Genetic Origins of the Japanese a Partial Support

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Genetic Origins of the Japanese: A Partial Supportfor the Dual Structure Hypothesis

KEIICHI OMOTO1* AND NARUYA SAITOU 2

1 International Research Center for Jap anese Stu dies, Kyoto, 610-11 J apan;2 National Institute of Genetics, Mishima, 411 Japan

KEY WORDS genetic dista nce; origins of J apa nese; Ainu;

Ryukyua n; Asian populations

A B S T R A C T Based on the morphological char acteristics of the skull a nd

teeth, Hanihara ([1991] Japan Review 2:1–33) proposed t he ‘‘dua l str uctu re

model’’ for th e forma tion of modern J apa nese populations. We examine this

model by dividing it into two independent hypotheses: 1) the Upper Paleo-

lithic population of Ja pan tha t gave r ise to the N eolithic J omon people was of

s ou t h e a s t As ia n or i gi n , a n d 2 ) m o de r n Ai n u a n d R yu k y u a n (O k in a w a )populations are direct descendan ts of the J omon people, while H ondo (Main

I sland) -J apanese ar e mai nly der ived fr om the migr ants fr om the nor theast

Asian cont inent after t he Aeneolithic Yayoi period. Our a im is to examine t he

extent to which the model i s suppor ted by genetic evidence f r om moder n

populations, part icularly from J apa n a nd other Asian area s. Based on genetic

dista nce an alyses u sing da ta from u p to 25 ‘‘class ic’’genet ic ma rk ers, we find

fi r s t t h a t t h e t h r e e J a p a n e s e p op u la t i on s i n cl u di n g Ai n u a n d R yu k y u a n

clear ly bel ong t o a nor theast Asian cluster gr oup. This negates the fir st

hypothesis of the model . Then, we find that Ainu and Ryukyuans shar e a

group contrasting with Hondo-Japanese and Korean, supporting the second

hypoth esis of th e model. Based on t hese r esult s, we propose a m odified version

of the dual structure model which may explain the genetic, morphological,

and archaeological evidence concerning the formation of modern Japanese

populat ions. Am J Ph ys Anth ropol 102:437–446, 1997. r 1997 Wiley-Liss, Inc.

Questions about t he or igins of moder n

Japanese have a long history of debate (for

references see Han ihara , 1991). In short, th e

cont rover sies wer e between ‘‘cont inu ity’’an d

‘‘adm ixture’’models.Th e advocat es ofth e former

model believed that the inhabitants of th e

Ja panese Islands were genetically u nchanged

from prehistoric to historic times, while their

morphology showed secular changes (e.g., Su-

zuki, 1969). The advocates of the latter model

empha sized the dra stic changes in morphologyand cultur e which took place synchronically

about 2,300 years a go, mainly in the western

part ofJ apa n, and considered these as evidence

for a dmixtu re (e.g., Kana seki et a l., 1960).

In 1991, Hanihara proposed a hypothesis

for the formation of Japanese populations,

which h e called t he ‘‘dua l st ru ctur e m odel.’’

I t i s c l e a r l y o n t h e s i d e o f t h e a d m i x t u r e

school and is the most comprehensive cur-

rent hypothesis on th e forma tion of modern

Japanese populations.

To test this hypothesis, we divide it into

t w o p a r t s t h a t a r e b r i e fl y s u m m a r i z e d a s

follows: 1) the U pper Pa leolithic populat ions

of J apa n came from somewhere in southea st

As ia a n d g a ve r is e t o J o m on e se , o r t h e

people oft he Neolithic J omon period (12,000–

2,300 year s BP) , and 2) moder n Japanesepopulations were formed by the mixture of

mainly two population groups with different

*Correspondence to: K. Omoto, Intern ational Research Cent erfor Ja pa ne se St udi e s, 3-2 Oe ya ma -cho, Goryo, Ni shi kyo-ku,Kyoto, 610-11 Japa n. Ema il: ko8516@nichibu n.ac.jp

Received 14 November 1995; accepted 2 Febr uar y 1997.

