Genes Genet. Syst. (2015) 90, p. 147–152

Human genetic diversity in the Japanese Archipelago:
dual structure and beyond
Timothy A. Jinam1*, Hideaki Kanzawa-Kiriyama2 and Naruya Saitou1
1

Division of Population Genetics, National Institute of Genetics, Yata 1111, Mishima 411-8540, Japan2
Department of Anthropology, National Museum of Nature and Science,
4-1-1 Amakubo, Tsukuba, Ibaraki 305-0005, Japan(Received 30 January 2015, accepted 9 March 2015)

The Japanese Archipelago stretches approximately 3,000 kilometers from
Hokkaido in the north to the Ryukyu Islands in the south, and has seen humanactivity since at least 30 thousand years ago (KYA). The Jomon period from 16
to 3 KYA is associated with cord-marked pottery and the people at that time, whowere hunter-gatherers, occupied a range of locations across the JapaneseArchipelago. The Yayoi period from 3 to 1.7 KYA saw the introduction of migrants
from the Asian Continent who brought rice agriculture to the archipelago. The
dual-structure model, which is based on craniofacial measurements, proposes that
admixture between the Jomon and Yayoi people resulted in current-day Japanese.
Subsequent genetic studies using uniparental and autosomal markers in currentday and ancient human samples are widely in support of the dual-structure
model. These genetic data have also unveiled the uniqueness of the indigenous
Ainu and Ryukyuan people while further demonstrating the genetic substructure
within the Mainland Japanese.
Key words:

Japanese Archipelago, Japanese, Ainu, Ryukyu, population genetics

INTRODUCTION
The Japanese Archipelago is made up of more than
6,000 islands that lie east of the Asian Continent. The
northernmost main island, Hokkaido, is flanked by
Sakhalin and the Kuril Islands of Russia, whereas thesouthernmost tip is made up of the Ryukyu Islands,
which extend to neighboring Taiwan. Most of theapproximately 120 million Japanese people reside in thefour largest islands: Hokkaido, Honshu, Shikoku andKyushu. Honshu is the largest island and can be divided
into Tohoku, Kanto-Koshinetsu, Tokai-Hokuriku, Kinki
and Chugoku regions (Fig. 1). The Japanese people
whose ancestral lineages are originally from Honshu,
Shikoku or Kyushu islands are referred to as Hondo
Japanese (‘mainland’ in Japanese). Besides the Hondo
Japanese, there are indigenous groups in the Ryukyu
Islands and Hokkaido named Ryukyuan and Ainu,
respectively.
Demographic events during the Jomon and Yayoi periods have left their impact on the genetic diversity of current human populations in the Japanese Archipelago.
Researchers have mainly considered these two historicalperiods when inferring the origins of the Japanese
Edited by Hiroshi Iwasakii* Corresponding author. E-mail: tjinam@nig.ac.jp

people. This review will discuss the impact of prehistorical migration events on the genetic diversity of theJapanese, the unique characteristics of the indigenous
Ryukyuan and Ainu populations, and finally the origins
and genetic substructure of the Hondo Japanese. Early
population genetic studies relied on either uniparental
markers (mitochondrial DNA (mtDNA) and Y-chromosome)(Hammer and Horai, 1995; Horai et al., 1996) or dozens
of polymorphic autosomal markers such as blood groups
and red blood cell enzymes (Misawa and Hayashida,1968; Omoto and Harada, 1972; Omoto et al., 1973).
With the advancement of high-throughput genotyping
and sequencing technologies, a large amount of genetic
data of the Japanese has become available in projects
such as HapMap (The International HapMap Consortium,2005), Pan-Asian SNP (The HUGO Pan-Asian SNP Consortium, 2009) and the 1000 Genomes Project (1000
Genomes Project Consortium, 2012). Genetic data are
not limited to existing individuals, as more ancient DNA
has been successfully extracted from human remains thatdate back as far as the Jomon period. The availability
and detailed analyses of these data will prove invaluable
in forming a better understanding of the origins and history of the Japanese population.

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Fig. 1.

Map of the Japanese Archipelago.

