% and from the Japanese in the form of mtdna M7a1 with a frequency of 16%.

G may pertain to the so called Ezo or Emishi group which is purported to have been different than both south Jōmon and later Ainu. It was pushed northern by the ancestors of the Ryukyuans that would become the Japanese. It has a coalescence age of 35,000 years and probably came earlier to Japan that the other two mtdna haplogroups. G is mostly found in eastern Japan and around the Okhotsk sea and its frequency falls in western Japan and Korea but its diversity is lively in every place both in the islands and the mainland. It is a widespread haplogroup in northern East Asia and northeast Asia and would naturally occupy Japan as well which is roughly on the same latitude. But its diversity within Japan is also interesting. There are different branches attested like G1b and G4. G1b attains relatively high frequncy in the speakers of the Kamchatkan languages. But especially in the southern part of Kamchatka peninsula it increased more because of the Ainu who settled there coming from the Kurils.

Both distributions of N9b and G seem to correspond with the historically attested range of the Ainu languages and apparently they may have initially had different linguistic ancestors that nevertheless would both come from the Okhotsk region.

There were additionally smaller Jomon lineages, namely D4h2, M7b'c and M10. The rest of the haplogroups found in modern Japanese, D4, D5, M8, CZ, A, N9a, B and F are thought to have come with the Yayoi migrations.

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1. Genetic origins of the Ainu inferred from combined DNA analyses of maternal and paternal lineages, Tajima 2004
2. Mitochondrial Genome Variation in Eastern Asia and the Peopling of Japan, Tanaka 2004
3. Interdisciplinary study of the Jomon skeletons excavated from the Kanto region of Japan, Adachi 2013
4. Ancient genomic DNA analysis of Jomon people, Kanzawa 2013