Jomon: Paleolithic Contingent in Modern Japanese Oct 28, 2015 13:14:40 GMT
Post by Admin on Oct 28, 2015 13:14:40 GMT
Haplogroup N (mtDNA)
Haplogroup N (mtDNA) is the ancestral haplogroup to almost all European haplogroups and Jomon haplogroup frequencies are 50% (n = 2) for N9b and 50% (n = 2) for M7a2, which are called the Jomon genotype. While Haplogroup M is an Asian mtDNA haplogroup, Haplogroup N is a West Eurasian (Caucasian) mtDNA haplogroup, which can be also found at high frequencies in Scandinavia, and it can be considered that the Jomon people were half Caucasian in their genetic heritage. A 2003 sequencing on the mitochondrial DNA of two Cro-Magnons (Paglicci 52 and Paglicci 12) further identified the mtDNA as Haplogroup N.
We investigated mitochondrial DNA haplogroups of four Jomon individuals from the Sanganji shell mound in Fukushima, Tohoku district, Japan. Partial nucleotide sequences of the coding and control region of mitochondrial DNA were determined. The success rate of sequencing increased when we analyzed short DNA sequences. We identified haplogroups from all four samples that were analyzed; haplogroup frequencies were 50% (n = 2) for N9b and 50% (n = 2) for M7a2. Haplogroup N9b has been previously observed in high frequencies in the other Tohoku Jomon, Hokkaido Jomon, Okhotsk, and Ainu peoples, whereas its frequency was reported to be low in the Kanto Jomon and the modern mainland Japanese. Sub-haplogroup M7a2 has previously been reported in the Hokkaido Jomon, Okhotsk, and modern Udegey (southern Siberia) peoples, but not in the Kanto Jomon, Ainu, or Ryukyuan peoples. Principal component analysis and phylogenetic network analysis revealed that, based on haplogroup frequencies, the Tohoku Jomon was genetically closer to the Hokkaido Jomon and Udegey people, than to the Kanto Jomon or mainland modern Japanese. The available evidence suggests genetic differences between the Tohoku and Kanto regions in the Jomon period, and greater genetic similarity between the Tohoku Jomon and the other investigated ancient (Hokkaido Jomon, Okhotsk) and modern (Siberian, Udegey in particular) populations. At the same time, the Tohoku and Hokkaido Jomon seem to differ in sub-haplotype representations, suggesting complexity in Jomon population structure and history.
Figure 1 Geographical location of Sanganji site, and other sites of Tohoku Jomon people.
Two of the four Sanganji Jomon individuals belonged to haplogroup N9b (Table 5, Table 6). Haplogroup N9b has been observed in the northern Jomon populations at high frequencies: Hokkaido Jomon, 64.8% (Adachi et al., 2011); Tohoku Jomon, 63.2% (Adachi et al., 2009a); and we found this haplogroup in high frequency (50.0%) in the Sanganji Jomon, although based on a small sample size. On the contrary, the frequency of haplogroup N9b was low in the Kanto Jomon at 5.6% (Shinoda and Kanai, 1999, Shinoda, 2003). In modern populations, haplogroup N9b is present in the Japanese archipelago at low frequencies (<10%) (Maruyama et al., 2003; Tajima et al., 2004; Umetsu et al., 2005), but at a high frequency (30.4%) in the Udegey from southern Siberia. It seems that haplogroup N9b was one of the main haplogroups in ancient and modern Northeast Asian populations.
We further subdivided the haplogroup N9b observed in the two Sanganji Jomon individuals using specific primers into four sub-haplogroups (N9b1, N9b2, N9b3, and N9b*) (Table 4). Samples which could not be designated to sub-haplogroups N9b1, N9b2, and N9b3 were classified as sub-haplogroup N9b*. Of the two Sanganji Jomon samples, one was classified as sub-haplogroup N9b2 and another was classified as sub-haplogroup N9b*. In the Hokkaido Jomon, although sub-haplogroup N9b* was observed, sub-haplogroup N9b2 has so far not been observed. The Sanganji results may hint at some population differentiation among the northern Jomon populations.
Figure 2 A map of East Eurasia and geographic locations of the East Asian and Siberian populations compared in the present study.
Haplogroup M7a is classified into three sub-haplogroups, M7a1, M7a2, and M7a*. Individuals who were not classified into sub-haplogroups M7a1 and M7a2 were classified into sub-haplogroup M7a*. We found that two Sanganji individuals belonged to haplogroup M7a2 (Table 5, Table 7). In modern populations, haplogroup M7a1 was observed in modern Japanese populations at a high frequency: Ainu, 15.7% (Tajima et al., 2004); mainland Japanese, 9.5% (Maruyama et al., 2003); Ryukyuan, 26.6% (Horai et al., 1996, Matsukusa et al., 2010). However, haplogroup M7a2 was scarcely observed in the mainland Japanese (0.5%), and this haplogroup was not observed in the Ryukyuan. On the contrary, haplogroup M7a2 was observed in the Udegey from southern Siberia at high frequency (19.6%, Starikovskaya et al., 2005).
