ANTHROPOLOGICAL SCIENCE
Vol. advpub(0), 000–000, 2013

Advance Publication

Ancient mitochondrial DNA sequences of Jomon teeth samples
from Sanganji, Tohoku district, Japan
Hideaki KANZAWA-KIRIYAMA1,2, Aiko SASO3,4, Gen SUWA4, Naruya SAITOU2,1,3*
1

Department of Genetics, School of Life Science, Graduate University for Advanced Studies, Mishima 411–8540, Japan
2
Division of Population Genetics, National Institute of Genetics, Mishima 411–8540, Japan3
Department of Biological Sciences, The University of Tokyo, Tokyo 113–0033, Japan
4
The University Museum, The University of Tokyo, Tokyo 113–0033, Japan
Received 18 May 2012; accepted 13 November 2012

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 andcontrol 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 themodern 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 Jomonand 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 andHokkaido Jomon seem to differ in sub-haplotype representations, suggesting complexity in Jomon
population structure and history.
Key words: Mitochondrial DNA, ancient DNA, Sanganji shell mound, Jomon, Tohoku region
2003; Adachi et al., 2008, 2009a, b, 2011). Analyses ofancient materials are useful, because they directly clarify
maternally inherited mtDNA haplogroups. So far, Jomon
materials from three regions, the Hokkaido, Tohoku, andKanto regions (Figure 1), have been analyzed (Shinoda andKanai, 1999; Shinoda, 2003; Adachi et al., 2008, 2009a, b,2011). Comparisons of mtDNA haplogroup frequencies
with other East and Northeast Asian populations indicatethat the genetic structure of the Hokkaido Jomon (the northernmost of the Jomon populations) exhibited some similarities with indigenous modern Siberian populations inhabiting
the lower Amur riverine system, particularly the Ulchi andUdegey people (Adachi et al., 2011). However, the genetic
affinity of the other Jomon people, especially of the Tohoku
Jomon, was not sufficiently classified in Adachi et al.
(2009a). Furthermore, the mtDNA haplogroups N9b andM7a, characteristic of the Tohoku Jomon, are scarce in theother modern populations except the modern Japanese (including Ainu and Ryukyuan people) and Udegey. In order tofurther understand the origin of the Jomon people based on
ancient DNA, additional analyses of the Tohoku Jomon are
essential.
In this study, we analyzed samples taken from skeletal
remains of the late to final Jomon period Sanganji shellmound site of Fukushima Prefecture, Tohoku district, Japan.

Introduction
The question of the origin of the Jomon people has been
debated for several decades. The Jomon are widely thought
to have settled the Japanese archipelago c. 15700 to 2350
years BP (Kobayashi, 2008) and ranged geographically from
Hokkaido to Okinawa. Morphological studies of dental variation have suggested that the Jomon people were of southern
origin (Turner, 1987, 1990; Hanihara, 1991; Matsumura,2007; Matsumura et al., 2009). On the other hand, archaeology, genetics, and recent cranial morphology studies suggestthat the Jomon people were of northern origin (Nei, 1995;
Imamura, 1996; Omoto and Saitou, 1997; Hanihara and
Ishida, 2009; Nakashima et al., 2010).
To investigate more directly the origin of the Jomon froma genetic standpoint, mitochondrial (mt) DNA from ancientskeletal remains have been analyzed in the last few decades(Horai et al., 1989, 1991; Shinoda and Kanai, 1999; Shinoda,* Correspondence to: Naruya Saitou, Division of Population Genetics, National Institute of Genetics, 1111 Yata, Mishima 411–8540,
Japan.
E-mail: saitounr@nig.ac.jp
Published online 7 March 2013
in J-STAGE (www.jstage.jst.go.jp) DOI: 10.1537/ase.121113© 2013 The Anthropological Society of Nippon

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H. KANZAWA-KIRIYAMA ET AL.

Figure 1. Geographical location of Sanganji site, and other sites of Tohoku Jomon people.

The remains that we examined are part of the skeletal collection excavated in 1952 and 1954, and have been stored in
The University Museum, The University of Tokyo for morethan 50 years. It is known that excessive handling and longterm storage may influence the ability to obtain authentic endogenic DNA (Melchior et al., 2010). Because the successrates of ancient DNA studies increase when shorter DNA regions are analyzed (Pääbo et al., 2004; Haak et al., 2010), we
focused on determining nucleotide sequences of the shorter
mtDNA regions. As a result, in our sample of four, we wereable to determine haplogroups with a 100% success rate.
Our new results from the Sanganji Jomon materials, added
to previous data (Adachi et al., 2009a), allow for more detailed population comparisons.

Table 1. Information of analyzed Sanganji Jomon teeth samples
Sample ID

Sex131421-1
131421-2
131421-3
131464

Female?
Male
Male
FemaleTooth
Date ofablation type excavation
0a
0a
?b
2Cc

1954
1954
1954
1952

Analyzed
tooth part
Right M3
Right M3
Right M2
Right M2

Materials and MethodsaThere are no tooth extractions in the mandibular anterior teeth (allalveoli present), inferring ablation of only the upper canines (or a rarecase at Sanganji of no ablation).
b
The left I1 alveolus is closed after tooth loss, while the left I2 isintact. The right side mandible is not preserved. This suggests either
individual tooth ablation interpreted as mourning ablation (Harunari,2002), a rare case at Sanganji of transitional stage of the 4I pattern (allfour lower incisors extracted), or type 0 with natural loss of the left I1.
c
All lower anterior teeth (canine and incisors) were extracted,
implying the 2C ablation type (all lower anterior teeth and upper
canines).

