AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 102:437–446 (1997)

Genetic Origins of the Japanese: A Partial Support
for the Dual Structure Hypothesis
KEIICHI OMOTO1* AND NARUYA SAITOU2
1International Research Center for Japanese Studies, Kyoto, 610-11 Japan;
2National Institute of Genetics, Mishima, 411 Japan

KEY WORDS
genetic distance; origins of Japanese; Ainu;
Ryukyuan; Asian populations
ABSTRACT
Based on the morphological characteristics of the skull andteeth, Hanihara ([1991] Japan Review 2:1–33) proposed the ‘‘dual structure
model’’ for the formation of modern Japanese populations. We examine thismodel by dividing it into two independent hypotheses: 1) the Upper Paleolithic population of Japan that gave rise to the Neolithic Jomon people was ofsoutheast Asian origin, and 2) modern Ainu and Ryukyuan (Okinawa)
populations are direct descendants of the Jomon people, while Hondo (Main
Island)-Japanese are mainly derived from the migrants from the northeast
Asian continent after the Aeneolithic Yayoi period. Our aim is to examine theextent to which the model is supported by genetic evidence from modern
populations, particularly from Japan and other Asian areas. Based on genetic
distance analyses using data from up to 25 ‘‘classic’’ genetic markers, we findfirst that the three Japanese populations including Ainu and Ryukyuan
clearly belong to a northeast Asian cluster group. This negates the first
hypothesis of the model. Then, we find that Ainu and Ryukyuans share agroup contrasting with Hondo-Japanese and Korean, supporting the second
hypothesis of the model. Based on these results, we propose a modified versionof the dual structure model which may explain the genetic, morphological,
and archaeological evidence concerning the formation of modern Japanese
populations. Am J Phys Anthropol 102:437–446, 1997. r 1997 Wiley-Liss, Inc.

Questions about the origins of modern
Japanese have a long history of debate (forreferences see Hanihara, 1991). In short, thecontroversies were between ‘‘continuity’’ and‘‘admixture’’models. The advocates of the former
model believed that the inhabitants of theJapanese Islands were genetically unchanged
from prehistoric to historic times, while theirmorphology showed secular changes (e.g., Suzuki, 1969). The advocates of the latter modelemphasized the drastic changes in morphology
and culture which took place synchronically
about 2,300 years ago, mainly in the westernpart of Japan, and considered these as evidence
for admixture (e.g., Kanaseki et al., 1960).
In 1991, Hanihara proposed a hypothesis
for the formation of Japanese populations,which he called the ‘‘dual structure model.’’r 1997 WILEY-LISS, INC.

It is clearly on the side of the admixture
school and is the most comprehensive current hypothesis on the formation of modern
Japanese populations.
To test this hypothesis, we divide it into
two parts that are briefly summarized asfollows: 1) the Upper Paleolithic populationsof Japan came from somewhere in southeast
Asia and gave rise to Jomonese, or thepeople of the Neolithic Jomon period (12,000–
2,300 years BP), and 2) modern Japanese
populations were formed by the mixture of
mainly two population groups with different*Correspondence to: K. Omoto, International Research Center
for Japanese Studies, 3-2 Oeyama-cho, Goryo, Nishikyo-ku,
Kyoto, 610-11 Japan. Email: ko8516@nichibun.ac.jp
Received 14 November 1995; accepted 2 February 1997.

K. OMOTO AND N. SAITOU

438

TABLE 1. Nei’s standard genetic distances (lower diagonal matrix) and modified Cavalli-Sforza distances(above diagonal matrix) for the four populations

