Man In India, 95 (4): 205–228© Serials Publications

LANGUAGE DIVERSITY OF THE JAPANESEARCHIPELAGO AND ITS RELATIONSHIP WITH HUMANDNA DIVERSITY
Naruya Saitou and Timothy A. Jinam
Introduction
The Japanese Archipelago stretches over 4000 km from north to south, and is thehomeland of three human populations; Ainus, Mainlanders, and Okinawans. The
origins of these people have been studied for a long time. The standard theory
based on craniofacial data is the "dual structure model" propagated by Japanesephysical anthropologists, notably Hanihara (1991). According to this model, firstmigrants to the Japanese Archipelago came from somewhere in Southeast Asia
in Upper Paleolithic age more than 30,000 years ago, and were probably
ancestors of the Jomon people. The second wave of migration is believed to havetaken place later in the Yayoi period (3000-1700 BP), where the people arrived
from Northeast Asia. Indigenous Jomon people and new migrants in and after
Yayoi period gradually mixed with each other. This model provides a reasonable
explanation for the morphological similarity between the Ainu people of
Hokkaido at the northernmost main island of Japanese Archipelago, and the
Okinawan people in Southwest Archipelago, despite of large geographicaldistance. Similarity of these peoples was already noticed more than one hundredyears ago by von Baelz (1911) who proposed the Ainu-Okinawan common
origin theory.
We recently determined genome-wide single-nucleotide polymorphisms(SNPs) for Ainus and Ryukyuans (see Figure 1), and analysed these data withexisting data sets (Japanese Archipelago Human Population Genetics
Consortium 2012; Jinam et al. 2015). Major findings were: (1) Recent admixture
with Mainlanders was observed for more than one third of Ainu individuals; (2)Ainus and Okinawans are tightly clustered with a high statistical support
followed by Mainlander and Korean in the phylogenetic tree of East Asian
populations; (3) Ainu population probably experienced admixture with otherpopulations distributed north of Hokkaido. We further analysed these data, andfound that Ainu people are genetically different from Mainlanders living in
Tohoku, northern part of the Honshu Island, and the estimated age of starting
admixture between Ainu and Mainlander ancestral populations was ca. 6th
centrury A.D. (Jinam et al. 2015). We also determined partial nuclear genome
DNA sequences of Jomon period people from DNA extracts used for
mitochondrial DNA haplotype determination (Kanzawa-Kiriyama et al. 2013),
and found that the Ainu people are genetically closest to the Jomon people, and206

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Figure 1

the mainlanders are sandwiched between Jomon and East Eurasian continental
populations (Kanzawa-Kiriyama et al., 2016).
Another aspect is the genome diversity of Japanese Archipelago Mainlander
populations. Yamaguchi-Kabata et al. (2008) reported genome-wide SNP data
analysis of 7,000 Japanese, and they computed Fst distances among people fromseven geographical areas (see Figure 1). Figure 2 is a phylogenetic network
based on these genetic distances using Neighbour-net (Bryant and Morton 2004).
The Okinawan population is far apart from the remaining six populations, as
expected. Kyushu area, which is geographically closest to Okinawa, is also
genetically closest to Okinawa. Interestingly, Tohoku area, which is

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Figure 2

geographically far apart from Okinawa, shares a short split with the Okinawa
population. If modern Tohoku people inherited DNAs of the Emishi who lived in
Tohoku area more than 1,000 years ago, this pattern suggests a genetic affinity
between the Emishi people and the ancestral Okinawans.
Nakaoka et al. (2013) analysed HLA data of ten regions in Japan, and foundvarious interesting diversity among these regions. First of all, Okinawa was quite
different from the remaining nine regions. Shikoku and Hokuriku were outliers
and were different with each other. Shikoku was somewhat closer to Okinawa,
while Hokuriku was most distant from Okinawa.
We recently examined the genome-wide SNP data of the Izumo population
who are distributed relatively close to East Korea (see Figure 1). It should be
noted that Izumo area is in the Chugoku-Shikoku District which was not
examined by Yamaguchi-Kabata et al. (2008). Figure 3 is a Principal Component
Analysis based on preliminary 21 Izumo individual data with four other East
Asian populations: Tokyo (Nishida et al. 2008), Korea (Bae et al. 2011), North
China (HapMap Consortium, 2005), and South China (Teo et al. 2009). The
PCA coordinates of three continental populations (Koreans, Northern Chinese,and Southern Chinese) and Japanese Mainlanders in Tokyo shown in Figure 3
are in good agreement with their geographical relationship. In contrast, Izumo
people are genetically more apart from Koreans than Japanese Mainlanders inTokyo, although Izumo is geographically between Tokyo and Korea. The PCA
plot of Figure 3 suggests the existence of some heterogeneous migrants to theJapanese Archipelago Mainland.

