Hum Genet (1998) 102 : 647–652
ORIGINAL INVESTIGATION
Burkhard Rolf · Basil Horst · Antonin Eigel
T. Sanguansermsri · Bernd Brinkmann · Jürgen Horst
Microsatellite profiles reveal an unexpected genetic relationship
between Asian populations
Received: 10 June 1997 / Accepted: 15 March 1998
Abstract Allelic frequencies for up to five short tandem
repeat systems (HumTH01, HumVWA, HumF13B,
HumCD4, HumD21S11) were analyzed in seven popula-
tion samples from Asia using the polymerase chain reac-
tion and gel electrophoresis. No deviations from Hardy-
Weinberg equilibrium were observed. Two new alleles of
the CD4 and TH01 loci were detected, and sequenced and
their molecular structure is presented. A phylogenetic tree
based on Thai, Han Chinese (from the northeast of China),
Japanese, German and Ovambo allelic frequencies was
constructed and demonstrates the close relationship of the
Asian populations. Additionally, allelic frequency data for
the VWA and TH01 systems were determined for the
south Chinese minorities Bai, Dai and Qiang and for Kore-
ans and compared with the above data. The Bai and Dai
populations were clear outliers of the cluster of all other
Asians, indicating an unexpected pattern of genetic hetero-
geneity of the Chinese nation. Two clusters of Asian popu-
lations could be established: the Koreans and Japanese
together with the Han and Qiang Chinese, and, forming a
separate cluster, the Bai and Dai populations.
Introduction
Short tandem repeat (STR) polymorphic systems are used
in human identification/parentage testing (Gill et al. 1994),
linkage analysis (Hearn et al. 1992), and for the investiga-
B. Rolf · B. Horst · B. Brinkmann (✉)
Institut für Rechtsmedizin, Westfälische Wilhelms-Universität,
von Esmarch Str. 86, D-48149 Münster, Germany
Fax: +49-251-8355158
A. Eigel · J. Horst
Institut für Humangenetik, Westfälische Wilhelms-Universität,
Vesaliusweg 12-14, D-48149 Münster, Germany
T. Sanguansermsri
Human Genetic Unit, Faculty of Medicine,
Chiang Mai 50002, Thailand
© Springer-Verlag 1998
tion of human evolution (Bowcock et al. 1994). In some
cases, they have been found to cause, or to be associated,
with disease (for review see Richards and Sutherland
1996). Population genetic data based on these systems of-
fer a tool to demonstrate parallels or differences between
ethnic groups in an evolutionary context (Meyer et al.
1995; Brinkmann et al. 1996).
Asia is the largest continent and was peopled by archa-
ic Homo species before the arrival of the modern Homo
sapiens sapiens (Cavalli-Sforza et al. 1994). Today, it is
generally accepted that at least two independent waves
brought modern humans into Asia. A southern wave,
50,000–70,000 years ago, brought people along the south-
ern coastal line to New Guinea and Australia. A second
expansion, starting in western Asia/northern Africa 50,000
years ago, brought people to the whole of Asia, the Arctic
and also to America (Cavalli-Sforza et al. 1994), where the
ancestors of today’s Amerinds arrived 20,000–25,000
years ago (Forster et al. 1996). Peoples of this second
wave might have mixed with descendants of the first,
southern wave out of Africa into Asia but not into high-
land Papua New Guinea and Australia.
Population genetic data based on protein polymor-
phisms have revealed that differences in eastern Asia are
mainly observed between the northern and the southern
populations. Cavalli-Sforza et al. (1994) found divergence
between north and south Chinese and a clustering of both
of these with neighboring populations. Zhao and Lee
(1989) assumed that the modern Chinese nation originated
from two distinct populations during early Neolithic times,
one population originating from the northern Yellow river
valley and one originating from the southern Yangtze river
valley, respectively. Nevertheless, information on nuclear
DNA polymorphisms, such as, STR allelic frequencies, of
these populations are still rare. Only a few reports dealing
with STR allelic frequencies in Asian populations, mainly
Japanese and Chinese, have been published (Brinkmann et
al. 1996; Hou and Walter 1996; Takahashi et al. 1996).
Considering the size and the variety of Asian populations,
the amount of information is poor. The aim of the present
work was to determine the allelic frequencies of up to five
Table 1 Allelic frequencies in the five short tandem repeat (STR) polymorphic systems HumTH01, HumVWA, HumF13B, HumCD4 and HumD21S11. (n number of chromosomes investi-
648

gated)