Hondo-Japanese
KoreanAinu
Ryukyuan

Hondo-Japanese

KoreanAinu

Ryukyuan—
0.00404
0.00808
0.003360.00354—0.010430.00899

0.00747
0.01155—
0.006960.002170.007070.00642—

ancestries: Ainu and Ryukyuan are relatively pure descendants of Jomonese, while
Hondo (Main Island)-Japanese have received
strong genetic infusions from migrant populations who came to western Japan during the
Aeneolithic Yayoi period (300 BC–300 AD) and
the Proto-historic Kofun period (300–700 AD).
These migrants came from northeast Asia
via the Korean peninsula and from there
spread to eastern and southern Japan.
We believe that questions on the origins ofhuman populations are better addressed bygenetic approaches than by other approaches, be they morphological or, definitely, cultural (e.g., archaeological and linguistic) ones. In this paper, we present theresults of two genetic distance analyses thatuse ‘‘classic’’ genetic marker gene frequency
data. The first analysis tests whether Japanese populations have roots in southeast
Asia. The second one seeks to determine
whether there is a dual structure among
Japanese populations. On the basis of ourfindings, we propose that the first question
cannot but the second question can be supported. We discuss the anthropological significance of these results and present a
modified version of the dual structure model.
MATERIALS AND METHODSIn the first genetic distance analysis, 26
populations of the world, including three
Japanese (Ainu, Ryukyuan and HondoJapanese), were compared. The populations
examined other than Japanese were: three
African, four Indo-European, three native
American, nine east Asian, one native Australian, one New Guinean (Papuan), and
two Pacific populations. Gene frequency dataon a total of 20 polymorphic loci were available for these populations: eight blood groupsystems (ABO, MNSs, P, Fy, Rh, Jk, Di, K),seven red cell enzyme systems (ACP, PGD,
PGM1, PGM2, ADA, GPT, ESD), and fiveserum protein systems (Hp, Tf, Gc, Gm,

Inv). Most data on Japanese populations
were taken from the compilation by JIBP
Synthesis, Volume 2 (Watanabe et al., 1975).
The sources of some additional data were as
follows: GPT (Ueda et al., 1979) and ESD(Omoto et al., 1975). The data on blood
genetic markers of Koreans were taken from
Yuan et al. (1984) and Goedde et al. (1984).
The data on other populations were obtained
from Roychoudhury and Nei (1988) and Masatoshi Nei (personal communication), withthe exception of our unpublished data on
two Negrito populations of the Philippines.
In the second genetic distance analysis,
the three Japanese populations mentioned
above and Koreans were compared using
gene frequency data from 25 polymorphic
loci. In addition to those mentioned above,
we were able to use data from five polymorphic loci: pseudocholinesterase-1, cerumen,
PTC taste sensitivity, color blindness, and INH
inactivator types (Watanabe et al., 1975).
For calculation of genetic distances, Nei’sstandard distance (Dst) (Nei, 1972) and themodified Cavalli-Sforza distance (DA) (Nei etal., 1983) were used (Table 1). To cluster
each set of genetic distances, we employed
the neighbor-joining (NJ) method (Saitou
and Nei, 1987). This approach to tree construction has been shown to be superior toother methods such as the UPGMA method(Sokal and Sneath, 1963) in recovering thetrue branching pattern of the genetic relationship of populations (Saitou and Nei,
1987; Nei and Takezaki, 1994). To evaluate
the branching pattern statistically, we used
the bootstrap test (Efron, 1982). This test
determines the probability of reproducing
the particular branching pattern in the phylogenetic tree by using randomly recombined genefrequency data for the given populations.
RESULTSIn the first set of our calculations, a totalof 26 populations of the world were com-

GENETIC ORIGINS OF JAPANESE

439

Fig. 1. A neighbor-joining (NJ)
genetic tree for 26 populations of
the world based on standard genetic distance (Dst). Allele frequency
data of 20 polymorphic loci areused. Numbers along the branches
are bootstrap probability values(%).

pared (Figs. 1, and 2). In both genetic trees,using the genetic distances Dst and DA, theAfrican populations are very different from
non-African populations. The bootstrap value
for this separation is very high (93–96%).
Among non-Africans, the Indo-European
population group is first separated from therest, though the bootstrap probability values are not as high as those showing separation of the African groups. Further, Native
American populations including Eskimos are
separated from Asian/Pacific populations.
However, with regard to clustering of Native
Australian and New Guinean populations,the two trees show a noteworthy difference
from each other. In the tree based on Dst(Fig. 1), they are clustered with the northeast Asian group, which is unexpected, given
the anthropological view that the roots ofAustralian and New Guinean populations
are in southeast Asia. In the tree based on
DA, however, Australians and New Guineans are clearly separated from other AsianPacific populations (Fig. 2).
Among the rest of the Asian-Pacific populations, two cluster groups may be recognized, although the bootstrap values fortheir separation are low: northeast Asianand southeast Asian/Pacific groups. ThreeJapanese populations—Korean, Tibetan, andMongolian—form the northeast Asian cluster group, while southern Chinese, Thai,
Filipino, Indonesian, Micronesian, Polynesian, and two Negrito populations belong to
the southeast Asian/Pacific cluster group.
In the second set of phylogenetic analyses,
three ethnic groups of Japan (Ainu,
Ryukyuan, and Hondo-Japanese) are com-