Sample collection
The Sanganji shell mound is located in the northern partof Fukushima Prefecture, Tohoku district (Figure 1). The
chronological age of the burials, belonging to the late to final
Jomon period, is considered to lie within the range from4000 to 2500 years BP. The 1952–1954 excavations of
the Sanganji Jomon skeletal remains were carried out by theSpecial Committee for Jomon Chronology of the JapaneseArchaeological Association (1952 excavation), and by the
Department of Anthropology, The University of Tokyo(1954 excavation). To analyze mtDNA haplogroups, weused teeth from four Sanganji Jomon individuals housedin The University Museum, The University of Tokyo(Table 1). Three of these came from skeletal remains catalogued as UMUT-131421 (Endo and Endo, 1979), which

includes six to eight individuals from what is known assecondary burial C’ (Fukushima Museum, 1988). In the following analysis, we distinguish these three individuals by
suffixes, 131421-1, 131421-2, and 131421-3. The fourth
individual that we examined, UMUT-131464 (Endo andEndo, 1979), comes from secondary burial B, which includes approximately 10 individuals (Fukushima Museum,1988). A single, well-preserved molar tooth was removed
from the mandible of each individual (isolated teeth were
excluded to avoid the possibility of sampling from the same
individual). We chose mandibles which had both right- andleft-side molars, so that the antimere of the analyzed toothwould remain available for general morphological studies.

Vol. 121, 2013

The ablation patterns of the Jomon people have been discussed in relation to population movement (Harunari, 2002;
Funahashi, 2010). The tooth ablation type of individuals
131421-1 and 131421-2 (no mandibular teeth extracted) was
probably 0-type (only the upper canine extracted, no mandibular tooth extraction). According to Harunari’s (2002)
interpretations, this would indicate in-group status of theindividuals and not immigration through marriage. If so,these two individuals may have been born at Sanganji, and it
is possible that they were relatives.
DNA extraction
Tooth samples were soaked in a 13% sodium hypochlorite
solution for 3 minutes, rinsed several times with HPLCgrade water (Wako, Japan), then treated with ultraviolet radiation at least overnight, and allowed to air-dry under ultraviolet radiation for 60 minutes. The outer surface of thesamples was then removed using a heat-treated drill. Next,
the samples were again rinsed with HPLC-grade water andallowed to air-dry under ultraviolet radiation for 60 minutes.
The tip of the tooth root was cut horizontally using a cutting
disk; the dental pulp was reduced to powder with a drill andcollected in a tube. DNA extraction from the powderedsamples was carried out based on the method of Rohland andHofreiter (2007) with some modifications. The powderedsamples were dissolved with 0.5 M EDTA (pH 8.0) (Wako,
Japan) and 0.25 mg/ml proteinase K (TaKaRa, Japan) overnight at room temperature. The dissolved solution was centrifuged, and the supernatant was collected. The collected
solution was concentrated using VivaSpin6 (Sartorius,
Japan) to a volume less than 300 µl. The concentrated solution was added to 1.5 ml binding buffer (5 M GuSCN,
25 mM NaCl, and 50 mM Tris, pH 8.0) plus 100 µl silica
suspension (Sigma) and incubated under agitation for 3
hours at room temperature. The silica pellet was collected
via centrifugation, the supernatant was removed, and thepellet was washed twice with binding buffer. Subsequently,
the pellet was dried at room temperature for 15 minutes.
DNA was eluted with 50 µl 1 × TE buffer at room temperature for 10 minutes, and, after centrifugation, the aqueous
solution was transferred to a new tube. DNA was eluted
twice, and 100 µl of DNA extract was finally obtained fromeach sample.
PCR amplification and sequencing
Ancient DNA is invariably of shorter length, and thelength of the DNA sequences that can be amplified by polymerase chain reaction (PCR) is limited (Pääbo et al., 2004;
Haak et al., 2010). Moreover, as heavy handling and prolonged storage influence the ability to obtain authentic endogenic DNA (Melchior et al., 2010), we anticipated that theanalysis of Sanganji Jomon samples, excavated in 1952 and1954, would be difficult and the success rate would be low.
To overcome this problem, in addition to the primers thattarget long DNA segments (158–195 bp), we used shortlengths of target DNA (58–90 bp) containing haplogroupspecific SNPs, because shorter DNA regions are more readily amplified by PCR than longer DNA regions (Pääbo et al.,
2004; Haak et al., 2010).
To determine mtDNA haplogroups, hypervariable region

ANCIENT HUMAN MTDNA FROM TOHOKU, JAPAN3

Table 2. Primers used for PCR amplifications of mitochondrial
DNA hypervariable regions 1 and 2
PrimerID
L127
H257
L15998
H16142
L16120
H16239L16208H16367