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Figure 3

By combining these analyses with our new analysis on Ainu and otherpopulations in the Japanese Archipelago, a new scenario on the evolutionary
history of people on the Japanese Archipelago is emerging. This is shown in
Figure 4, and we would like to name this as “the inner dual structure” model of
the Japanese Mainlanders. Two phases of migrations are assumed to form thecurrent Japanese Mainlanders in this model. Phase 1 is the earlier migrants who
possibly arrived at the Japanese Archipelago in the late Jomon period (~4000
years ago), while phase 2 is later migrants who came to Northern Kyushu andlater spread eastward. Phase 2 migrants initially brought paddy field rice
agriculture around 3000 years ago, which started the Yayoi period. This phase 2
migration trend is assumed to continue to historical times of Japan. Saitou (2015)
proposed “three migration waves model” based on this inner dual structure
model for explaining the formation of Japanese Archipelago people.
It may be interesting to compare this new scenario based on DNA data withlinguistic data. Corresponding to three genetically defined human populations on
this Archipelago, there are three languages; Ainu, Japanese, and Ryukyuan. The
Ryukyu language is clearly close to the Japanese language, and they were once
considered to be just dialect differences. Lee and Hasegawa (2011) analysed
linguistic data of the Japanese and Ryukyuan that were compiled by Hirayama(1988, 1992), and concluded that the common ancestral language of the Japanese

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Figure 4

and Ryukyuan was introduced to the Japanese Archipelago with introduction ofrice agriculture. This was based on their estimated divergence time of ~2,000
years ago between the Japanese and Ryukyuan languages. Lee and Hasegawa(2011) criticised other hypotheses such as affinity of the Japanese language with
Austronesian and with Altaic languages. They never paid attention to the seminal
work of Robbetts (2005) on the Altai hypothesis.
They used BEAST software (Drummond and Rambaut 2007) whosemathematical framework was similar to that used by Gray and Atkinson (2003)
and Bouckaert et al. (2012), who both supported the Anatolian origin hypothesisof the Indo-European language. Recently, however, ancient DNA analysis ofEuropean individuals strongly supported the classic Steppe hypothesis (Haak et
al. 2015). If this is true, there was something wrong in the mathematical model
used by these studies on language phylogenies.
One clear drawback on the phylogenetic tree model is that there are often
reticulations in linguistic data. In fact, Lee and Hasegawa (2011) showed
phylogenetic networks of Ryukyuan and Japanese dialects using Neighbour-Net(Bryant and Moulton, 2004), and there were so many reticulations in Japanesedialects. We thus conduct more thorough phylogenetic network analysis oflinguistic data used by Lee and Hasegawa (2011) in this paper.