PREHISTORY OF THE JAPANESEARCHIPELAGOThe Japanese Archipelago has a long history of humanpresence (Ono et al., 2002; Kaifu and Mizoguchi, 2011;
Saitou, 2015). The earliest signs of human activity inthe archipelago are the presence of stone tools that dateback to 30 thousand years ago (KYA) (Imamura,1996). The oldest human remains found were also dated
to approximately 30 KYA, corresponding to the upper
Paleolithic period. The Ryukyu Islands, in particular,
yielded several of these old skeletal remains. The oldest
human fossils found in Japan are from Yamashita-cho
Cave on Okinawa Island, and carbon-14 dating suggested
an age of 32 KYA (Suzuki, 1983). Other sites such as
Pinza-abu on Miyako Island and Minatogawa Fissure on
Okinawa Island yielded human remains with ages that
range from 18 to 26 KYA (Kobayashi, 1974; Departmentof Education, Okinawa Prefectural Government, 1985;
Baba and Narasaki, 1991). Most recently, a site inShiraho-Saonetabaru cave on Ishigaki Island yieldedhuman remains dating to 20 KYA (Nakagawa et al.,2010). In Honshu Island, the oldest remains were foundin Mikkabi and Hamakita in Shizuoka prefecture, dating
to 7 to 14 KYA (Suzuki, 1962; Matsu’ura and Kondo,
2001). These archeological findings show that there wasalready a substantial human presence in the JapaneseArchipelago during the Paleolithic period. However, itremains unclear whether the Paleolithic people that
already inhabited the Japanese Archipelago at that time
were the direct ancestors of the Jomon people. Comparisons of tooth measurements show substantial difference
between the Paleolithic Minatogawa human from
Okinawa and Jomon samples (Suwa et al., 2011), andmay imply a discontinuity between the Paleolithic andJomon people.
The Jomon period from 16 to 3 KYA takes its namefrom the cord-marked pottery typically found in that time
period. The means of sustenance for the Jomon people
was primarily through hunting and gathering, and agriculture was rudimentary and limited. The Jomon people
were distributed across the Japanese Archipelago, basedon the artifacts (Habu, 2004) and human remains
found. The skeletal remains show a marked differenceHuman genetic diversity in the Japanese
between the Jomon people and present-day Hondo
Japanese. Similarities in the cranial measurements ofJomon and Polynesians (Hanihara, 1991) led to the hypothesis that the Jomon people originated from Southeast Asia.
The morphological structure of the Jomon was also
found to be close to the Ainu and Ryukyuans (Yamaguchi
and Dodo, 1980), suggesting that these two groups retain
more Jomon ancestry than the Hondo Japanese. These
ancient Jomon remains provided priceless data not only
for physical anthropologists, but also for geneticists.
Although a large majority of the DNA extracted fromthese ancient remains was derived from environmental
microorganisms and other contaminants, the small percentage of endogenous DNA that was extracted stillyielded useful and important data. Early studies ofancient DNA tended to focus on mtDNA, mainly due tolarger copy numbers of the molecule that remained in theancient samples compared to the nuclear genome.
mtDNA extracted from Jomon samples shows enrichment
for haplogroups N9b and M7a (Adachi et al., 2011;
Kanzawa-Kiriyama et al., 2013). These two haplogroups
are rarely found in other populations except in theJapanese Archipelago, which further supports the idea ofJomon ancestry in modern Japanese. Interestingly, haplogroup N9b is also found at high frequencies in the
Udegey, a group in southern Siberia (Tajima et al., 2004),
suggesting that the Jomon may have genetic links withpopulations from Northeast Asia. For prehistoric samples, most of the ancient DNA was extracted from Jomon
remains excavated from the Hokkaido and Tohoku areas(Fig. 1), where the lower temperatures and humidity inthese northern regions may have played a part in limiting
DNA degradation in the ancient human remains. However, as DNA extraction and sequencing methods keep
improving, we anticipate that ancient DNA can still be
extracted from poorly preserved samples and enable
genetic analyses of Jomon samples from a wider distribution in Japan. These kinds of improvements will help
address issues such as whether there was already population substructure during the Jomon period and theextent of Jomon genetic contributions to the modern
Japanese. Combined analyses with other ancient DNA
from the Asian continent (Fu et al., 2013) may also help
to answer questions regarding the origins of the Jomon
people.
The Jomon period was followed by what is known as the
Yayoi period, which lasted from approximately 3 to 1.7
KYA. The starting date of the Yayoi period is still debatable: previous estimates started from 2.5 KYA (Imamura,1996), while recent improvements in dating methods havesuggested a much older estimate, up to 3.2 KYA (Fujio,2011). This period is largely known as the time when
agriculture, in particular rice, was introduced to theJapanese Archipelago. Although the exact geographicalorigin of the Yayoi people is unclear, they are believed to149