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

r 1997 WILEY-LISS, INC.



a n ce s t r ie s : Ai n u a n d R yu k y u a n a r e r e la -

tively pu re descendan ts of Jomonese, while

Hondo (Main Island)-Japanese have received

strong genetic infusions from migrant popula-

tions who came to western J apan during the

Aeneolithic Yayoi period (300 BC–300 AD) and

the Proto-historic Kofun period (300–700 AD).

These migr ant s came f r om nor t heast Asia

v i a t h e K o r e a n p e n i n s u l a a n d f r o m t h e r e

spr ead to easter n and souther n Ja pan.We believe th at qu estions on th e origins of

huma n populations ar e better addr essed by

g en e t ic a p p r oa ch e s t h a n b y ot h e r a p -

pr oaches, be they mor phological or , defi-

nitely, cultural (e.g., archaeological and lin-

guistic) ones. In this paper, we present the

results of two genetic distance an alyses tha t

use ‘‘class ic’’gen etic m ar ker gene frequency

data. The fir st analysis tests whether J apa-

n e s e p op u la t i on s h a v e r oot s i n s ou t h e a s t

Asia. The second one seeks t o deter mine

w h et h er t h e re is a d u a l s t r u ct u r e a m on g

Japanese populati ons. On the basi s of our

findings, we propose that the first questioncannot but the second question can be sup-

ported. We discuss the ant hropological sig-

n ifi ca n ce of t h es e r e su lt s a n d p r es en t a

modified version of the dual st ructur e model.

MATERIALS AND METHODS

I n the fir st geneti c dist ance analysis, 26

populations of the wor ld, i ncludi ng thr ee

J a p a n e s e (Ai n u , R y u k yu a n a n d H on d o-

J apa nese), were compar ed. The populations

examined other than Japanese wer e: thr ee

Afr ican, four I ndo-Eur opean, thr ee native

American, nine east Asian, one native Aus-

t r a l ia n , on e N e w G u i n e a n (P a p u a n ), a n dtwo Pacificpopulations. Gene frequency data

on a total of 20 polymorphic loci were avail-

able for t hese p opulat ions: eight blood group

systems (ABO, MNSs, P, Fy, Rh, Jk, Di, K),

seven r ed cell enzyme systems (ACP, P GD,

PGM1, PGM2, ADA, GPT, ESD), and five

s e r u m p r ot e in s ys t e m s (H p , T f, G c, G m ,

I n v). M os t d a t a on J a p a n e se p op u la t i on s

wer e taken f r om the compilation by JI BP

Synt hesis, Volum e 2 (Wat an abe et al., 1975).

The sources of some additional da ta were as

follows: GPT (Ueda et al., 1979) and ESD

(Omoto et al ., 1975). The data on blood

genetic mar kers of Korean s were ta ken from

Yua n et a l. (1984) and Goedde et a l. (1984).

The data on other populations were obtained

from Roychoudhury and Nei (1988) and Ma-satoshi Nei (personal communication), with

the exception of our unpublished data on

two Negrito populations of the Philippines.

I n the second genetic distance analysis,

the thr ee Japanese populations mentioned

a b ov e a n d K or e a n s w er e com p a r e d u s in g

gene fr equency data fr om 25 polymor phic

loci. In addition to those mentioned above,

we were able t o use da ta from five polymor-

phic loci: pseudocholinesterase-1, cerumen,

PTC taste sensitivity, color blindness, and INH

inactivator types (Watanabe et al., 1975).

For calculat ion of genet ic dista nces, Nei’s

standar d distance ( Dst ) (Nei, 1972) and themodified Cava lli-Sforza dist an ce (DA) (Nei et

al., 1983) were used (Table 1). To cluster

each set of genetic distances, we employed

the neighbor-joining (NJ ) met hod (Saitou

and Nei, 1987). This approach to tree con-

str uction has been shown to be super ior t o

other methods such as the UPGMA method

(Sokal and Sneath, 1963) in recovering the

tr ue br anching patter n of the genetic r el a-

t ionship of populations (Saitou and Nei,

1987; Nei an d Takezaki, 1994). To evalua te

the branching pattern statistically, we used

the bootstr ap test ( Ef r on, 1982) . This t est

deter mines the pr obability of r epr oducingthe particular branching pattern in the phyloge-

netic tree by u sing ran domly recombined gene

frequency data for the given populations.