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Materials and Methods
We downloaded supplementary data of Lee and Hasegawa (2011), and computed
Manhattan distances from their 0/1 data. When missing data (indicated as “?”)were found in some words, that word was omitted from distance computation. In
total, we used 159 word data for linguistic distances after omitting 52 words
which included at least one piece of missing data. There were 49 words that had
identical 0/1 patterns, meaning that the remaining 110 words contributed to theobserved distances. There were 15 words which showed singleton patterns.
Therefore, in terms of cladistic thinking, 95 words were phylogeneticallyinformative; see Saitou (2014) for this concept. Distance matrices are available
upon request. Phylogenetic networks were drawn by using SplitsTree4 (Huson
and Bryant, 2006) based on the Neighbour-Net algorithm (Bryant and Moulton,
2004).
Results
Figure 5 shows the phylogenetic network of 10 Ryukyuan dialects. This figure isessentially similar to Figure 4B of Lee and Hasegawa (2011). Split a clusters
dialects in Okinawa and Naze, and splits b and c cluster dialects of Miyako andIshigaki Islands, respectively. The remaining two major splits d and e are
reticulative. Split d clusters Hateruma with Taketomi and Ishigaki Islands, while
split e clusters Hateruma with Yonaguni Island.
Figure 6 is a phylogenetic network for seven Kyushu prefectural dialects.
Split a separates northern prefectures (Fukuoka, Saga, and Nagasaki) fromsouthern four prefectures, and splits b and c cluster Miyazaki-Oita and MiyazakiKagoshima, respectively. Miyazaki Prefecture is geographically between
Kagoshima and Oita Prefectures, and coexistence of splits b and c is reasonable.
Split d clusters Oita and Fukuoka Prefectures which are geographically adjacent.
The four major splits (a-d) are all consistent with geographical propinquity ofprefectures.
Figure 7 is a phylogenetic network for seven Chugoku and Shikoku
prefectural dialects. As we saw in Figure 6, this network also shows dialect
clusters which are geographically close; split a clusters two San-in district
prefectures (Tottori and Shimane), and split c further clusters these two
prefectures with Yamaguchi prefecture which is adjacent to Shimane prefecture.
Two trios of Shikoku district prefectures, one is Kagawa, Kochi, and Ehime andthe other is Tokushima, Kagawa, and Kochi, are separated from the remaining
prefectures with split b and d, respectively.
There are only three major splits in Figure 8, in which the dialect network ofseven Kinki district prefectures are shown. Split a separates the central part ofLANGUAGE DIVERSITY OF THE JAPANESE ARCHIPELAGO

Figure 5

Figure 6

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Figure 7

Figure 8

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the Kinki district (Kyoto, Osaka, Nara, and Shiga) from peripheral ones
(Wakayama, Mie, and Hyogo), while split b seems to correspond to west andeast regions in the Kinki District. Finally, split c clusters dialects of Kyoto andOsaka, which were the cultural centers of Japan for a long time.
The phylogenetic network for the Chubu district dialects shown in Figure 9
is highly reticulated, and some splits show clusters in which their member
prefectures are not geographically adjacent. The longest split a clusters three
Hokuriku district prefectures (Fukui, Ishikawa, and Toyama), while the second
longest split b clusters Yamanashi, Aichi, and Gifu. Although Aichi and Gifu
prefectures are adjacent, Yamanashi is not. Among the remaining six splits (c-h),
those compatible with geographical adjacency are splits e, f, and h. Split cclusters dialect of the Hachijo Island with that of Toyama prefecture. Hachijo
Island dialect is well known to be quite distinct from all the other Japan
Mainland dialects, but this network suggests that it shares some elements with
Toyama dialect. It should be noted that Hachijo Island is on the Pacific, while
Toyama is facing the Japan Sea. Fukui and Yamanashi dialects are clusteredthrough split d, and Gifu and Shizuoka dialects are clustered through split g. If
these splits are not statistical artefacts, some non-geographical factors are
involved in forming these splits.
Phylogenetic networks of Kanto and Tohoku (including Hokkaido) districts
are shown in Figures 10 and 11, respectively. Splits for these two district dialects
are mostly representing geographical adjacency. However, there are some
exceptions; split a of Figure 11 clusters Fukushima and Hokkaido, and split dclusters Miyagi and Aomori.
We now move to compare dialects of two geographically adjacent districts.
Figure 12 is a phylogenetic network of Ryukyuan language dialects and Japanese
language dialects in Kyushu district. There are two short but interesting splits inthis figure. Yonaguni and Hateruma dialects are clustered with Saga prefecture
dialect at split a, and these two Ryukyuan dialects are clustered with all Kyushu
dialects at split b. This suggests some linguistic influence from Northern Kyushu
to these two islands. Figure 13 is a phylogenetic network of Kyushu andChugoku-Shikoku district dialects. Split a clusters Kyushu dialects except for
Nagasaki, and Nagasaki dialect is clustered with Setouchi area dialects(Hiroshima, Okayama, and Tokushima) at split b. This suggests that Nagasaki
dialect was influenced by Chugoku-Shikoku district dialects, especially by
Setouchi dialects.
Figure 14 is a phylogenetic network of Chugoku-Shikoku and Kinki
districts. Split a clusters five Kinki dialects, while Hyogo dialect clusters with
Okayama dialect at split b. This clustering is understandable, for Hyogo andOkayama prefectures are geographically adjacent. However, clustering of Mie