TH01 5 6 7 8 8.3 9 9.3 10 10.3 11 12 n

Ovambosa 0 0.037 0.401 0.38 0 0.151 0.021 0.01 0 0 0 192

Germansa 0.003 0.225 0.167 0.116 0.001 0.149 0.32 0.017 0.001 0.001 0 1388
Japanesea 0 0.21 0.275 0.051 0 0.417 0.04 0.007 0 0 0 276
Hanb 0 0.107 0.255 0.041 0 0.566 0.026 0 0 0.005 0 196
Thaisc 0 0.108 0.314 0.048 0 0.43 0.04 0.052 0 0.004 0.004 248
Baia 0 0.068 0.263 0.095 0 0.51 0.032 0.032 0 0 0 190
Dai 0 0.086 0.333 0.051 0 0.382 0.103 0.04 0.005 0 0 198
Qiang 0 0.053 0.313 0.056 0 0.483 0.088 0.007 0 0 0 284
Koreans 0 0.101 0.276 0.256 0 0.573 0.026 0 0 0 0 40

VWA 11 13 14 14’ 15 16 17 18 19 20 21 22 n

Ovambosa 0.055 0.035 0.065 0 0.2 0.225 0.195 0.115 0.085 0.025 0 0 200
Germansa 0 0.001 0.097 0 0.101 0.207 0.279 0.213 0.086 0.015 0.001 0.001 1298
Japanesea 0 0 0.214 0 0.025 0.178 0.278 0.239 0.062 0 0.004 0 256
Hanb 0 0 0.287 0 0.033 0.143 0.253 0.192 0.055 0.037 0 0 181
Thais 0 0 0.263 0.004 0.04 0.194 0.202 0.194 0.087 0.012 0.004 0 248
Baia 0 0 0.23 0 0.039 0.236 0.197 0.191 0.084 0.017 0.006 0 178
Dai 0 0 0.219 0 0.036 0.158 0.23 0.214 0.128 0.015 0 0 196
Qiang 0 0 0.205 0 0.026 0.234 0.234 0.186 0.091 0.026 0 0 280
Koreans 0 0.026 0.225 0 0.051 0.126 0.321 0.1506 0.076 0 0.026 0 40

CD4 4 5 6 7 8 9 10 11 12 13 14 15 n

Ovambosb 0 0.228 0.156 0.067 0.091 0.01 0.095 0.21 0.086 0.014 0.038 0.005 210
Germansb 0 0.348 0.305 0 0.003 0.003 0.307 0.023 0.009 0.002 0 0 600
Japaneseb 0 0.733 0.033 0 0 0.003 0.23 0.001 0 0 0 0 274
Hanb 0 0.715 0.005 0 0 0.005 0.265 0.01 0 0 0 0 200
Thais 0.012 0.606 0.016 0 0 0.004 0.35 0.012 0 0 0 0 248
 649

STR systems (HumTH01, HumVWA, HumF13B, Hu-

206
816
296
194
248
n
mCD4 and HumD21S11) in Chinese and Japanese as well
>33.2
as in the three Chinese minority populations, Bai, Dai and
0.081
0.005
0.003
0.005
0.012
Qiang, and in the neighboring Thai and Korean popula-
tions, for the reconstruction of the phylogenetic history of
several Asian populations.
0.001
0.027
0.043
0.057
0.076
33.2

Materials and methods

0.001
0.006

0.008
33

Population samples
0.084
0.097
0.177
0.129
0.184
32.2

The population samples were Ovambos (Bantu) from Namibia,

Caucasoid Germans from northwestern Germany, Han Chinese from
the Shenyang area, Bai and Dai Chinese from Yunnan Province, Qi-
0.005
0.011