440

K. OMOTO AND N. SAITOU

Fig. 2. A neighbor-joining (NJ)
genetic tree for 26 populations of
the world based on modified Cavalli-Sforza distance (DA). The genefrequency data used is the same as
in Fig. 1. Numbers along thebranches are bootstrap probability
values (%).

pared with the Korean sample as the control. We had to restrict our analyses to thesesamples because we wanted to maximize thegenetic data used in the analyses. Only 20
genetic loci are available for the other populations, but 25 loci have been examined inthese three Japanese and the Korean population samples. The NJ networks show that
Ainu and Ryukyuan samples are clustered
together in contrast to Hondo-Japanese andKorean. The two genetic distance measuresused (Dst and DA) gave essentially the same
topology, although the bootstrap values forthe separation of the Ainu/Ryukyuan branch
were slightly different: 74% for the one
based on Dst and 85% for DA (Fig. 3).

DISCUSSION
Background of the dual structure model
Hanihara’s model is primarily based on
findings arising from studies on cranial anddental features (Hanihara, 1991, 1992). The
basic observation supporting this model isthe morphological similarity of Ainus, and tosome extent of Ryukyuans, to the Neolithic
populations of the Jomon period, who areusually regarded as descendants of the Upper Paleolithic population of Japan represented by Minatogawa Man (Howells, 1966;
Suzuki, 1982; Hanihara, 1984). Furthermore, the difference in cranial morphology
between the Jomon and the Aeneolithic Yayoi

GENETIC ORIGINS OF JAPANESE

Fig. 3. The NJ genetic tree comparing three Japanese populations (Ainu, Ryukyuan, and Hondo-Japanese) with Korean as a control, based on allele frequency
data of 25 polymorphic loci. Genetic distance measuresused are DA (A) and Dst (B). Note that the bootstrap
probability values (85% for A and 74% for B) are muchhigher than those under the random expectation (33%).

populations in the western part of Japan isso remarkable and occurred so suddenly atabout 2,300 years BP that a continuity model
provides insufficient explanation. Hanihara(1987) also used computer simulation to estimate the number of migrant people who cameto the western part of Japan. He proposed thatover the 1,000 years elapsed since the beginning of the Yayoi period (300 BC) and the end of
the Kofun period (700 AD) an unexpectedly
large number of migrant people may haveentered Japan: 1.5 million, assuming theannual growth rate of the migrant Yayoi rice
farmers was 0.2 percent (Hanihara, 1987).

441

Although the validity of this figure can be
examined through more detailed simulation
studies, we think that Hanihara’s dual structure model is superior to many other models
on the origins of the Japanese that havebeen proposed because most of these arerather nonquantitative and speculative.
The strong advocate for the dual origin
and admixture model for the formation of
the Japanese populations, as well as theidea that the ancestors of the Jomon peoplecame from southeast Asia is Christy Turner(Turner, 1976, 1987, 1992). He demonstrated that east Asian populations can bedivided into two distinct groups on the basisof dental patterns: the northeast Asian groupexhibit ‘‘Sinodonty’’ and the southeast Asiangroup shows ‘‘Sundadonty.’’According to him,
the Ainu and Jomon populations are sundadonts, whereas the Hondo-Japanese aresinodonts (Turner, 1976).
Mitochondrial DNA (mtDNA) extracted
from ancient bones also seemed to suggest acommon origin for the Jomon and Ainu
populations (Horai et al., 1989, 1991). In
these studies, mtDNA was extracted fromthe bones of five Jomonese, carbon 14–dated
at about 6,000 years BP, and six earlymodern Ainu (seventeenth to eighteenth century AD). A 190 base-pair (bp) segment of theD-loop region of mtDNA was sequenced, andthe sequences were compared with those ofmodern individuals from various regions of
the world. An identical sequence was observed among four Jomonese, two Ainu, andthree southeast Asian as well as 15 nonAinu Japanese mtDNAs. Although Horaiand his colleagues are cautious about theirconclusions on the origins of Jomonese andAinu (Horai et al., 1989), this result has
been cited as positive evidence for the southeast Asian origin of the first population ofJapan (Hanihara, 1991). However, it is worth
noting that there is a big difference between
the phylogeny of molecules and the phylogeny of populations. It is well known thatmolecular splits may far antedate population splits (Nei, 1987). In the molecular
genetic tree of Horai et al. (1991), mtDNAs
of non-Ainu Japanese are scattered aroundthe whole tree, among mtDNAs of Europeans and Africans, and do not cluster.