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Figure 9

Figure 10

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Figure 11

Figure 12

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Figure 13

Figure 14

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Figure 15

and Tottori dialects at split c is puzzling. The unique status of Mie dialect is also
found in Figure 15 in which dialects of Kinki and Chubu were compared. Mie isnow clustered with Fukui dialect at split a, while it also clustered with
Wakayama and Hyogo dialects at split b.
Dialects of Chubu and Kanto districts are compared in Figure 16. Dialects ofthese two districts are separated at split a, while Shizuoka is clustered with
Ibaraki at split b and Tokyo, Yamanashi, and Aichi are clustered at split c. Figure
17 is a phylogenetic network of Kanto, Tohoku, and Hokkaido dialects. All
Kanto dialects are clustered at split a, while Tokyo is outside of the cluster
defined by split b and Fukushima is now included in the cluster. Split c defines
Tohoku dialects except for Fukushima, and Hokkaido dialect is clustered withdialects of Kanto district and Fukushima prefecture at split c. This intermediate
location of Hokkaido dialect between Kanto and Tohoku districts probably
reflects the cultural influence to Hokkaido both from Tohoku and from Kanto.
So far, only modern dialects were compared. We would like to add Old
Japanese and Middle Japanese to our comparison. Figures 18-24 are
phylogenetic networks of these two historical Japanese and dialects of seven
districts. In all cases, Old Japanese and Middle Japanese were clustered. Some
dialects showed closer relationship with these historical Japanese. Among
Ryukyuan dialects, Okinawa and Naze dialects are clustered with historical

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Figure 16

Figure 17

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Figure 18

Japanese at split a of Figure 18. Naze dialect is slightly closer to historicalJapanese, for it shares a short split b with them. Historical Japanese also clusterwith Hateruma and Yonaguni dialect at split c. This split probably corresponds tosplit b of Figure 12.
Nagasaki dialect is clustered with historical Japanese at split a of Figure 19,
and Miyazaki and Oita dialects cluster with Old Japanese at split b. Figure 20
shows that historical Japanese are quite different from Chugoku-Shikoku
dialects, yet Kochi and Ehime dialects showed a weak similarity with them asshown at split a. Kinki dialects are also quite different from historical Japanese
as shown in Figure 21, yet Mie and Nara dialects are somewhat similar to these
historical Japanese at split a.
Hachijo Island dialect is well known among those who study Japanesedialects to be quite unique and keeps old words. Split a of Figure 22 confirms
this pattern. Yamanashi dialect is also somewhat similar to historical Japanese as
shown at split b. The phylogenetic network of Kanto dialects and historicalJapanese (Figure 23) shows that Tokyo dialect is somewhat similar to historicalJapanese at split a. The same situation can be found for Hokkaido dialects at
Figure 24, in which Tohoku and Hokkaido dialects were compared withhistorical Japanese.

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Figure 19

Figure 20

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Figure 21

Figure 22

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Figure 23

Figure 24

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Figure 25

Finally, we constructed a phylogenetic network of Ryukyuan dialects,
modern Japanese dialects, and two historical Japanese, as shown in Figure 25.
Ryukyuan dialects are clearly more diverged with each other than Japanesedialects. Hachijo island dialect is located at a unique position among Japanesedialects; it is located between Ryukyuan and Japanese. Old Japanese is moreclosely related to Ryukyuan language than Middle Japanese as depicted by splita. Split b separates historical Japanese, Nagasaki dialect, and dialects of easternJapan (Chubu, Kanto, Tohoku, and Hokkaido) from the rest, while split c
separates Ryukyu dialects, Hachijo island dialect, and Kyushu dialects except for
Nagasaki dialect from the rest.
Discussion
The Japanese Mainland and Okinawa Islands has been populated for thousandsof years. Therefore, if the original languages spoken in the Jomon period evolved
to Japanese and Ryukyuan languages, they are expected to have diverged morethan 3,000 years ago. However, Japanese and Ryukyu languages are much moreclosely related. Hattori (1959) estimated the divergence of these two languages(he used the term “dialects”) to be around 1500 years ago (5th Century A.D.) by
applying the glottochronological technique which was popular in 1950s. Lee andHasegawa (2011) estimated that divergence to be around 2200 years ago.