have migrated from the Asian mainland through the
Korean peninsula and into the Japanese Archipelago via
the Kyushu and/or Chugoku regions (Fig. 1). Bone morphological structure shows that the Yayoi people weremarkedly different from the preceding Jomon people(Hanihara, 1991; Dodo et al., 1992). Unfortunately,
studies of ancient DNA samples from the Yayoi period(e.g., Oota et al., 1995) are not as extensive as those of
Jomon samples, but this should change in the future.
Besides introducing rice agriculture, the Yayoi migrants
also brought new technologies and tools (Imamura, 1996);
but just as importantly, they made a significant contribution the genetic makeup of the present-day Japanese.
The origin of the current Hondo Japanese population
was inferred based on interactions between the Yayoi
migrants and the Jomon people who were already present
in the Japanese Archipelago at that time. Currently, thewidely accepted model for the origin of Hondo Japaneseis the admixture model, also known as the dual-structure
model (Hanihara, 1991). According to this model, Hondo
Japanese are the result of admixture between the ancestral Yayoi and Jomon people (Fig. 2). The current Ainu
and Ryukyuan groups are believed to retain more Jomon
components, based on morphological measurements.
Alternative models include the replacement theory, which
posits that the Yayoi migrants totally displaced theJomon populations, and the transformation theory, inwhich the early Paleolithic humans continually evolved
into current Hondo Japanese with minimal gene flowfrom Yayoi migrants (Suzuki, 1963; Mizoguchi, 1986). As
discussed in the later sections, the admixture model iscurrently the most widely accepted model and is well supported by genetic data.
THE INDIGENOUS GROUPS OF JAPANThe Ainu and Ryukyuan populations are indigenous
groups who now mostly reside in Hokkaido and theFig. 2. Model representing the origins of human populations in
the Japanese Archipelago. Horizontal blue arrows indicate
recent admixture events between the different groups.

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Ryukyu Islands, respectively. Because of similarities intheir cranial and skeletal morphologies with those of the
Jomon people (Yamaguchi and Dodo, 1980; Hanihara,1991), they are thought to be the more direct descendantsof the Jomon people than the Mainland Japanese. In
fact, early anthropologists already noticed that the similarities between the Ainu and Ryukyuans might be due toshared ancestry (von Baelz, 1911). The Ainu in particular exhibit physical features that are distinct from the
Hondo Japanese, leading to various hypotheses regarding
their origins, including genetic links to West Eurasians.
The Ainu have traditionally been associated with a hunting-gathering lifestyle that is common to other populations surrounding the Sea of Okhotsk, such as the Nivkhi
in Sakhalin. Rather than being an isolated group, theAinu most likely experienced cultural and genetic
exchange with their neighboring populations. A study ofdental measurements showed similarities between the
Ainu and the Okhotsk culture people from the 5th to 12th
century A.D. (Hanihara, 2010), while mtDNA analysis
showed phylogenetic clustering of the Ainu, Nivkhi andOkhotsk people (Adachi et al., 2011). A study of the
ABCC11 gene that is responsible for ear wax type further
suggests gene flow from Northeast Asia (possibly by
Okhotsk people) into the Ainu in Hokkaido (Sato et al.,2009).
Early mtDNA analysis of the Ainu using a limited number of restriction enzymes showed similarities with Hondo
Japanese (Harihara et al., 1986), but later studies showed
high affinities between the Ainu and Nivkhi from Sakhalin(Tajima et al., 2004), supporting previous suggestions ofgenetic influence from North Eurasian populations.
Analysis using another uniparental marker, the Ychromosome, showed the presence of haplogroup D-M125
in the Ainu. This Y-haplogroup is endemic to theJapanese Archipelago and is found in high frequencies in
the Ainu and Ryukyuans (Tajima et al., 2004; Hammer etal., 2006), further adding support for the idea of sharedancestry between these two groups. This was further
supported by a genome-wide single nucleotide polymorphism (SNP) study that showed the Ainu and Ryukyuans
cluster with 100% bootstrap probability on the phylogenetic tree (Jinam et al., 2012). Furthermore, autosomal
SNP data also revealed signs of recent admixture
between the Ainu and Hondo Japanese (Jinam et al.,2015).
The Ryukyu Islands can be geographically classified
into four main clusters, but the most populated island is
Okinawa Island. Archeological findings suggest that
there were different cultures that developed in the northern part of the Ryukyu Islands (closer to Kyushu andHonshu) and the southern part (closer to Taiwan) (Asato,2003). Previous genetic studies mostly focused on individuals from Okinawa Island and found that they havehigh genetic similarities with the Ainu in Hokkaido, eventhough these two groups are geographically very distant(Omoto, 1995; Omoto and Saitou, 1997). Genome-wide
SNP studies show that the Okinawans form a distinct
cluster from the Hondo Japanese (Yamaguchi-Kabata etal., 2008), while a more detailed genetic survey of individuals from three main islands in the Ryukyu cluster founddifferentiation between the island groups that was attributed to genetic drift (Sato et al., 2014).
However, none of those genetic studies demonstrated
any links between the Ainu and Ryukyuans and current
Southeast Asian populations, which runs counter to the
hypothesis derived from archeological and anthropological data (Hanihara, 1991). It may be possible that any
shared genetic loci between the indigenous Japanese andSoutheast Asians have become ‘hidden away’ in the
genome due to recombination, assuming that these twogroups diverged a long time ago. A more detailed
sequence analysis and good-quality ancient DNA from
Jomon period samples should contribute to solving thisparticular conundrum.
ORIGINS OF THE HONDO JAPANESE AND THEIRGENETIC SUBSTRUCTURE
Previous studies employed genetic markers such as
mitochondrial, Y-chromosomal and autosomal DNA totackle the issues surrounding the origins of the Japanese.
Support for the dual-structure hypothesis included studies based on mtDNA sequences (Horai et al., 1996;
Tanaka et al., 2004), Y-chromosomal SNPs and short tandem repeat polymorphisms (Hammer et al., 2006). Analyses involving classical protein markers led to partial
support for the dual-structure model, supporting theshared ancestry of the Ainu and Ryukyuans dating backto the Jomon people, but found no close relationshipbetween them and Southeast Asians (Omoto and Saitou,
1997).
A genome-wide SNP study of three Japanese groups(Hondo Japanese mostly from Tokyo, Ainu and Ryukyuan)(Jinam et al., 2012) adds support to the dual-structure
model. Phylogenetic tree analysis shows that the Hondo
Japanese are located between an Ainu-Ryukyuan cluster
and continental Asians, suggesting that they are admixed
between these two population clusters. A follow-up tothat study used a formal test for admixture (Patterson etal., 2012) to show that the Hondo Japanese are indeed theresult of admixture between the ancestors of the Ainu and
Han Chinese or Korean: the Jomon and Yayoi people,
respectively. Furthermore, they estimated the proportion of Jomon component in the Hondo Japanese to beapproximately 18% and that the admixture event
occurred at least 1.4 KYA (Jinam et al., 2015). Other studies have tried to estimate the proportion of Jomon ancestry
in the Japanese population. Using Y-chromosomal markers in the Ainu, Ryukyuan and Hondo Japanese from sev-