Sequencea

Nucleotide
positionsb

AGCACCCTATGTCGCAGTAT
128–256
TCTGTGTGGAAAGCGGCTGT
CCATTAGCACCCAAAGCTA 15999–16141
ATGTACTACAGGTGGTCAAG
TTACTGCCAGCCACCATGAA 16121–16238
TGGCTTTGGAGTTGCAGTTG
CCCCATGCTTACAAGCAAG 16209–16366
CTGAGGGGGGTCATCCAT

Product
size
169
182
158
195

a

Primers of Adachi et al. (2009b) were referred.
Numbers of nucleotide positions are relative to the revised Cambridge Reference Sequence (rCRS) (Andrews et al., 1999).
b(HVR)-1, HVR-2, 28 haplogroup/sub-haplogroup-specificsingle nucleotide polymorphisms (SNPs), and a 9 bp repeat
variation in the noncoding cytochrome oxidase II/tRNALys
intergenic region, were analyzed following previous
publications (Umetsu et al., 2005; van Oven and Kayser,
2008; Adachi et al., 2009a, b, 2011; Haak et al., 2010). The
primers used to amplify HVR-1, HVR-2, and haplogroupdetermining regions are listed in Table 2 and Table 3. Analyzed haplogroups were compared with those of modern
Japanese and Jomon people (Horai et al., 1996; Shinoda andKanai, 1999; Shinoda, 2003; Maruyama et al., 2003; Tajima
et al., 2004; Tanaka et al., 2004; Adachi et al., 2008, 2009a,b, 2011; Matsukusa et al., 2010). To further characterize thesub-haplogroups within N9 and M7a, we used additional
primers listed in Table 4.
A total of 1 µl of the extracted DNA was used as the template for PCR. Amplifications were carried out in a total reaction volume of 20 µl containing of 0.5 µM of each primer,
and the Multiplex PCR assay kit (TaKaRa) reagents. The
PCR conditions were incubation at 94°C for 30 sec, followed by 42 cycles of 94°C for 30 sec, 54°C for 20 sec,
72°C for 15 sec, and 1 cycle of 72°C for 10 min. An aliquot(2.5 µl) of the PCR product was checked on a 2% agarosegel, and the remainder (17.5 µl) was then purified with
Monofas (GL Sciences). The PCR products of SNP analysis
were used as template for direct nucleotide sequencing, but
we performed cloning of the PCR products of HVR-1 andHVR-2 because of these small quantities. Sequencing reactions were performed with BigDye Terminators v. 1.1 Cycle
Sequencing kit (Applied Biosystems, Foster City, CA), and-21M13 and M13RVN primers were used in direct sequencing. All sequencing reactions were carried out using 3130
DNA Sequencer (Applied Biosystems), and the sequence ofeach region was compared with the revised Cambridge Reference Sequence (CRS) (Andrews et al., 1999).
Contamination precautions
During each sample-handling step, the following precautions were taken to minimize the risk of contamination.
1. The equipment used (drill, pipettes, centrifuge, vortex
machine, and PCR rack) were treated with a DNA contamination removal solution (DNA-AWAY, Molecular

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Table 3. Primers used for PCR amplifications of mitochondrial DNA haplogroup specific SNPs
Haplogroup

Haplogroup-defining
mutations

M/D5

10400/10397

N

10873

A/G

4824/4833

B

8281–8289 deletion

D

5178

D4/E

3010/3027

F

10310

M7

9824

M7a

2772

M7c

5442

M8

15487T

M9

3394

M10

15071

M12/M7bN9abc4170/4164
5417

PrimerID

Sequence (5′–3′)

M13-L10382
M13R-H10421
M13-L10870
M13R-H10888
M13-L4812
M13R-H4842
M13-L8268
M13R-H8295
M13-L5171
M13R-H5204
M13-L3005
M13R-H3029
M13-L10298
M13R-H10326
M13-L9816
M13R-H9851
M13-L2742
M13R-H2778
M13-L5434
M13R-H5471
M13-L15450
M13R-H15489
M13-L3376
M13R-H3397
M13-L15057
M13R-H15077
M13-L4151
M13R-H4177
M13-L5385
M13R-H5422(-21M13)bAAGTCTGGCCTATGAGTGACTACAA(M13RVN)cTGAGTCGAAATCATTCGTTTTG(-21M13)CCACAGCCTAATTATTAGCATCATC(M13RVN)GCTAAATAGGTTGTTGTTGATTTGG(-21M13)TAGCCCCCTTTCACTTCTGA(M13RVN)AAGAAGCAGGCCGGATGT(-21M13)AATAGGGCCCGTATTTACCCTATA(M13RVN)AGGTTAATGCTAAGTTAGCTTTACAGTG(-21M13)ACCCTACTACTATCTCGCACCTGA(M13RVN)CTAGGGAGAGGAGGGTGGAT(-21M13)CTCGATGTTGGATCAGGACA(M13RVN)TCGTTGAACAAACGAACCTT(-21M13)CCCTACCATGAGCCCTACAA(M13RVN)GGATGATGATTAATAAGAGGGATGA(-21M13)TTTTGTAGCCACAGGCTTCC(M13RVN)GGCGGATGAAGCAGATAGTG(-21M13)GAGAAGACCCTATGGAGCTTTAAT(M13RVN)TAATGCAGGTTTGGTAGTTTAGGA(-21M13)AAATGACAGTTTGAACATACAAAACC(M13RVN)AAAGGGGAGATAGGTAGGAGTAGC(-21M13)GCCCTCGGCTTACTTCTCTT(M13RVN)CTGGGTCGCCTAGGAGGT
M13-GGCATTCCTAATGCTTACCG(M13RVN)GGGCCTTTGCGTAGTTGTAT(-21M13)ATCGGGCGAGGCCTATATTA(M13RVN)ATGCCGATGTTTCAGGTTTC(-21M13)GAACAGCATACCCCCGATT(M13RVN)TGCTAGGGTGAGTGGTAGGAA(-21M13)TCCACCTCAATCACACTACTCC(M13RVN)TGGGGTGGGTTTTGTATGTT