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Although their new estimate, which applied a new mathematical framework andlinguistic data, is more than 500 years older than Hattori’s estimate, its 95%
confidence interval was 1200 - 4200 years ago, and Hattori’s estimate is within
this range.
Glottochronological studies were heavily criticised in linguistics, and a new
Bayesian method seems to be also problematic. When Drummond and Rambaut(2007) intoduced a new software called BEAST, they used 17 dengue virus env
protein amino acid sequences reported by Lanciotti et al. (1997) as an example.
The env protein data consisted of 495 amino acid sequences with no gap, andthose 17 viral strains were collected between 1956 and 1994. The genome ofdengue virus is RNA, and the evolutionary rates of RNA viruses are usually very
high, so only scores of years are enough for viral proteins to accumulate aminoacid changes. One of us once conducted influenza virus (also RNA genome)
sequence analysis and estimated its evolutionary rates (Saitou and Nei 1986).
Therefore, basic assumptions used in BEAST is understandable. Lee andHasegawa (2011) applied BEAST to linguistic data of only 110 words, and thedivergence time estimation was based on only one time period; between Old
Japanese and Middle Japanese. Linguistic data used by Lee and Hasegawa(2011) were quite scanty compared to molecular data which are expected for
BEAST applications.
When Hattori (1959) estimated the divergence time between Ryukyu andJapanese languages, he implicitly assumed the constancy of the word changing
rate. If we use the neighbor-joining method (Saitou and Nei 1987) to the same
distance matrix used for the phylogenetic network shown in Figure 25, a tree
shown in Figure 26 was produced. MEGA6 (Tamura et al. 2013) was used to
draw that tree. If the root of this tree is between Japanese dialect cluster and
Ryukyuan dialect cluster, the rate of word change is clearly faster in Ryukyu
dialects than Japanese dialects.
The branching pattern of this unrooted tree is different from that of Figure 2
tree of Lee and Hasegawa (2011) in many respects. Middle Japanese and modern
Japanese dialects were clustered in their tree (corresponding to split a of Figure25), while middle Japanese clustered with Old Japanese in the neighbour-joining
tree. The latter clustering was also observed in split d of Figure 25. Anothernoteworthy difference is the placement of Hachijo island dialect. It is outside of
all modern Japanese dialects and historical Japanese in Figure 26, and thispattern is consistent with the unique and old feature of this dialect. In contrast,
Hachijo island dialect was clustered with Shizuoka dialect in the tree shown by
Lee and Hasegawa (2011). Another puzzling pattern of their BEAST-produced
tree is the clustering of Hokkaido, Yamanashi, and Tokyo dialects which arebasal to all the other modern Japanese dialects. In the neighbour-joining tree,
Hokkaido dialect is within the Tohoku cluster, and Tokyo and Yamanashi dialect

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Figure 26

cluster is just outside of this Tohoku-Hokkaido cluster. They further cluster withother Kanto and Chubu dialects and formed East Japan dialect cluster.
It is generally accepted in molecular phylogenetic studies that tree topologies
may be acceptable while the divergence time estimates frequently have various
problems even when we have relatively large molecular sequence data. If theoriginal molecular data are the outcome of a tree-like evolutionary history,
reconstructed trees are often concordant irrespective of methods used. The
existence of many discrepancies between the neighbour-joining tree (Figure 26)
and the BEAST tree (Figure 2 of Lee and Hasegawa 2011) suggests that theword data used include many reticulations. This feature is in fact shown in thispaper. Therefore, we should be careful of any divergence time estimates not
only for molecular data but for linguistic data. When tree topology is quite
different among various tree-making methods, tree topology is also not easy toinfer.
Language evolution on the Japanaese Archipelago can be interpreted byapplying the elite dominance model in linguistics; people on the Ryukyu Islands
once spoke language(s) totally different from the Japanese language. Later, their
original language changed to the Japanese language by Mainlanders who
influenced the Ryukyu people genetically and culturally. If we accept thisassumption, the language shift possibly occurred when Kinki area was the226

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political center and when the government expanded their territory to Ryukyu
Island. This may have occurred between 5th and 10th century A.D., which ismuch later than the divergence estimate of Lee and Hasegawa (2011).
In conclusion, linguistic difference between Japanese and Ryukyu languages
may not reflect DNA difference between Mainlanders and Okinawans, for the
language change in Okinawa probably occurred after the Phase 2 migration
started. However, this language change coincided with gene flow from theMainland to Ryukyu Archipelago that resulted in close genetic relationshipbetween them, although the Okinawans still retained more Jomon genetic
components.
Address for communication
Naruya Saitou and Timothy A. Jinam, National Institute of Genetics, Mishima, Japan.

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