RESULTS

In the first set of our calculations, a total

of 26 populations of the wor ld wer e com-

TAB LE 1. Nei’s standa rd genetic distances (lower diagonal m atrix) and m odified Cavalli-Sforza distances(above diagonal m atrix) for the four populations

H on do-J a pa n ese Kor ea n Ain u Ryu k yu a n

H on do-J a pa n ese — 0.00354 0.00747 0.00217Kor ea n 0.00404 — 0.01155 0.00707Ain u 0.00808 0.01043 — 0.00642Ryu kyu a n 0.00336 0.00899 0.00696 —

43 8 K. OMOTO AND N. SAITOU



pared (Figs. 1, and 2). In both genetic trees,

using the genet ic dist ances D st a n d DA, t h e

African populations are very different from

non-African populations. The bootstrap value

for th is separ ation is very h igh (93–96%).

Among non-Afr icans, the I ndo-Eur opean

population group is first separated from the

r est , t hough the bootstr ap pr obability val-

ues are n ot as high as those showing separa-

tion of the African groups. Further, Native

American popula tions including Esk imos are

separa ted from Asian/Pacific populations.However, with rega rd t o clust ering of Na tive

Austr alian and New Guinean populations,

the two trees show a noteworthy difference

f r o m e a c h o t h e r . I n t h e t r e e b a s e d o n D st

(Fig. 1), th ey ar e cluster ed with the nor th-

east Asian group, which is un expected, given

t he anthr opol ogical view that t he r oots of

Austr alian and New Guinean populat ions

ar e in southeast Asia. I n the tr ee based on

DA, h owever, Austr alians and New Gui n-

eans are clearly separated from other Asian-

Pa cific populat ions (Fig. 2).

Among the rest of the Asian-Pacific popu-

lations, two cluster gr oups may be r ecog-

n i ze d , a l t h ou g h t h e b oot s t r a p v a lu e s for

their separ ation ar e low: nor theast Asian

and southeast Asian/Pacific gr oups. Thr ee

Japanese populations—Korean, Tibetan, and

Mongolian—form the northea st Asian clus-ter gr oup, while souther n Chinese, Thai,

Filipino, Indonesian, Micronesian, Polyne-

sian, an d t wo Negrito populations belong t o

the southeast Asian/Pacific cluster group.

In t he second set of phylogenetic ana lyses,

t h r ee e th n ic gr ou p s of J a p a n (Ain u ,

Ryukyuan, and Hondo- Japanese) ar e com-

Fig. 1. A neighbor-joining (NJ )genetic tree for 26 populations of th e w o rld b a se d o n sta n d a rd g e-neticdistan ce (Dst ).Allele frequencyd a ta o f 2 0 p olym o rp h ic loc i a reused. Numbers along the branchesa re b oo tstra p p ro ba b ility v a lu es

(%).

43 9GENETIC ORIGINS OF JAPANESE



par ed wit h the Kor ean sample as the con-

trol. We ha d to restr ict our a na lyses to these

samples because we wanted t o maximize the

genet ic data used in the analyses. Only 20

genetic loci are available for the other popu-

lations, but 25 loci have been examined in

t hese thr ee J apanese and the Kor ean popu-

lation samples. The NJ networks show that

Ainu and Ryukyuan samples ar e cluster ed

together in contrast to Hondo-Japanese and

Korean. The two genetic distance measures

used (Dst a n d DA) gave essentially the same

topology, a lthough the bootstr ap values for

the separa tion of the Ainu/Ryukyuan bran ch

wer e sl ightly di ffer ent : 74% f or the one

based on Dst an d 85% for DA (Fig. 3).