Nucleotide
positionsa

Product
size

10383–10420

85

10871–10887

67

4813–4841

68

8269–8294

78

5172–5203

76

3006–3028

60

10299–10325

72

9817–9850

74

2743–2777

83

5435–5470

86

15451–15488

76

3377–3396

60

15058–15076

59

4152–4176

77

5386–5421

78

Numbers of nucleotide positions are relative to the revised Cambridge reference sequence (rCRS) (Andrews et al., 1999).
(-21M13) sequence represents 5′-TGTAAAACGACGGCCAGT-3′.
(M13RVN) sequence represents 5′-TGTGGAATTGTGAGCGG-3′.

BioProducts, San Diego, CA) and with ultraviolet irradiation.
2. Some heat-resistant implements (tube rack made of stainless steel, drill tips, cutting disk, and glass bottle) were treated with dry heat sterilization at 200°C for 12 hours.
3. Disposable equipment (tubes and filtered pipette tips) was
irradiated with ultraviolet rays.
4. The working area was divided into pre-PCR and postPCR areas.
5. The clean-bench was treated with overnight ultraviolet radiation.
6. Gloves, face masks, and clean-room items (coats, caps,
shoes, and socks) were also used when ancient DNA samples were handled.
7. Clean-room items were treated with ultraviolet irradiation
overnight.
8. To exclude any possible contamination from modern human DNA, simultaneous negative controls during DNA extraction and PCR amplification steps were added.

Data analysis
To investigate the relationship between the Tohoku
Jomon people and the other ancient and modern East Asians,
we compared mtDNA haplogroup frequencies (Appendix 1)
using Arlequin v. 3.11 (Excoffier et al., 2005). For pairwise
population comparisons, the Fst formula used in Arlequin is
identical to the weighted average F-statistic over loci, θw,
defined by Weir and Cockerham (1984) (Michalakis andExcoffier, 1996). The equation to calculate Fst-values is asfollows:∑ auuθ̂ W = ---------------------------------------(a∑ u + bu + cu )

(1)

u

n⎧ 2
1
r–1 2 1 ⎫a u = ---- ⎨ s – ------------ p ( 1 – p ) – ----------- s – --- h ⎬
nc ⎩
n–1
4 ⎭
r

(2)

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ANCIENT HUMAN MTDNA FROM TOHOKU, JAPAN

5

Table 4. Primers used for PCR amplifications of mitochondrial DNA sub-haplogroup specific SNPs
Haplogroup
M7a1

14364
16324

M7a2

15422
16140

N9a

5231

N9b

13183

N9b1

12501

N9b2

16294

N9b3

14996

Y

8392

a
b
c

Primer

Haplogroup-defining
mutationsID

Sequence (5′-3′)

M13-L14357
M13R-H14399
M13-L16302
M13R-H16346
M13-L15401
M13R-H15427
M13-L16119
M13R-H16170
M13-L5217
M13R-H5238
M13-L13147
M13R-H13188
M13-L12492
M13R-H12524
M13-L16292
M13R-H16327
M13-L14965
M13R-H14998
M13-L8380
M13R-H8395(-21M13)bCCACCCCATCATACTCTTTCA(M13RVN)cGGTTGAGGTCTTGGTGAGTGT(-21M13)CAAACCTACCCACCCTTAACA(M13RVN)GGGACGAGAAGGGATTTGAC(-21M13)CCTCCCATTCCGATAAAATCA(M13RVN)AAGTAAGCCGAGGGCGTCT(-21M13)ATTACTGCCAGCCACCATGA(M13RVN)AGGGGGTTTTGATGTGGATT(-21M13)AATTCCATCCACCCTCCTCT(M13RVN)GGGCAAAAAGCCGGTTAG(-21M13)CCCCCTAGCAGAAAATAGCC(M13RVN)AGACTGCTGCGAACAGAGTG(-21M13)TCAGTCTCTTCCCCACAACA(M13RVN)GGCTCAGTGTCAGTTCGAGA(-21M13)CACTAGGATACCAACAAACCTACCC(M13RVN)TTTGACTGTAATGTGCTATGTACGG(-21M13)CCCACATCACTCGAGACGTA(M13RVN)AGAATATTGAGGCGCCATTG(-21M13)CAGTGAAATGCCCCAACTAAAT(M13RVN)GGAGTATGGGGGTAATTATGGTG