0.036
0.008
0.04

ang Chinese from Sichuan, Thais from the Chiang Mai Province,
32

Koreans from Seoul, South Korea, and Japanese from the Shiga area.
0.034
0.095

0.062
0.064
31.2

0.06

DNA extraction

DNA was isolated according to standard procedures from peripheral

0.076
0.090
0.097
0.108
0.044

blood lymphocytes (Miller et al. 1986) or from dried blood on cotton

31

(Walsh et al. 1991) and quantified using the slot-blot technique

(Waye et al. 1989).
0.001
0.033

0.005
0.048
30.2

DNA amplification and electrophoresis

0.187
0.221
0.311
0.255
0.294

The polymerase chain reaction (PCR) conditions for the respective

30

STR systems have been described previously: HumTH01 (Edwards

et al. 1992; Wiegand et al. 1993); HumVWA (Kimpton et al. 1992;
0.005

Möller et al. 1994a); Hum F13B (Nishimura and Murray 1992);

29.3

202
804
274
200
248

HumD21S11 (Sharma and Litt 1992; Möller et al. 1994b) and Hu-
0
0
0
0

mCD4 (Edwards et al. 1991). The PCR products were resolved by

high-resolution polyacrylamide gel electrophoresis according to
0.001
0.004
0.013
0.005
0.004

0.001

0.004
29.2

Allen et al. (1989) and visualized by silver staining (Budowle et al.

11

1991). Alleles were identified by side-to-side comparison with an al-

0

0
0

lelic ladder.
0.187
0.205
0.197
0.301
0.195

0.001
0.001

0.005
10K
29

Sequence analysis
0.433
0.795

0.644
28.2

0.02

0.05

Alleles showing unusual migrational behavior were isolated from the

0.7
10

gels as described elsewhere (Möller and Brinkmann 1994). After

0
0

0
0

reamplification under the same conditions, sequencing was carried

out on an ABI 373 DNA Sequencer using the Taq Dye Deoxy Termi-
0.172

0.032
0.063

0.005
0.001

0.004
0.26

0.03

nator Cycle Sequencing Kit (Perkin Elmer/Applied Biosystems, Fos-

9K
28

0
0

ter City, Calif.).

0.001

0.385
0.225
0.146

0.228
27.2

0.22

Statistics
0

0
0
0

For evaluation of the Hardy-Weinberg equilibrium the Exact Test

0.073
0.037

0.005

0.045
0.224
0.055
0.075
0.104

was used (Guo and Thompson 1992) with HWE Analysis 3.2 soft-
27

ware (C. Puers, Münster, Germany); no deviations from the equilib-

Data from Brinkmann et al. (1996)
Data from Brinkmann et al. (1998)

rium were observed (P>0.05). Allelic frequency data were used to

calculate a distance matrix between the populations using the pro-
Data from Horst et al. (1997)
0.004
0.003

0.116
0.012
0.004

0.004

gram DISPAN (genetic distance and phylogenetic analysis; Ota

26

0
0

1993) and the Da distance measure (Nei et al. 1983). Based on this
Table 1 (continued)

matrix, a phylogenetic tree was constructed using the neighbor-join-

0.005

0.398
0.103

0.012

ing method (Saitou and Nei 1987).

<26

0
0
0
0

0
0
Ovambosb

Ovambosb
Germansb

Germansb
Japaneseb

Japaneseb
D21S11

Thaisc
Thais
Hanb

Hanb
F13B

b
a

c
650
Table 2 Distance matrix for five
populations based on five loci Ovambos Germans Japanese Han Thai Bai Dai Qiang
(61 alleles, upper right triangle)
or for nine populations based on Ovambos - 0.1492 0.2644 0.2553 0.2246
two loci (23 alleles, lower left
Germans 0.1286 - 0.0965 0.1082 0.0809
triangle). Calculations were
done using the program DISPAN Japanese 0.1461 0.0763 - 0.0195 0.0273
(Ota 1993). The measurement of Han 0.1550 0.1144 0.0238 - 0.0240
distance used is Da (Nei et al. Thais 0.1300 0.0881 0.0196 0.0241 -
1983) Bai 0.1111 0.1218 0.0698 0.0609 0.0462 -
Dai 0.1232 0.0820 0.0505 0.0639 0.0357 0.0169 -
Qiang 0.1224 0.0803 0.0267 0.0180 0.0172 0.0594 0.0465 -
Koreans 0.1545 0.1241 0.0254 0.0275 0.0385 0.0698 0.664 0.0380

