Category Archives: Genetics

Genetic Origins of Jomon and Japanese



Journal Publications on Genetic Origins of Jomon and Japanese

We have been very interested in the Jomon culture of Japan. There seem to be pockets here and there with significant Jomon components in current society, for example in Hida and in Tohoku. Anecdotally people have mentioned “Jomon DNA” and we wondered what is it? We have surveyed the literature on the genetics of the Jomon indigenous people of the Japanese archipelago and we present a brief summary of our findings.

1.  Hammer et al, 1995, Y chromosomal DNA variation and the Peopling of Japan, Note paternal ancestry.

Discussion.  YAP element is present in 42% of Japanese and absent in Taiwanese. YAP is absent in non-Japanese Asians inc. Taiwanese, Chinese, and Koreans. YAP is a marker of Jomon male lineages. Y-chromosome of modern Japanese is 39% Yayoi, 61% Jomon. YAP+ entered Japan with (only) Jomon, YAP- with both Jomon and Yayoi.

A broad picture of gene flow to Japan:

30K YA — Jomon enter on land bridges

20K YA — YAP+ and YAP- occur in Jomon

10K YA — Isolation of Jomon due to end of ice age

2.3 K YA — Yayoi enter and bring more YAP-

2.  Tanaka et al, 2004, Mitochondrial genome variation in eastern Asia and the peopling of Japan, A long and important paper on the peopling of Japan based on maternal ancestry.

Abstract of Abstract:  New clades and subclades emerged. Confirmed present-day Japanese have closest genetic affiity to northern Asian populations, esp. Koreans. Revealed a high degee of differentiation in Paleolithic Japanese. Detected ancient southern and northern migrations (Ryukyu, Ainu). Found direct connections with Tibet, like that of Y-chromosomes. Suggests that “Japan could be included in an area of migratory expansion to Continental Asia. All the theories that have been proposed up to now to explain the peopling of Japan seem insufficient to accommodate fully this complex picture.”

Archaeological record:  attests that humans reached Japan 30,000 YA when still connected to Continent by two land bridges, north and south. Neolithic period in Japan is known as the Jomon period. Later, Continental people arrived, initiating the Yayoi period.

Results for Macrohaplogroup M  (D, …) :

M12 is a rare haplogroup, only in mainland Japanese, Koreans, and Tibetans (Tibetans having highest frequency 8% and diversity 50%). p. 1847 says that it is the mitochondrial counterpart of the Y-chromosome marker YAP+, a marker from C. Asia to mainland Japan.

Results for Macrohaplogroup N:  (A, Y, N9a, N9b, F, B) :

F is a subgroup of R9. Six mutations define F1. Only subhaplogroup F1b is well represented in the Japanese inc. Ainu and Ryukyuan. Highest diversities are in eastern China including Taiwan (100%).

Lineage Sorting and Population Pooling

Japanese, inc Ainu and Ryukyuans, part of a big group of Korean, Buryat, Tibetans, and N. Chinese. Ainu was the first differentiated, and Ryukyuans separated later. Japanese and Koreans still comprised a single group

The Peopling of Japan

Table 4 Frequency results.  Japanese relate by far to Koreans, less so to northern Chinese. Ryukyuans present smallest distance to Buryats, then S Chinese. Ainu cloest to mainland Japanese, Koreans, and N. Chinese. 

Table 4 Sequence matches.  Japanese relate first to Koreans and second to Buryats. Ryukyuans to Buryats then to Koreans. Ainu greatest affinities toward Kamchatka. Ryukyuans had a dual northern and southern Asian background previous to  admixture with mainland Japanese. Great distance and low identity values for Ainu-Ryukyuan pairs, indicating notable maternal isolation.

Some conclusions:  Ancient Japanese inhabitants came from northern Asia, later immigration came from southern Asia. Ainu have a rather recent Siberian influence. Ryukyuans show an older radiation from southern China. Macrohaplogroup N is larger in Ainu (50%) than in Ryukyuans (15%). Both of these populations are considered largely isolated but “they most probably had different maternal origins.”


“… the actual Japanese population is the result of a complex demographic history…” The Ryukyuans and Ainu are well differentiated from the mainland Japanese, yet that have common pecularities shared with the mainland Japanese (highest frequences in Asia for M7a, M7b2, and N9b. For both, their closest relatives are northern populations. “…our results are strikingly coincident with the previously proposed northern origin and influences received by the Japanese.” Horai’s (1997) mt studies demonstrated closest relation with Koreans. Some of these are substantially recent roots. Although it is well-documented that there was substantial immigration from Korea during the Yayoi period, mainland Japanese do share some of their haplotypes exclusively with Southern China (2.5%), N. China (1.5%), C Asia (1.5%), and Indonesia.

“In summary, Japan could have received several northern and southern Asian maternal inputs since Paleolithic times, with notable northern Asian immigrations through Korea in the late Neolithic and more specific gene flows from western Asia, Siberia, and southern Islands.”

3.  Hammer, 2006, Dual origins of the Japanese: common ground for hunter-gatherer and farmer Y chromosomes,

Haplogroup D as a Jomon marker. Haplogroups D and C began expansions in Japan ~20,000 and ~12,000 years ago, respectively. These are the Jomon hunter-gatherers with Central Asian origin. The Yayoi farmers with haplogroup O and SE Asian origin began to expand only 4,000 years ago. These are the dual origins. D presence in Japanese males was 35%, ranging from 75% in Ainu to 26% in Tokushima. Outside Japan, D is extremely rare. Presence of haplogroup O was 52% overall of six populations (Ainu, Aomori, Shizuoka, Tokushima, Kyushu, Okinawa). O is not found in Ainu. Kyushu 62%, Honshu 51%, Okinawa 38%.

4.  Stoneking and Delfin, 2010, The human genetic history of East Asia: Weaving a complex Tapestry,  A review paper.

East Asia encompasses the region bordered by Ural Mountains in west, by Himalayan Plateau in SW, by Bering Strait in NE, and SE Asia. Presents two figures: mtDNA haplogroups and Y-chromosome haplogroups. Note in the latter, the yellow D-M174 in Tibet and Japan, very dissimilar to Korea.

5.  Adachi, Noboru, et al, Mitochondrial DNA analysis of Hokkaido Jomon skeletons: Remnants of archaic maternal lineages at the southwestern edge of former Beringia, 2011.  Abstract only. 

~22,000 YA is coalescence time of haplogroups N9b, D4h2, G1b, and M7a which were observed in the Jomon skeletons. All of these haplogroups except M7a were observed with high frequencies in SE Siberians but were absent in SE Asians. This implies that the Hokkaido Jomon were direct descendants of Paleolithic Siberians.  

Illustration above is from Wa-pedia.