DISCUSSION

Background of the dual structure model

Hanihar a’s model is pr imar ily based on

findings arising from st udies on cranial an d

denta l featu res (Han ihara , 1991, 1992). The

basic observation supporting this model is

the morphological similarity ofAinus, and to

some extent of Ryukyuans, to the Neolithic

populations of th e J omon per iod, who ar e

usually r egar ded a s descendants of the Up-

per Paleoli thic population of Japan r epr e-

sented by Minatogawa Man (Howells, 1966;

S u zu k i , 1 98 2; H a n i h a r a , 1 98 4). F u r t h e r -

more, the difference in cranial morphology

between the J omon an d the AeneolithicYayoi

Fig. 2. A neighbor-joining (NJ)genetic tree for 26 populations of the world based on modified Cav-alli-Sforza distance (DA). The genefrequency data used is th e same asi n F ig . 1 . N u m be r s a lon g t h ebranches are bootstrap probability

values (%).




populations i n t he wester n pa r t of Japa n is

so r emar kable an d occur r ed so suddenly at

about 2,300 years BP that a continuity model

provides insu fficient explan ation. H aniha ra

(1987) also used computer simulation to esti-

mate the number of migrant people who came

to the western part of Japan . He proposed that

over the 1,000 years elapsed since the begin-ning of the Yayoi period (300 BC) and the end of

the Kofun period (700 AD) an unexpectedly

l ar ge number of migr ant peopl e may have

e n t e r e d J a p a n : 1 . 5 m i l l i o n , a s s u m i n g t h e

an nu al growth ra te of th e migran t Yayoi rice

far mer s was 0.2 per cent (Hanihar a , 1987).

Although the validity of this figur e can be

examined th rough more detailed simulation

studies, we think th at H aniha ra’s dual stru c-

tur e model is su perior t o many other models

o n t h e o r i g i n s o f t h e J a p a n e s e t h a t h a v ebeen pr oposed because most of these ar e

rather nonquantitative and speculative.

The str ong advocate for the dual or i gi n

and admixtur e model f or the f or mation of

t h e J a p a n e s e p op u la t i on s , a s w el l a s t h e

idea that the ancestors of the Jomon people

came from south east Asia is Christy Turn er

(Tu r n e r , 1 9 76 , 1 9 87 , 1 9 92 ). H e d e m on -

str ated that east Asian populations can be

divided into two distinct groups on the basis

of dental pattern s: the northeast Asian group

exhibit ‘‘Sinodonty’’an d th e s outh east Asian

group sh ows ‘‘Su nd ad onty.’’Accordin g t o him ,

the Ainu and Jomon populations are sunda-

d on t s , w h er e a s t h e H on d o-J a p a n e s e a r e

sinodonts (Tur ner, 1976).

Mitochondrial DNA (mtDNA) extra cted

from an cient bones a lso seemed t o suggest a

com m on or i gi n for t h e J o m on a n d Ai n u

populations (Hor ai et al ., 1989, 1991). I n

these studies, mtDNA was extr acted f r om

the bones of five Jomonese, carbon 14–dated

a t a b ou t 6 ,0 00 ye a r s B P, a n d s ix e a r ly-

modern Ainu (seventeenth to eighteent h cen-

t u r y AD). A 190 base-pair (bp) segmen t of the

D-loop region of mt DNA was sequ enced, and

the sequences were compared with those of modern individuals from var ious regions of

the wor ld. An identical sequence was ob-

served am ong four J omonese, two Ainu, a nd

t h r e e s o u t h ea s t A s ia n a s w el l a s 1 5 n o n -

Ai n u J a p a n e s e m t D N As . A lt h ou g h H or a i

and his colleagues are cautious about their

conclusions on the origins of Jomonese a nd

Ainu (Hor ai et al ., 1989), th is r esult has

been cited as p ositive evidence for the s outh -

east Asian origin of the first population of

J apa n (Han ihar a, 1991). However, it is worth

noting tha t ther e is a big difference between

the phylogeny of molecules a nd the phylog-

eny of populations. I t is well kn own thatmolecular spli ts may f ar antedate popul a-

tion spli ts (Nei, 1987). I n the molecul ar

genetic tree of Horai et al. (1991), mt DNAs

of non-Ainu J apanese ar e scatter ed ar ound

the whole tree, among mtDNAs of Europe-

ans and Africans, an d do not cluster.