Results

DNA samples were amplified in each of the five STR sys-

tems and identified by gel electrophoresis and sizing with
allelic ladders. Table 1 summarizes the allelic frequencies. Fig. 1 A phylogenetic tree based on the distance matrix from Table
Parts of the data have been published earlier but are in- 2 for Ovambos, Germans, Han Chinese, Thais and Japanese. The
cluded in the table for easy comparison. The respective tree is based on the neighbor-joining method (Saitou and Nei 1987).
The numbers at the branches are the bootstrap values
references are indicated in Table 1.
In the HumTH01 system, the most abundant allele in
the Ovambo sample was allele 7 (40%) and in the German
sample allele 9.3 (32%). In all Asian populations tested,
allele 9 exhibited the highest frequency, with up to 57% in
the Korean sample. One allele migrating outside the range
of the allelic ladder was observed in the Thai sample. Se-
quencing revealed a structure consisting of 12 (AATG) re-
peats.
In the VWA system, differences were less prominent as
alleles 16, 17 and 18 were present at high frequencies
(about 15–25%) in all populations tested. Nevertheless, al-
lele 14 was present in the Asian populations at more than
20%, whereas this allele was only present at 9.5% in Ger- Fig. 2 A phylogenetic tree based on the distance matrix from Table
mans and 6.5% in Ovambos. 2 for Ovambos, Germans, Han Chinese, Japanese, Bai Chinese, Dai
In the HumCD4 system, alleles 5 and 10 were the most Chinese, Qiang Chinese, Thais and Koreans. The tree is based on the
neighbor-joining method (Saitou and Nei 1987). The numbers at the
abundant alleles in all populations; however, one allele branches are the bootstrap values
could not be identified in the Thai population sample, as it
migrated faster than the smallest allele (no. 5) present in
the allelic ladder. Sequencing of this allele revealed the
previously unknown structure of four (TTTTC) repeats. tions using the program DISPAN (Table 2). The distance
Alleles 29 and 30 exhibited the highest frequencies measure used was Da (Nei et al. 1983). Based on this ma-
(20–30%) in the D21S11 system in all populations, fol- trix, a phylogenetic tree was constructed, using the neigh-
lowed by allele 31 with about 10%. In the German and bor-joining method (Saitou and Nei 1987). The tree pro-
Ovambo samples, allele 28 was present at 17% and 28%, vides strong evidence for a close relationship between
respectively, whereas this allele in the Asian populations Thais and the two other Asian populations, the Japanese
was only observed at 3–6%. and the Han Chinese (Fig. 1). Interestingly, the Han Chi-
In the F13B system, allele 10 was found at 40–80% in nese and the Japanese populations are clustered together
the Asian and German samples; in the Ovambos, this al- and the Thai population is outside of this cluster. The
lele was only present at 5%. The highest frequencies for branching pattern observed is supported by the high boot-
alleles 8 (22%) and 9 (38%) were observed in Germans strap values of 100 and 99, indicating that these findings
and Ovambos, respectively. are significant.
Allelic frequency data for the five STR loci determined A distance matrix for seven Asian populations and Ger-
in this study for the Thai population and earlier for the mans and Ovambos based on the STR systems HumVWA
Ovambo, German, Chinese and Japanese populations were and HumTH01 (Table 2) was used to construct an addi-
used to calculate a distance matrix between the popula- tional phylogenetic tree, shown in Fig. 2. The branching

