蓝海人类学在线 Ryan WEI's Forum of Anthropology

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发表于 2013-10-22 03:04 | 显示全部楼层 |阅读模式
Ancient mitochondrial DNA sequences of Jomon teeth samples from Sanganji, Tohoku district, Japan


Abstract 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.




 楼主| 发表于 2013-10-22 03:08 | 显示全部楼层
 楼主| 发表于 2013-10-22 03:30 | 显示全部楼层
本帖最后由 natsuya 于 2013-10-22 03:48 编辑

 楼主| 发表于 2013-10-23 02:22 | 显示全部楼层
 楼主| 发表于 2013-10-24 21:44 | 显示全部楼层

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 subhaplogroups
N9b1, N9b2, and N9b3 were classified as subhaplogroup
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, subhaplogroup
N9b2 has so far not been observed. The Sanganji
results may hint at some population differentiation among
the northern Jomon populations.
 楼主| 发表于 2013-10-24 21:47 | 显示全部楼层

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).

In ancient East Asian populations, haplogroup M7a
(which includes M7a1, M7a2, and M7a*) is widely observed
in the Jomon people (Hokkaido Jomon, 7.4%; Tohoku
Jomon, 31.6%; Kanto Jomon, 3.7%). That the Sanganji
Jomon (present study) also had this haplogroup apparently at
high frequency (50.0%) supports the suggestion of Adachi et
al. (2009b) that haplogroup M7a is a putative ‘Jomon genotype.’
However, we have now identified the occurrence of
sub-haplogroup M7a2 for the first time in the Tohoku
Jomon, which enables some further considerations.

Although the currently available data is still limited, interestingly,
the frequencies of haplogroups M7a1 and M7a2
appear quite different among the Jomon people (Table 7).
This may indicate that during the later Jomon period, M7a1
was mainly distributed in the middle to southern part of the
Japanese archipelago, and haplogroup M7a2 (and also
M7a*) was distributed further north, from the Tohoku and
Hokkaido regions of the Japanese archipelago and southern
Siberia. Adachi et al. (2011) suggested that haplogroup M7a
was of southern origin, and that this haplogroup was introduced
to Japan around the last glacial maximum (LGM). If
we accept this suggestion, haplogroup M7a2, which is observed
in the northern Jomon people, might have originated
after the introduction of M7a into the Japanese archipelago.
The sub-haplotype then subsequently became distributed
further northward by migration, and must have reached
southern Siberia.

The tooth ablation type of Sanganji individuals 13142-1
and 13142-2 was both probably the 0-type (only the upper
canine extracted, no mandibular tooth extraction), which
suggests an in-group status of the individuals according to
Harunari’s (2002) interpretation of ablation patterns. On the
other hand, individual 13142-3 did not exhibit a clear pattern
and 131464 was the 2C-type, which suggests an out-group
status. Therefore, individuals 13142-1 and 13142-2, both
possibly born at Sanganji and with the same haplotype,
could have been relatives. However, since sub-haplogroup
M7a2 might have been the major type in that region, it is
also possible that they shared the same haplotype without
having any genealogical relationship.

The genetic transition from the Jomon people to modern
Japanese is explained by the ‘dual structure model,’ according
to which a substantial number of Yayoi people migrated
into the Japanese archipelago via the Korean peninsula
about 3000 years ago, and admixed with Jomon people
(Hanihara, 1991). This model also suggests that the effect of
the Yayoi immigrants is small in the Ainu and Ryukyuan
peoples, who live at the margins of the Japanese archipelago
and retain more Jomon components than the mainland Japanese.
In fact, this expected pattern was recently observed
from the comparison of genome-wide autosomal SNP data
for the Ainu, the Ryukyuan, and the mainland Japanese populations
(Japanese Archipelago Human Population Genetics
Consortium, 2012). Therefore, high frequencies of the
‘Jomon genotype’ (haplogroup N9b and M7a) in the Ainu
and Ryukyuan peoples have been considered to partially
support this model (Adachi et al., 2009b). Thus, it is expected
that the Ainu people who live in Hokkaido, the northernmost
Japanese archipelago, would have haplogroups M7a*
and M7a2 in high frequencies, because the northern Jomon
populations have been so far shown to have these haplogroups.
However, the Ainu people have only haplogroup
M7a1 (Table 7). This may indicate either sample bias, or
that the haplogroup M7a of the Ainu was not derived from
the indigenous northern Jomon genotype, and that this haplogroup
was introduced into the Ainu population after the
Jomon period. The latter interpretation implies that the genetic
effect from mainland Japan after the Jomon period was
stronger than previously considered.
 楼主| 发表于 2013-10-24 21:51 | 显示全部楼层
To investigate the relationships between the Jomon people
from the Tohoku region (Sanganji Jomon, present study;
the Tohoku Jomon, Adachi et al., 2011) and other East and
Northeast Asian ancient and modern populations, a statistical
analysis based on haplogroup frequencies (Appendix 1)
was performed. In this analysis, we merged sub-haplogroups
N9b1, N9b2, N9b3, and N9b* into haplogroup N9b, and
sub-haplogroups M7a1, M7a2, and M7a* into haplogroup
M7a, because sub-haplogroup frequency data were missing
in some populations used in the statistical analysis (Table 6,
Table 7). The approximate geographical locations of these
populations are shown in Figure 1 and Figure 2.
 楼主| 发表于 2013-10-24 21:54 | 显示全部楼层
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 subhaplogroup
determinations and better temporal control of
the Jomon materials.
 楼主| 发表于 2013-10-24 21:56 | 显示全部楼层
We (H.K.-K. and N.S.) initially suspected that the DNA
analysis of materials such as those of the Sanganji Jomon
would be difficult because of their prolonged storage in museums.
However, albeit with a small sample size of four, the
success rate of mtDNA haplogroup detection increased to
100% when focusing on short DNA regions.
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 subhaplotype
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
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.
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