F ig . 3 . T h e N J g e n e tic tre e com p a rin g th re e Ja p a -

n e se p op u la tion s (Ain u , R yu k y u a n , a n d H o n do -Ja p a -nese) with Korean as a control, based on allele frequencydata of 25 polymorphic loci. Genetic distan ce measur esu s e d a r e DA (A) a n d Dst (B). N o te th a t th e b o o tstra pprobability values (85% for A an d 74% for B) a re muchhigher tha n t hose under th e random expectat ion (33%).




The question of northernor southern origins

Contr ar y to the assumpt ions of the dual

stru cture model, classic genetic mark er da tashow that J apanese popul ations, i ncluding

Ainu, h ave definite norther n affinities. Mat-

sumoto (1984, 1988) found th at serum gam-

maglobulin (Gm) types showed a clear-cut

north/south dichotomy of east Asian popula-

t ion s a n d t h a t J a p a n e se b elon ge d t o t h e

nor ther n gr oup. He also showed t ha t J apa-

n e s e p op u l a t ion s a r e r e la t i ve ly h om og e-

neous i n the dist r ibution of Gm allele fr e-

quen cies, which contr adicts Han iha ra ’s dual

stru cture model. Matsum oto’s conclusion,

t hat the homeland of al l Japanese popula-

tions ma y have been in the Lak e Baikal area

in Siberia, h owever, met with strong objec-tion from J apa nese a nth ropologists, includ-

i ng Kazur o Ha ni har a. We also beli eve tha t

conclusions a bout t he origins ofh um an popu-

lations should be based on information from

many genetic loci r ather than a si ngle ge-

net ic locus.

Nei an d Roychoudhu ry (1993) an alyzed 26

populations fr om a r ound t he wor ld u sing

gene fr equency data fr om 29 pol ymor phic

loci of class ic genetic ma rker s an d exam ined

t h e r e s u lt i n g d e n d r og r a m s b y b oot s t r a p

t ests. Among east Asians, t hey compar ed

J apa nese (Hondo-J apa nese), Korean s, Mon-

golian s, Tibetan s, southern Chinese, Thais,

Filipinos, and I ndonesians. They did not

r e cog n iz e n or t h e r n a n d s ou t h e r n cl u st e r

gr oups and used the tr adit i onal ter m Mon-

goloid to denote all east Asian and Pacific

populations.

Recently, Nei published phylogenetic tr ees

t h a t s h ow t h e r e la t ion s h ip s of J a p a n e se

populations (Nei, 1995). This time, he com-

p a r e d Ai n u , ‘‘J a p a n e s e of O k in a w a , ’’

(Ryuk yua n) an d ‘‘J ap an ese ofTokyo’’(Hond o-

J apa nese) with neighboring populations u s-

ing dat a from 18 polymorphic loci. He sh owed

t h a t t h e t h r ee J a p a n e se p op u la t ion s a r ecl ose t o Kor ean, while souther n Chinese,

N a t iv e Ta i wa n e s e, T h a i, a n d F il ip in o

samples cluster as a separate group. On the

basis of thi s r esult , he chal lenged Han iha-

r a’s hypothesis as a whole with r espect to

t he or igi ns and the dual str uctur e of Japa-

nese populations.

Omoto (1995) examined the pr oblem of

the origins of Ainu in detail. He compared

Native Australian, New Guinean, Microne-

sian, an d Polynesian populations plus 11

east Asian populations on the basis of NJ

t r e e s w i t h DA distances, using classic ge-

netic m ar ker s fr om 23 polymor phic loci .

Ainu clear ly f ell in to the nor theast Asian

group, with Korean , Mongolian , and Tibetan

samples, while south ern Chinese, Thai, Fili-

pino, Indonesian, a nd two Negrito populations

were linked with the southeast Asian group.

The over all Hondo-J apanese admixtur e

ra te in t he original sam ple of about 500 Ainu

fr om the Distr ict of Hidaka on Hokkaido,

which is the n or ther nmost island of Japan,

was estimated to be approximately 30–40%

(Omoto, 1972). Omoto (1995), however, deter-mined the impact of admixture on the posi-

t ion of the Ainu population in the tr ee by

correcting gene frequencies for admixtur e.