Adachi et al. (2009a) mentioned that three regional Jomon populations shared some haplogroups (M7a and N9b), and that genetic similarity decreased gradually with increased geographical distance. However, since sub-haplogroups M7a2 and N9b2 have so far not been shown to be shared between the Tohoku and Kanto Jomon people, it may be that, in terms of the maternal lineage, the gene flow between the geographically close Tohoku and Kanto regions was limited in the Jomon period. In addition, in the population comparison analysis, although we found genetic similarity between the Hokkaido and Tohoku Jomon, so far they lack shared haplogroups at the sub-haplogroup level (M7a*, D4h2, and G1b of the Hokkaido Jomon were not seen in the Tohoku Jomon, and N9b2 and D4b of the Tohoku Jomon were not seen in the Hokkaido Jomon). Again, this may be indicating comparatively limited gene flow in the Jomon period. This interpretation is consistent with the results of the population differentiation test, and the observation of inter-regional heterogeneity among the ancient Japanese archipelago populations. However, the above interpretations need to be confirmed and refined by larger samples of sub-haplogroup determinations and better temporal control of the Jomon materials.
Compared to modern East Asian populations, the Tohoku and Hokkaido Jomon people were genetically close to the Udegey of southern Siberia (Udegey and Tohoku Jomon, Fst = 0.088, P = 0.01; Udegey and Hokkaido Jomon, Fst = 0.138, P = 0.00) (Appendix 2). The Udegey is also geographically closer to the Jomon populations than are the other southern Siberian populations (Figure 2). In the phylogenetic network shown in Figure 4, based on shared mtDNA haplogroups M7a and N9b (Appendix 1), it seems possible that the Udegey represents admixture of southern Siberian populations and the northern (Hokkaido and Tohoku) Jomon people. This implies some degree of gene flow between the Udegey people ancestors and the northern Jomon. Moreover, as we mentioned earlier, haplogroups N9b and M7a2 are hardly observed in the other East Asian populations except in the Japanese archipelago (Table 6, Table 7). One interpretation would be that a northern population with haplogroups N9b and M7a2 migrated into the Tohoku region via Hokkaido, although a southern origin has been considered for the M7a haplotype (see above for discussion of the southern haplogroup hypothesis). This would be compatible with the conclusion of previous studies that the Jomon people were (largely) of northern origin (Nei, 1995; Omoto and Saitou, 1997; Hanihara and Ishida, 2009; Nakashima et al., 2010; Adachi et al., 2011).
Figure 3 Principle Component Analysis of 18 East Asian populations based on Fst values.
The Sanganji results and related analyses presented above suggest that the history of the Jomon people is more complex than previously considered (see also Adachi et al., 2011). Our knowledge of Tohoku and Kanto Jomon sub-haplogroup representations is still limited, and we do not know the genetic background of the Jomon people from west of the Kanto region or the Sea of Japan coastal areas. Therefore, further data accumulation, not only mitochondrial DNA but also nuclear DNA (Sato et al., 2010; Kazuta et al., 2011), and ancient DNA analysis based on larger samples with both adequate temporal control and more extensive geographical regions are necessary to clarify an apparently complex Jomon population history.
Moreover, since next-generation sequencing technology makes it possible to analyze tiny amounts of ancient DNA (e.g. Green et al., 2010), it is quickly becoming practicable to analyze not only Jomon mtDNA, but also nuclear DNA, which contains much more genetic information. Since the success rate of mtDNA haplotyping of four Sanganji Jomon samples was 100%, skeletal remains materials from sites such as Sanganji may also contain nuclear DNA. With this prospect of an expanded range of materials suitable for ancient nuclear DNA analysis with the emergence of next-generation sequencing, further studies on the Tohoku and other Jomon materials may enable a better resolution to the issues discussed herein.
Figure 4 Phylogenetic network of 18 East Asian populations based on Fst values.
Our observation of genetic similarity between the Tohoku Jomon and some of the indigenous southern Siberian peoples is compatible with previous interpretations that the Jomon people originated in Northeast Asia. However, statistical analysis of Jomon populations suggests: (1) the existence of inter-regional heterogeneity within the Jomon people; (2) genetic similarity among the two northern Jomon populations (Tohoku and Hokkaido) much more so than with the Kanto Jomon, implying comparatively limited gene flow between the Kanto and more northern regions; and (3) despite their relative closeness, the presence of sub-haplotype differences between the two northern Jomon populations. The emerging implication seems that the history of the Jomon people may have been more complex than previously considered.
In the modern Japanese, mtDNA haplogroups N9b and M7a2, common in the Sanganji and Hokkaido Jomons, are uncommon. Therefore, it seems that the genetic influence of the northern Jomon populations to the modern mainland Japanese is limited in the maternal linage. However, the samples analyzed in the present study are limited, and current and previous reports are confined mostly to Jomon skeletal materials of the east coast of the Tohoku region. In order to clarify the characteristics of the Tohoku Jomon as well as their genetic influence on modern populations, larger and geographically wider-based samples need to be investigated.
Anthropological Science Vol. 121 (2013) No. 2 p. 89-103