Nucleotide
positionsa

Product
size

14358–14398

83

16303–16345

84

15402–15426

65

16120–16169

90

5218–5237

58

13148–13187

80

12493–12523

71

16293–16326

84

14966–14997

72

8381–8394

59

Numbers of nucleotide positions are relative to the revised Cambridge reference sequence (rCRS) (Andrews et al., 1999).
(-21M13) sequence represents 5′-TGTAAAACGACGGCCAGT-3′.
(M13RVN) sequence represents 5′-TGTGGAATTGTGAGCGG-3′.

n - p ( 1 – p ) – r---------– 1- s 2 – -------------2n – 1- h
b u = ----------n–1
r
4n

(3)

c u = 1--- h2(4)

where au, bu, and cu are the observed components of variance(au for between populations, bu for between individuals
within populations, and cu for between gametes within individuals); n bar is the average sample size; nc is the squared
coefficient of variation of sample sizes; p bar is the average
sample frequency of alleles; s2 is the sample variance ofallele frequencies over populations; h bar is the average
heterozygote frequency for alleles. For further details, see
Weir and Cockerham (1984).
Three ancient populations, the Hokkaido (Adachi et al.,2011), Tohoku (present study; Adachi et al., 2009a), andKanto Jomon (Shinoda and Kanai, 1999; Shinoda, 2003),
the Okhotsk people (Sato et al., 2009), and the following 14
modern populations were compared: Ainu (Tajima et al.,2004), mainland Japanese (Maruyama et al., 2003),
Ryukyuan (Umetsu et al., 2005), Korean (Lee et al., 2006),
northern Chinese (Yao et al., 2002), Yangtze River region
Chinese (Yao et al., 2002), southern Chinese (Yao et al.,2002), Aboriginal Taiwanese (Trejaut et al., 2005), northern
Siberians (Starikovskaya et al., 1998), Kamchatkans (Schurr
et al., 1999), Ulchi (Starikovskaya et al., 2005), Udegey(Starikovskaya et al., 2005), Nivkhi (Starikovskaya et al.,2005), and Negidal (Starikovskaya et al., 2005). Principal

component analysis (PCA) scatterplots and phylogenetic
networks were constructed with R (R Development Core
Team, 2010) and splitstree4 (Huson and Bryant, 2006), respectively, based on pairwise Fst-values.

Results and Discussion
PCR and SNP typing
We successfully determined the mtDNA haplogroup of all
four individuals that we examined (Table 5), using the primer pairs targeting short DNA segments (58–90 bp). In eachindividual, all SNP sites were consistent with previously observed haplogroups, and this thus reduces the chance of contamination. When we used the primer pairs targeting long
DNA segments (158–195 bp) in the analysis of HVR, theamplification efficiency and quantity of PCR products decreased dramatically, possibly due to the sample conditions.
This corresponds to the observations of Pääbo et al. (2004)
and Haak et al. (2010). To estimate the level of modern DNA
contamination, long PCR products were sequenced withcloning. In these analysis, some PCR products contained sequences that were inconsistent with the SNP analysis. This
indicates that, to reduce the effect of contamination in theanalysis of ancient DNA, focusing on short DNA regions isbetter, and we need to reduce the number of PCR cycles.
Population comparison based on haplogroup frequencies
Two of the four Sanganji Jomon individuals belonged to
haplogroup N9b (Table 5, Table 6). Haplogroup N9b has

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Table 5. Observed nucleotide mutations of four Sanganji Jomon individuals

Haplogroup

Nucleotide positiona

SampleSanganji131421-1

Sanganji131421-2

Sanganji131421-3

Sanganji131464

Sex

F?

M

M

f

Tooth ablation type

0

0

4I?

2C

T
C
A
2
C
ND
A
ND
G
A
C
T
G
T
G
C
C
ND
A
ND
T
A
G
—
—
—
—
—
—

T
C
A
2
C
ND
A
ND
G
A
C
T
G
T
G
C
C
ND
A
ND
T
A
G
—
—
—
—
—
—

C
T
A
2
C
ND
A
ND
G
A
T
—
—
—
—
—
C
—
A
ND
T
A
A
G
G
G
C
G
ND

C
T
A
2
C
ND
A
ND
G
A
T
—
—
—
—
—
C
—
A
ND
T
A
A
G
G
G
—
G
ND

ND
ND
ND
ND

146
ND
ND
ND

ND
ND
ND
ND

CRS
ND
ND
16256, 16294

M7a2

M7a2

N9b*

N9b2

rCRSb
M
N
A
B
D
D4
D5
E
F
G
M7
M7a
M7a1
M7a2
M7b
M7c
M8
M9
M10
M12
N9
N9a
N9b
N9b1
N9b2
N9b3
Y
HVR

Haplogroup

10400
10873
4824
8281–8289 deletion
5178
3010
10397
3027
10310
4833
9824
2772
14364
16324
15422
16140
4164
5442
15487T
3394
15071
4170
5417
5231
13183
12501
16294
14996
8392
128–256
15999–16141
16121–16238
16209–16366

C
T
A
2
C
G
A
T
G
A
T
C
G
T
A
T
C
T
A
T
T
A
G
G
A
G
C
G
G

ND, not determined; —, not analyzed; diagnostic polymorphisms are emphasized by bold type. Haplogroup B has a 9 bp (CCCCCTCTA) deletion. ‘1’ denotes the presence of the 9 bp deletion, and ‘2’ denotes nondeletion (i.e. two repeats of the 9 bp fragment).
a
Numbers of nucleotide positions are relative to the revised Cambridge reference sequence (rCRS) (Andrews et al., 1999).
b
The sequences of rCRS