442

K. OMOTO AND N. SAITOUThe question of northernor southern origins
Contrary to the assumptions of the dual
structure model, classic genetic marker data
show that Japanese populations, including
Ainu, have definite northern affinities. Matsumoto (1984, 1988) found that serum gammaglobulin (Gm) types showed a clear-cut
north/south dichotomy of east Asian populations and that Japanese belonged to thenorthern group. He also showed that Japanese populations are relatively homogeneous in the distribution of Gm allele frequencies, which contradicts Hanihara’s dual
structure model. Matsumoto’s conclusion,that the homeland of all Japanese populations may have been in the Lake Baikal areain Siberia, however, met with strong objection from Japanese anthropologists, including Kazuro Hanihara. We also believe that
conclusions about the origins of human populations should be based on information frommany genetic loci rather than a single genetic locus.
Nei and Roychoudhury (1993) analyzed 26
populations from around the world using
gene frequency data from 29 polymorphic
loci of classic genetic markers and examined
the resulting dendrograms by bootstrap
tests. Among east Asians, they comparedJapanese (Hondo-Japanese), Koreans, Mongolians, Tibetans, southern Chinese, Thais,
Filipinos, and Indonesians. They did notrecognize northern and southern clustergroups and used the traditional term Mongoloid to denote all east Asian and Pacificpopulations.
Recently, Nei published phylogenetic treesthat show the relationships of Japanese
populations (Nei, 1995). This time, he compared Ainu, ‘‘Japanese of Okinawa,’’(Ryukyuan) and ‘‘Japanese of Tokyo’’ (HondoJapanese) with neighboring populations using data from 18 polymorphic loci. He showedthat the three Japanese populations areclose to Korean, while southern Chinese,
Native Taiwanese, Thai, and Filipino
samples cluster as a separate group. On thebasis of this result, he challenged Hanihara’s hypothesis as a whole with respect tothe origins and the dual structure of Japanese populations.

Omoto (1995) examined the problem of
the origins of Ainu in detail. He compared
Native Australian, New Guinean, Micronesian, and Polynesian populations plus 11
east Asian populations on the basis of NJ
trees with DA distances, using classic genetic markers from 23 polymorphic loci.
Ainu clearly fell in to the northeast Asiangroup, with Korean, Mongolian, and Tibetan
samples, while southern Chinese, Thai, Filipino, Indonesian, and two Negrito populations
were linked with the southeast Asian group.
The overall Hondo-Japanese admixture
rate in the original sample of about 500 Ainu
from the District of Hidaka on Hokkaido,
which is the northernmost island of Japan,
was estimated to be approximately 30–40%(Omoto, 1972). Omoto (1995), however, determined the impact of admixture on the position of the Ainu population in the tree bycorrecting gene frequencies for admixture.
No change occurred even when an admixture estimate of 40% was employed andAinu remained in the northeast Asian cluster group. However, the branch length to the
Ainu elongated considerably. When a hypothetical admixture rate of 60% was used tocorrect gene frequencies, the Ainu remainedin the northeast Asian cluster group, but theNative Australian/New Guinean cluster
moved near the root of the long branchleading to the Ainu. The genetic relationships of other populations were essentiallyunchanged. Although it is not possible todraw a conclusion from such a simulation, it
lends support the view that Ainu and Native
Australians/New Guineans both are derived
directly from the Upper Paleolithic populations of east Asia (Omoto, 1995). The possibility that Ainu origins lie in ancestral population groups in northeast Asia has also beenshown recently by a DNA-based study of
HLA Class II genes (Bannai et al., 1996).
Our study confirms that three Japanese
populations, including Ainu and Ryukyuan,
belong to the northeast Asian group, alongwith Koreans, Mongolians, and Tibetans.
This group appears separated from thesoutheast Asian group comprising southernChinese, Thai, Filipino, Indonesian, Micronesian, Polynesian, and two Negrito populations, although the bootstrap probability forGENETIC ORIGINS OF JAPANESE