No change occur r ed even when an admi x-

t u r e e s t im a t e of 4 0 % w a s e m p loy ed a n d

Ainu remained in the northeast Asian clus-

ter group. However, the bra nch length t o the

Ainu elongated considerably. When a hypo-

thetical admixtur e r ate of 60% was used t o

correct gene frequencies, the Ainu remained

in the north east Asian cluster group, but the

N a t i v e A u s t r a l ia n / N e w G u i n e a n c lu s t e r

m ov ed n e a r t h e r oot of t h e l on g b r a n ch

leading to the Ainu. The genetic r elation-ships of other populations were essentially

unchanged. Although i t is not possibl e to

draw a conclusion from such a simulation, it

lends support the view that Ainu a nd Na tive

Austr alians/New Guinean s both ar e derived

directly from the Upper Pa leolithic popula-

tions of eas t Asia (Omoto, 1995). The p ossibil-

ity tha t Ainu origins lie in a ncestral popula-

tion groups in northeast Asia has also been

shown r ecently by a DNA-based stu dy of

HLA Class II genes (Banna i et a l., 1996).

O u r s t u d y c o n fi r m s t h a t t h r e e J a p a n e s e

populations, including Ainu and Ryukyua n,belong to the northeast Asian group, along

with Kor eans, Mongolians, and Tibet ans.

T h is g r ou p a p p ea r s s e pa r a t e d fr om t h e

southeast Asian group comprising southern

Chinese, Thai, Filipino, Indonesian, Microne-

sian, Polynesian, and two Negr ito popul a-

tions, although the bootstrap probability for




t his separ ation i s r a ther l ow and i s statist i-

cally not significant (22% in Fig. 2).

With regard to th e origins of the Mongol-

oid populations, the current ly popular view

assumes th at southeast Asia was t he centerof dispersa ls (e.g., Turn er, 1995). This view,

which is based primarily on morphological

traits, was examined by Omoto (1995). He

considered genetic evidence and favored a

model which assumes independent origins

of n or t h e a s t As ia n , s ou t h e a s t As ia n , a n d

Nat ive Amer ican population gr oups. Nei

( 1995) seems to be skept ical about the di-

chotomy of northern and southern Mongol-

oi d g r ou p s b eca u s e t h e b r a n ch i n g y ie ld s

relat ively low bootst ra p valu es. However, in

view of the genetic, archaeological, and lin-

guistic evidence for large-scale dispersals of

northern groups into south east Asia and th e

Pacific dur ing the l ast 10,000 year s (e.g.,

Bellwood, 1979, 1996), we ass um e as a work-

i ng hypothesis t h at the dichot omy in our

genetic tr ee (Fig. 2) ha s h istorical validity.

H a n i h a r a ’s v ie w t h a t t h e U p p er P a l eo-

lithic population of Japan originated some-

w h er e i n s o u t h e a st As ia m a y h a v e b e e n

based par tly on the obser vation of Suzuki

(1 98 2 ) o n M in a t o ga w a M a n (H a n i h a r a ,

1991) . Suzuki consider ed that the skull of

Mi natogawa No. 1 dated at appr oximately

18,000 years BP is morphologically similar

toJomonese. He further assumed that Mina-togawa Man is more closely related to Liu-

ja n g M a n of s ou t h e rn C h in a t h a n t o t h e

specimen No. 101 of Upper Ca ve of Zhoukou-

dian, nor ther n China. However , we doubt

that observations on a single skull can pro-

vide all that needs to be known about or i-

gins. After examining our genetic data, we

propose a count erhypothesis tha t th e Upper

Paleolithic populations of Ja pan are derived

fr om th ose of nor theast Asia and did not

necessar ily or iginat e in southeast Asia. A

critical exam ination of the t hree specimens

from Upper Cave are pa rticularly importan t

in this regard.We believe tha t our h ypothesis is more in

agreement with preh istoric evidence th an is

Han ihara ’s. According to most archa eolo-

g is t s i n J a p a n , s t on e -t ool cu l t u r es of t h e

Upper P aleolithic an d t he s uccessive Jomon

period show definite n orther n a ffinities (Cho-

suke Ser izawa, per sonal communication) .