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 foundthis 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 etal., 2003; Tajima et al., 2004; Umetsu et al., 2005), but at ahigh 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 wasclassified 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.
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

4

25.0

n

N9b1
N9b2
N9b3
N9b*

b

(63.2)

19

Adachi et al.,
2009a

9.3

55.6

54

Adachi et al.,
2011

Hokkaido
Jomon

(5.6)

54

b

Shinoda andKanai, 1999;
Shinoda, 2003

Kanto Jomona(10.8)

37bSato et al.,
2009

Okhotsk

Udegey

b

(6.9)

87

(30.4)

46b

Starikovskaya Starikovskaya
et al., 2005
et al., 2005

Ulchi

Southern Siberian

4

50.0

n

M7a1
M7a2
M7a*c

Adachi et al.,2009a(31.6)b19b

Ancient East Asians

1.9
5.6

54

Adachi et al.,
2011

3.7

54
5.4

37

Shinoda and Sato et al., 2009
Kanai, 1999;
Shinoda, 2003

Okhotsk

19.6

46

Starikovskaya etal., 2005

UdegeyPopulations

15.7

51

Tajima et al.,
2004

Ainua

Ryukyuan

KoreanRyukyuana(4.6)b326

Korean(0.3)b

591

9.5
0.5

211

1.1

26.6

274

0.2

1.3

591

Maruyama et al., Horai et al., 1996; Lee et al., 2006
2003
Matsukusa et al.,2010

MainlandJapanese

Modern populations

1.3
0.6
0.3
0.4

672

Tanaka et al., Umetsu et al., Lee et al., 2006
2004
2005

MainlandJapanese

Modern East AsiansaThe haplogroups observed at the highest frequency in each population are emphasized by bold type.
For these populations, haplogroups were inferred from the sequences of hypervariable regions (Adachi et al., 2009a, b).
b
The mtDNA sequence data of Tohoku Jomon people are insufficient to classify them into each sub-haplogroups, and the frequency of Tohoku Jomon people is the total of haplogroup M7a1,
M7a2, and M7a*.
c
Individuals that are not classified into sub-haplogroups are denoted M7a*.

This study

(7.8)

51

Tajima et al.,
2004

Ainua

Table 7. Frequencies (%) of M7a sub-haplogroups in ancient and modern East Eurasian populations

Sanganji Jomon Tohoku Jomon Hokkaido Jomon Kanto Jomona

Referencesa

The sub-haplogroups observed at the highest frequency in each population are emphasized by bold type.
For these populations, haplogroups were inferred from the sequences of hypervariable regions (Adachi et al., 2009a, b).
b
The mitochondrial DNA sequence data of these populations were insufficient to classify them into each sub-haplogroup.

25.0This study

References

Sanganji Jomon Tohoku Jomon

Ancient East Asians

Populations

Table 6. Frequencies of N9b sub-haplogroups (%) in ancient and modern East Eurasian populations

Vol. 121, 2013
ANCIENT HUMAN MTDNA FROM TOHOKU, JAPAN7

8

H. KANZAWA-KIRIYAMA ET AL.

sub-haplogroup M7a*. We found that two Sanganji individuals belonged to haplogroup M7a2 (Table 5, Table 7). In
modern populations, haplogroup M7a1 was observed inmodern 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%), andthis haplogroup was not observed in the Ryukyuan. On thecontrary, 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 observedin 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 athigh frequency (50.0%) supports the suggestion of Adachi etal. (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 theJapanese archipelago, and haplogroup M7a2 (and alsoM7a*) was distributed further north, from the Tohoku andHokkaido 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 originatedafter the introduction of M7a into the Japanese archipelago.
The sub-haplotype then subsequently became distributed
further northward by migration, and must have reachedsouthern 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), whichsuggests an in-group status of the individuals according toHarunari’s (2002) interpretation of ablation patterns. On theother hand, individual 13142-3 did not exhibit a clear patternand 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 isalso 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

ANTHROPOLOGICAL SCIENCE

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, orthat the haplogroup M7a of the Ainu was not derived fromthe 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 wasstronger than previously considered.
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 andNortheast 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, andsub-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.
Within the Japanese archipelago, contrasting opinions on
the population structure of the Jomon have been proposed:
the Jomon people were relatively homogeneous (Dodo,
1982; Yamaguchi, 1982; Kondo, 1994; Ossenberg et al.,2006; Matsumura, 2007) or heterogeneous (Adachi et al.,2009a, b; Hanihara and Ishida, 2009; Nakashima et al.,2010). When comparing the ancient populations of theJapanese archipelago (Kanto, Tohoku, and Hokkaido
Jomons and Okhotsk), the population differentiation test
demonstrated that they were statistically different from eachother (highest P-value was 0.007 between the Tohoku andHokkaido Jomon). This indicates inter-regional heterogeneity of the ancient Japanese archipelago populations, consistent with results of recent genetic (Adachi et al., 2009a, b)
and morphological (Hanihara and Ishida, 2009; Nakashima
et al., 2010) research.
Next, in order to obtain, for the first time, an indication of
overall genetic similarities of the Jomon regional populations as seen from the mtDNA haplotypes, we computed Fst
values between population pairs. The P-values between the
Tohoku Jomon and the other ancient or modern comparative
populations were less than 5%, based on 100 permutationsof the Arlequin software. The results showed a close genetic
similarity between the Tohoku and Hokkaido Jomon people(Fst = 0.061, P = 0.036 ± 0.015) (Appendix 2), and support
previous interpretations that the Jomon ancestors of thenorthern part of Japan (Hokkaido) might have expanded

Vol. 121, 2013

ANCIENT HUMAN MTDNA FROM TOHOKU, JAPAN

9

Figure 2. A map of East Eurasia and geographic locations of the East Asian and Siberian populations compared in the present study.