Human genetic diversity in the Japaneseeral locations, Rasteiro and Chikhi (2009) estimated theJomon component in the Hondo Japanese using likelihood-based methods and reported a range of 20% to50%. A study by He et al. (2012) used approximately
50,000 autosomal SNPs to estimate a value of 23% to 40%
Jomon component in the Hondo Japanese. These studies
generally agree with the dual-structure model and add
further details such as admixture proportions, but thedual-structure model alone may not be sufficient to
explain the genetic substructure observed in Hondo
Japanese.
Using more than 500,000 SNP data in 7,003 Japanesethroughout the Japanese Archipelago, YamaguchiKabata et al. (2008) showed that the differentiation
between Hondo Japanese from different regions was
small (Fst values ranged from 0.00023–0.00077), yet they
can still be distinguished in principal component analysis
plots. Between the different Hondo Japanese clusters,
the highest amount of differentiation was observed
between Japanese from Tohoku and Tokai-Hokuriku (Fig.
1). Unfortunately, this study did not include Japanesefrom the Chugoku and Shikoku areas, which are geographically closer to the Korean peninsula. Anotherstudy sampled a wider coverage of individuals throughout
Japan but used five highly polymorphic immune-related
genes. The authors showed that the Japanese from
Shikoku and Hokuriku are differentiated from other
Hondo Japanese (Nakaoka et al., 2013). It is clear fromthese studies that the Japanese people are not homogeneous, but to establish whether the observed differentiation can be explained purely by genetic drift or othermigration waves will require further study.
CONCLUSION
Genetic analyses of both current populations andancient remains has greatly enriched our understandingof the history and diversity of human populations in theJapanese Archipelago. In general, genetic data strongly
support the dual-structure model proposed by Hanihara(1991) whereby the Hondo Japanese are the result of
admixture between the Jomon and Yayoi ancestral populations (Fig. 2). The indigenous Ainu and Ryukyuan
populations retain a genetic identity that most likely
traces back to Jomon ancestors, while at the same timeshow indications of recent admixture with the Hondo
Japanese (Jinam et al., 2015). Some questions remainunanswered, however, such as the origins of the Jomon
people and the genetic affinities of the Yayoi people.
These questions can hopefully be addressed by morecomprehensive and expansive ancient DNA studies.
Large-scale genetic surveys have also unearthed genetic
substructure within the Hondo Japanese (YamaguchiKabata et al., 2008; Nakaoka et al., 2013). Such studies
are of interest not only to population geneticists and151

anthropologists, but also to medical geneticists who may
utilize such data to improve diagnosis and personalized
treatment of diseases. The genetic substructure in the
Hondo Japanese also hints at a more complex model ofhuman migrations and interactions than the dualstructure model implies. Future efforts to sample
Japanese groups not represented in previous genetic
studies will greatly benefit our understanding of humanpopulation history in the Japanese Archipelago.

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