The m icroblade tra dition accompanying th e

Ar aya type bur in was widely distr ibuted

fr om easter n Siber ia to the Ja panese ar chi-

pelago from t he postglacial period u ntil t he

beginning of the J omon per iod (appr oxi-mat ely 20,000–12,000 years BP). No stone-

tool culture of southeast Asian affinities has

been discover ed in J apan for this per iod

(Kimur a, 1993; Tan ak a et a l., 1995).

Dual structure of the Japanesepopulations

O m ot o (1 97 2, 1 99 2) a n d O m ot o a n d

Misawa ( 1976) have shown that Ainu and

Ryukyuan peoples ar e genetically r ath er

similar to each other but are different from

Hondo-Japanese. This finding seemed to fit

well with th e admixtu re model for the form a-tion of the Japanese populations. I n these

previous reports, however, the dichotomy of

Ainu/Ryukyuan and Hondo-J apanese was

emphasized, without the relationship being

tested statist ically. I n the pr esent study,

three Japanese populations are compared to

each other, with Korean as the control on the

basis of the lar gest data set ever used: 25

polymorphic loci. Also, the separa tion be-

tween the Ainu/Ryukyuan cluster and the

Hondo-J apanese/Kor ean gr oup in the NJ

network was stat istically evaluat ed by boot-

strap probabilities (Fig. 3). While two ge-

netic distance measur es, D st a n d DA, gaveessentially th e sa me topology, th e bootstrap

value is sl ightly higher (85%) in the tr ee

u s in g DA t h a n t h a t u s in g D st (74%). Al-

though this difference in bootstrap values is

statistically not significant, we have noted

t ha t DA is s u pe r ior t o Dst in pr oducing

reliable genetic relationships of populations

(Figs. 1, 2). Since th e expected value of the

bootstrap probability for four populations

un der no genet ic relationsh ip (‘‘sta r p hylog-

eny’’) is 33%, the observed valu es a re mu ch

higher than this r andom expectation. Re-

cently, theoretical studies on the bootstrap

test have been extensively conducted (e.g.,S it n i k ov a e t a l ., 1 99 5; Zh a r k i k h a n d L i,

1995; Efron et al., 1996). However, it is still

not clear how bootstr ap pr obabilit ies for

g en e t ic t r e e s s h ou l d b e t r e a t e d w i t h t h e

usual statistical tests. Therefore, we do not

consider reliance on bootstrap probabilities

as critical. In any case, we believe that our




r esul ts give suppor t f or the separ ation be-

tween Ainu/Ryukyuan and Hondo-J apan ese/

Korean cluster s. If this clustering is r eal, it

i n tur n gives a par tial suppor t f or Haniha-

r a’s dual str uctur e model, in t er ms of theduality of the J apan ese populations.

It is worth n oting th at our conclusions are

different from those of Nei (1995). He pub-

lished a phylogenetic tree ba sed on 18 poly-

morphic loci th at shows th e relat ionsh ips of

Ain u , H on d o-J a p a n e s e, a n d O k in a w a n

(Ryukyuan) with neighboring populations.

He expr essed his doubt about Hanihar a ’s

dual structure model as a whole (Nei, 1995).

However , when t he hypothesi s i s br oken

into two components, the evidence, we sug-

ge st , s h ow s t h a t t h e re m a y i n fa ct b e a

duality in J apa nese populations. This differ-

e n ce i n i n t er p r e t a t ion w il l b e cl ea r e d b y

f ut ur e studi es wi th much mor e and better

d a t a . A t t h i s m o m e n t , w e t h i n k t h a t t h e

deta ils of a populat ion’s origin ar e un likely

to be revealed by using a worldwide data set

such as used by Nei (1995). To understand

local biological history, one has to examine

the genetic profiles of the populations that

have been hypothesized to be an cestra l to it

a n d t o d o t h is w it h a s la r ge a n u m be r o f

genetic loci as possible. Of course, we do not

consider our findings to be final, particularly

becau se of our relatively low bootstrap val-

ues. Pr obably, our stu dy represent s a micro-scopic rather than a macroscopic approach

in reconstructing the population history of

J a p a n .