Figure 3. Principle Component Analysis of 18 East Asian populations based on Fst values.

southward to Honshu Island with a series of bottlenecks(Hanihara and Ishida, 2009; Nakashima et al., 2010). However, genetic similarity between the Tohoku Jomon and thegeographically adjacent Kanto Jomon was not observed(Fst = 0.268); the differences are shown in the PCA plot andthe phylogenetic network (Figure 3, Figure 4). These results
are an indication of genetic differences between the Kanto

and northern Jomon populations.
Adachi et al. (2009a) mentioned that three regional Jomon
populations shared some haplogroups (M7a and N9b), andthat 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

10

ANTHROPOLOGICAL SCIENCE

H. KANZAWA-KIRIYAMA ET AL.

Figure 4. Phylogenetic network of 18 East Asian populations based on Fst values.

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 lackshared 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 ofthe population differentiation test, and the observation ofinter-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.
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 theother 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 possiblethat 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 in-terpretation 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 etal., 2010; Adachi et al., 2011).
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 subhaplogroup representations is still limited, and we do notknow the genetic background of the Jomon people from westof 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 thesuccess 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 thisprospect of an expanded range of materials suitable forancient nuclear DNA analysis with the emergence of nextgeneration sequencing, further studies on the Tohoku andVol. 121, 2013

ANCIENT HUMAN MTDNA FROM TOHOKU, JAPANother Jomon materials may enable a better resolution to theissues discussed herein.

Conclusion
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, thesuccess rate of mtDNA haplogroup detection increased to100% when focusing on short DNA regions.
Our observation of genetic similarity between the Tohoku
Jomon and some of the indigenous southern Siberianpeoples 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 thanwith the Kanto Jomon, implying comparatively limited geneflow 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 considered.
In the modern Japanese, mtDNA haplogroups N9b andM7a2, common in the Sanganji and Hokkaido Jomons, areuncommon. Therefore, it seems that the genetic influence ofthe northern Jomon populations to the modern mainland
Japanese is limited in the maternal linage. However, thesamples 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 orderto clarify the characteristics of the Tohoku Jomon as well as
their genetic influence on modern populations, larger andgeographically wider-based samples need to be investigated.

Acknowledgments
We would like to thank Dr. Shintaroh Ueda, Departmentof Biological Sciences, The University of Tokyo, Dr. Ryuichi
Masuda, Department of Biological Sciences, Hokkaido University, and Dr. Kenta Sumiyama, National Institute of Genetics, for their suggestions about our experiments. We arealso grateful to Drs. Tomoya Baba, Katsuhiko Yanagihara,
and Yasuo Shirakibara of the National Institute of Genetics,
for kindly providing us access to their experimental rooms.