this separation is rather low and is statistically not significant (22% in Fig. 2).
With regard to the origins of the Mongoloid populations, the currently popular viewassumes that southeast Asia was the centerof dispersals (e.g., Turner, 1995). This view,which is based primarily on morphologicaltraits, was examined by Omoto (1995). He
considered genetic evidence and favored amodel which assumes independent origins
of northeast Asian, southeast Asian, andNative American population groups. Nei(1995) seems to be skeptical about the dichotomy of northern and southern Mongoloid groups because the branching yields
relatively low bootstrap values. However, inview of the genetic, archaeological, and linguistic evidence for large-scale dispersals ofnorthern groups into southeast Asia and thePacific during the last 10,000 years (e.g.,
Bellwood, 1979, 1996), we assume as a working hypothesis that the dichotomy in our
genetic tree (Fig. 2) has historical validity.
Hanihara’s view that the Upper Paleolithic population of Japan originated somewhere in southeast Asia may have been
based partly on the observation of Suzuki(1982) on Minatogawa Man (Hanihara,1991). Suzuki considered that the skull of
Minatogawa No. 1 dated at approximately
18,000 years BP is morphologically similar
to Jomonese. He further assumed that Minatogawa Man is more closely related to Liujang Man of southern China than to thespecimen No. 101 of Upper Cave of Zhoukoudian, northern China. However, we doubtthat observations on a single skull can provide all that needs to be known about origins. After examining our genetic data, we
propose a counterhypothesis that the Upper
Paleolithic populations of Japan are derived
from those of northeast Asia and did notnecessarily originate in southeast Asia. A
critical examination of the three specimensfrom Upper Cave are particularly importantin this regard.
We believe that our hypothesis is more inagreement with prehistoric evidence than is
Hanihara’s. According to most archaeologists in Japan, stone-tool cultures of theUpper Paleolithic and the successive Jomon
period show definite northern affinities (Chosuke Serizawa, personal communication).

443

The microblade tradition accompanying the
Araya type burin was widely distributed
from eastern Siberia to the Japanese archipelago from the postglacial period until the
beginning of the Jomon period (approximately 20,000–12,000 years BP). No stonetool culture of southeast Asian affinities has
been discovered in Japan for this period(Kimura, 1993; Tanaka et al., 1995).
Dual structure of the Japanese
populations
Omoto (1972, 1992) and Omoto andMisawa (1976) have shown that Ainu and
Ryukyuan peoples are genetically rather
similar to each other but are different from
Hondo-Japanese. This finding seemed to fit
well with the admixture model for the formation of the Japanese populations. In theseprevious reports, however, the dichotomy of
Ainu/Ryukyuan and Hondo-Japanese wasemphasized, without the relationship being
tested statistically. In the present study,
three Japanese populations are compared toeach other, with Korean as the control on thebasis of the largest data set ever used: 25
polymorphic loci. Also, the separation between the Ainu/Ryukyuan cluster and the
Hondo-Japanese/Korean group in the NJ
network was statistically evaluated by bootstrap probabilities (Fig. 3). While two genetic distance measures, Dst and DA, gave
essentially the same topology, the bootstrap
value is slightly higher (85%) in the treeusing DA than that using Dst (74%). Although this difference in bootstrap values isstatistically not significant, we have notedthat DA is superior to Dst in producing
reliable genetic relationships of populations(Figs. 1, 2). Since the expected value of thebootstrap probability for four populations
under no genetic relationship (‘‘star phylogeny’’) is 33%, the observed values are muchhigher than this random expectation. Recently, theoretical studies on the bootstrap
test have been extensively conducted (e.g.,
Sitnikova et al., 1995; Zharkikh and Li,
1995; Efron et al., 1996). However, it is still
not clear how bootstrap probabilities forgenetic trees should be treated with theusual statistical tests. Therefore, we do notconsider reliance on bootstrap probabilities
as critical. In any case, we believe that our444