Recently, a d eta iled genetic compa rison of

As ia n p op u l a t ion s , i n cl u d in g Ai n u a n d

R yu k y u a n , w h ich u s e d m t D N A s e qu e n ce

data was pu blished (Horai et al., 1996). The

r e s u lt s fr om t h i s s t u d y a r e i n a g r ee m en t

with ours in th at H ondo-Japa nese and Kore-

ans are genetically very close to each other

and the admixtur e model of the forma tion of

t he moder n J apanese is f avor ed. However ,

with regard to the relationship between the

Ai nu and the Ryukyuan, no evidence f or acommon ancestr y is f ound. Fut ur e studies

a r e n e ed ed t o cle a r u p t h e p os it ion of

Rykyuans.

Fina lly, when origins a re considered, ques-

tions about linguistic evidence commonly

ar ise. Our view can be summar i zed as f ol-

lows. If a lar ge number of migrant s to J apa n

actually came from northeast Asia, perhaps

v ia t h e K or e a n p e n in s u l a s t a r t in g a r ou n d

2,300 year s BP, a s Hanihar a ’s dual st r uc-

tur e model maintains, why is the language

of Hondo-Japanese (i.e., Japanese) so differ-ent from Korean or other Altaic langua ges?

In our view, language chan ges during popu-

lation mixture are complex social phenom-

ena that cannot be simply defined or mea-

sur ed chr onologically, as can biological

phenomena. Given the almost complete ab-

sence of quan titative and stat istical compari-

sons between J apa nese (including Ainu a nd

R yu k y u a n ) a n d ot h e r l a n gu a g es i n As ia ,

except for th e work of Biten Yas um oto, which

h a s n o g en e ra l s u pp or t a m on g J a p a n e se

l in g u is t s , w e h a v e a t p r e se n t n o c le a r a n -

swer, either pro or con, to our question. It is

in t er e st in g t o n ot e t h a t , on t h e b a sis of

stat istical compar isons of basic words a mong

east Asian langua ges including the Ainu, h e

r eached the conclusion that Ainu and Ko-

r ean languages may have common ancient

a n ce s t r y i n w h a t h e ca l ls t h e P a l eo-F a r -

E a s t e r n la n g u a ge g r ou p (Ya s u m ot o a n d

Honda , 1978; Yasu moto, personal commu ni-

ca t ion ). F or t h is r e a son , w e d o n ot p u t

e m p h a s is on l a n gu a g e n ow a n d h a v e f o-

cussed our a tt ent ion on genet ic, morphologi-

cal an d a rcha eological evidence.

CONCLUSIONS

We propose a modified version of the dual

str uctur e model of the or igins of Japanese

populations. Two fundam ental populat ion

g r ou p s a r e a n c es t r a l t o m od e r n J a p a n e s e

populations (Ainu, Ryukyuan, and Hondo-

Japanese) . One gr oup, r epr esented by the

J omonese wh o gave rise to the modern Ainu

a n d p r ob a bl y a l s o t h e R yu k y u a n p op u la -

tions, ha s its origin in the Upper P aleolithic

populations of northea st Asia, which were

not necessarily derived from southeast Asia.

The other group is the later migrants of the

Yayoi an d Kofun per iods who also came from

northeast Asia but were different geneticallyand mor phologically fr om the fir st gr oup.

I nter mixtur es occur r ed between these t wo

g r ou p s , b u t t h e g en e t ic i n flu e n ce of t h e

second group is pr edominan t in the m ajority

of m od e r n J a p a n e s e (H on d o-J a p a n e s e ).

Clearly, furt her stud ies are necessary which

include more informa tion, part icularly on




a n cien t a n d m od er n DN As of Ain u ,

Ryukyuan, and other popul ations of J apan

and east Asia, to clar i f y the or i gi ns of the

Japanese people.

ACKNOWLEDGMENTS

We th an k P rofessor Masat oshi Nei of The

Pennsylvania State Univer sity ( St ate Col-

l ege, PA) for pr oviding u s with gene fr e-

quency data. We also than k two anonymous

reviewers who read the original man uscript

critically and gave us invaluable commen ts.

Thanks ar e also due to Dr . Akiko Uchida,

Chiba University, for help in preparing the

origina l man uscript.

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