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16.7

4.3

7.4

33.3

1.9
9.3

1.4

2.0

2.0
21.6
3.9

24.3

1.9

7.8
19.6
3.9
2.0

15.7
3.9

51

Ai

13.7
3.9

10.8
43.2
8.1
2.7
5.4

5.4

37

Okhotsk

18.5

7.4
9.3

5.6

3.7
1.9

54

Kanto
Jomon

0.5
0.8
0.6

2.5
0.6
0.9
0.6
1.8

0.3
4.6
0.6
6.7
14.1
0.3
36.2
2.1

1.9
1.9
0.5
9.0
10.9
0.9
36.0
5.2

5.2
6.6
3.8
0.5
0.9
1.4

23.3
4.0
0.6

326

Ry

10.0
2.8
0.5

211

MJ

Population

0.3
1.3
1.0

7.6
2.4
5.9
1.2
1.7
1.5
0.7

1.2

7.3
0.3
1.9
8.5
15.7
2.7
25.9
5.2

1.5
3.9
2.7

591

Ko

2.6
3.7
1.3

6.6
6.0
3.3
3.3
0.7

9.3

2.0
5.3
13.9
3.3
23.2
7.3

4.6

3.3
2.6

151

NC

Modern East Asians

3.1

3.1

0.6
2.5

13.6

8.4

0.8
1.7
0.8
2.5
0.8
1.7
4.2

23.5

0.8
26.1
1.7
7.6
5.0
0.8
0.8

0.8
2.5

0.6
1.9
1.9
12.3
17.3
6.2
19.8
7.4

6.7
2.5

119

SC

5.6
0.6

162

YC

0.3

2.5

0.6

0.2

12.0
25.2

1.3
4.1

32.0

1.4

1.6

11.1
7.8

640

TA

4.1

6.2
16.6

73.1

145

NS

5.9

48.0

31.2
1.0

8.4
5.4

202

Ka

1.1
10.3
1.1
4.6

4.6

13.8
17.2

6.9
37.9

1.1
1.1

87

Ul

15.2
8.7

17.4

30.4
8.7

19.6

46

Ud

Siberian

5.4

23.2

5.4

66.1

56

Ni

27.3

18.2

12.1
15.2
6.1

21.2

33

Ne

b

Total of haplogroup M7 except for haplogroup M7a, M7b, M7c, and M7d.
Haplogroup D4 includes haplogroup D1, D2, and D3.
cTotal of haplogroup D except for haplogroup D4, D5, and D6.
dTotal of haplogroup G except for haplogroup G1.
e
It is difficult to estimate the specific haplogroup.
Tohoku Jomons (present study, Adachi et al., 2009a), Hokkaido Jomons (Adachi et al., 2011), Kanto Jomons (Shinoda and Kanai, 1999; Shinoda, 2003), Okhotsk people (Sato et al., 2009),
Ainu (Ai) (Tajima et al., 2004), mainland Japanese (MJ) (Maruyama et al., 2003), Ryukyuan (Ry) (Umetsu et al., 2005), Korean (Ko) (Lee et al., 2006), northern Chinese (NC), Yangtze Riverregion Chinese (YC), southern Chinese (SC) (Yao et al., 2002), Taiwanese Aboriginals (TA) (Trejaut et al., 2005), northern Siberian (NC) (Starikovskaya et al., 1998), Kamchatkan (Schurr et al.,1999), Ulchi (Ul), Udegey (Ud), Nivkhi (Ni) and Negidal (Ne) (Starikovskaya et al., 2005).
Northern Chinese, Liaoning, Qingdao and Zibo; Yangtze River region Chinese, Wuhan and Shanghai; southern Chinese, Gongdong, Guangdong, Guangzhou and Hong Kong; northern Siberian, Chukchi and Eskimos; Kamuchatkan, Koryak and Itel’men.

a

64.8

60.9

11.1

7.4

34.8

M7a
M7b
M7c
M7d
M7*a
N9a
N9b
Y
A
B
C
D4b
D5
D6
D*c
E
F
G1
G*d
M8a
M9
M10
M11
M12
R
Z
Otherse54

23

Hokkaido
Jomonn

TohokuJomon

Ancient East Asians

Appendix 1. Frequencies (%) of mitochondrial DNA haplogroups in ancient and modern East Eurasian populations

14
H. KANZAWA-KIRIYAMA ET AL.
ANTHROPOLOGICAL SCIENCE

n
0.061
0.268
0.292
0.194
0.276
0.088
0.479
0.308
0.382
0.533
0.239
0.216
0.238
0.241
0.251
0.280
0.295

TJ

0.267
0.287
0.204
0.258
0.138
0.463
0.295
0.349
0.507
0.224
0.231
0.218
0.229
0.241
0.283
0.294

HJ

0.203
0.115
0.159
0.149
0.333
0.157
0.271
0.350
0.082
0.107
0.072
0.061
0.082
0.116
0.158

KJ

0.034
0.028
0.137
0.105
0.049
0.152
0.404
0.174
0.205
0.153
0.153
0.156
0.193
0.209

Ok

0.044
0.086
0.187
0.039
0.135
0.343
0.060
0.079
0.066
0.066
0.078
0.119
0.150

Ai

0.118
0.091
0.045
0.171
0.376
0.120
0.151
0.105
0.100
0.113
0.164
0.194

Ul

0.299
0.137
0.224
0.409
0.150
0.146
0.136
0.122
0.134
0.165
0.193

Ud

0.171
0.344
0.530
0.282
0.304
0.243
0.252
0.262
0.302
0.300

Ni

0.079
0.401
0.120
0.160
0.096
0.096
0.100
0.126
0.152

Ne

0.395
0.219
0.264
0.196
0.210
0.207
0.251
0.260

Ka

Appendix 2. Pairwise Fst values between each pair of populations

0.262
0.292
0.228
0.275
0.241
0.359
0.342

NS

0.013
0.012
0.019
0.029
0.090
0.136

MJ

Fst P-value of all comparisons except for Ko–NC and NC–YC are <0.05.
a
The individuals that were not classified into specific haplogroups (‘others’ in Table 5) were removed from the population comparison analysis.

Tohoku Jomon (TJ)
23
Hokkaido Jomon (HJ)
54
Kanto Jomon (KJ)
50
Okhotsk (Ok)37
Ainu (Ai)
51
Ulchi (Ul)87
Udegey (Ud)46
Nivkhi (Ni)56
Negidal (Ne)33
Kamchatkan (Ka)202
Northern Siberian (NS)145
Mainland Japanese (MJ)211
Ryukyuan (Ry)324
Korean (Ko)585
Northern Chinese (NC)149
Yangtze River region Chinese (YC) 157
Southern Chinese (SC)109
Taiwanese Aboriginals (TA)
638

a

0.040
0.050
0.060
0.117
0.156

Ry

0.000
0.008
0.047
0.085

Ko

0.005
0.038
0.079

NC

0.026
0.063

YC

0.012

SC

Vol. 121, 2013
ANCIENT HUMAN MTDNA FROM TOHOKU, JAPAN15