K. OMOTO AND N. SAITOU

results give support for the separation between Ainu/Ryukyuan and Hondo-Japanese/
Korean clusters. If this clustering is real, it
in turn gives a partial support for Hanihara’s dual structure model, in terms of the
duality of the Japanese populations.
It is worth noting that our conclusions aredifferent from those of Nei (1995). He published a phylogenetic tree based on 18 polymorphic loci that shows the relationships ofAinu, Hondo-Japanese, and Okinawan(Ryukyuan) with neighboring populations.
He expressed his doubt about Hanihara’s
dual structure model as a whole (Nei, 1995).
However, when the hypothesis is broken
into two components, the evidence, we suggest, shows that there may in fact be a
duality in Japanese populations. This difference in interpretation will be cleared by
future studies with much more and betterdata. At this moment, we think that thedetails of a population’s origin are unlikely
to be revealed by using a worldwide data set
such as used by Nei (1995). To understandlocal biological history, one has to examine
the genetic profiles of the populations thathave been hypothesized to be ancestral to it
and to do this with as large a number ofgenetic loci as possible. Of course, we do notconsider our findings to be final, particularly
because of our relatively low bootstrap values. Probably, our study represents a microscopic rather than a macroscopic approachin reconstructing the population history ofJapan.
Recently, a detailed genetic comparison of
Asian populations, including Ainu and
Ryukyuan, which used mtDNA sequence
data was published (Horai et al., 1996). The
results from this study are in agreementwith ours in that Hondo-Japanese and Koreans are genetically very close to each otherand the admixture model of the formation of
the modern Japanese is favored. However,with regard to the relationship between the
Ainu and the Ryukyuan, no evidence for acommon ancestry is found. Future studies
are needed to clear up the position of
Rykyuans.
Finally, when origins are considered, questions about linguistic evidence commonlyarise. Our view can be summarized as follows. If a large number of migrants to Japanactually came from northeast Asia, perhaps
via the Korean peninsula starting around2,300 years BP, as Hanihara’s dual structure model maintains, why is the languageof Hondo-Japanese (i.e., Japanese) so different from Korean or other Altaic languages?
In our view, language changes during population mixture are complex social phenomena that cannot be simply defined or measured chronologically, as can biologicalphenomena. Given the almost complete absence of quantitative and statistical comparisons between Japanese (including Ainu and
Ryukyuan) and other languages in Asia,
except for the work of Biten Yasumoto, which
has no general support among Japanese
linguists, we have at present no clear answer, either pro or con, to our question. It isinteresting to note that, on the basis ofstatistical comparisons of basic words amongeast Asian languages including the Ainu, hereached the conclusion that Ainu and Korean languages may have common ancientancestry in what he calls the Paleo-FarEastern language group (Yasumoto andHonda, 1978; Yasumoto, personal communication). For this reason, we do not putemphasis on language now and have focussed our attention on genetic, morphological and archaeological evidence.
CONCLUSIONSWe propose a modified version of the dual
structure model of the origins of Japanese
populations. Two fundamental populationgroups are ancestral to modern Japanese
populations (Ainu, Ryukyuan, and HondoJapanese). One group, represented by the
Jomonese who gave rise to the modern Ainu
and probably also the Ryukyuan populations, has its origin in the Upper Paleolithic
populations of northeast Asia, which were
not necessarily derived from southeast Asia.
The other group is the later migrants of the
Yayoi and Kofun periods who also came from
northeast Asia but were different geneticallyand morphologically from the first group.
Intermixtures occurred between these twogroups, but the genetic influence of thesecond group is predominant in the majorityof modern Japanese (Hondo-Japanese).
Clearly, further studies are necessary which
include more information, particularly on

GENETIC ORIGINS OF JAPANESE

ancient and modern DNAs of Ainu,
Ryukyuan, and other populations of Japanand east Asia, to clarify the origins of theJapanese people.
ACKNOWLEDGMENTS
We thank Professor Masatoshi Nei of The
Pennsylvania State University (State College, PA) for providing us with gene frequency data. We also thank two anonymous
reviewers who read the original manuscript
critically and gave us invaluable comments.
Thanks are also due to Dr. Akiko Uchida,
Chiba University, for help in preparing theoriginal manuscript.
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