pattern is still the same as that observed above for the five
populations using the five STR systems. The addition of
four populations and the use of fewer loci did not change
the basic phylogenetic relationship. The Koreans are clus-
tered together with the Han Chinese from the Shenyang ar-
ea in 75% of the bootstraps; these two are then clustered
together with the Japanese with the same bootstrap proba-
bility. The Chinese minorities Bai and Dai are clear outli-
ers to the cluster of the other Asians. The high bootstrap
value of 100 indicates the significance of this finding. The
Thai and the Chinese minority population Qiang from Si-
chuan Province are not included in this branch. Although
the bootstrap probability for the Qiang is not significant,
they are placed outside the northeast Asian cluster (Han,
Koreans and Japanese) and the cluster of the Bai and Dai.
Discussion
The proposed model for the mutation of microsatellites is
the so-called single step mutation model, in which muta-
tions change the number of repeats mainly by one unit
(Weber and Wong 1993; Valdes et al. 1993). The two new
alleles observed here in this study in the Thai sample, al-
lele 4 at the CD4 locus and allele 12 at the TH01 locus,
differ from the known allelic size range by one repeat unit.
This finding might support the single step mutation model,
although other mechanisms are also possible. Pedigree
analysis revealed mutation rates of 10–5–10–2 for the sys-
tems (Weber and Wong 1993). The two new alleles de-
scribed here could have originated recently de novo in
Asia/Thailand. However, we cannot exclude the possibility
that these alleles originated in an African precursor popu-
lation and that they were then subject to genetic drift, and
are thus no longer present in all populations.
The tree provides strong evidence for the close relation-
ship between the Asian populations. The branching pattern
observed in the tree in Fig. 1 reflects the geographic loca-
tion of the population samples, as the Han Chinese sample
is from the northeast of China, much closer to Japan than
to Thailand. In the two-loci tree in Fig. 2, the Koreans are
clustered together with the Han Chinese in 75% of the
bootstraps and these two are then clustered together with
the Japanese with the same bootstrap probability. Studies
on mtDNA polymorphisms indicate that a major part of
the Japanese gene pool is derived from Yayoi people, who
migrated to Japan from the Korean peninsula/northeast
China about 2300 years ago (Horai et al. 1996). Genes of
the older Neolithic Japanese population, the Jomon peo-
ple, are less frequent in modern Japanese. These findings
are also supported by studies on Y-chromosomal variation
in Japanese males (Hammer and Horai 1995). The phylo-
genetic relationship based on data for the autosomal STRs
reveals a similar pattern. Koreans and Japanese are speak-
ers of an Altaic language (according to Ruhlen 1987),
whereas the Chinese speak a Sinotibetan language; thus at
least the genetic relationship between Koreans and Japa-
nese is supported by linguistic evidence.
651
The major ethnic group in China are the Han, making
up 93% of the population. The remaining 7% comprise 55
minority ethnic groups (Matsumoto et al. 1995). The Bai
and Dai minorities are from the Yunnan Province in China,
close to Thailand. The Bai and the Qiang from Sichuan
Province are speakers of a Tibetoburmese language. The
Dai population consists of two, closely related groups, the
southern Dai, who are related to the northern Thai, and the
western Dai, who are related to the Shan of Burma and ex-
hibit a higher frequency of the HbE gene (Yongvanit et al.
1989, G. Flatz, personal communication). The Dai sample
in this study is from the cities of Dali and Weishan in the
western part of the province, 150 km west of Kunming.
Therefore, they belong to the Shan. Interestingly, the Bai
and Dai populations are placed outside all other Asian
populations with a bootstrap probability of 100%, al-
though both the Thai and the Dai populations speak a Daic
language. The Dai population comprises 760,000 people
and the Bai 1,000,000 (Etler 1992); thus, recent effects of
drift due to the small size of these populations are proba-
bly not the reason for the phylogenetic difference. Selec-
tion resulting from climatic influence on genetic composi-
tion has not been described for the neutral STR markers.
As the STRs described here do not code for proteins and
are mainly in the introns of genes, hitchhiking would be
the only possible mechanism of selection, but this has not
been described so far.
The genetic diversity observed reflects only in part the
geographical and linguistic relationships of the Asian pop-
ulations. China is genetically very heterogeneous, and the
Chinese are much more closely related to their neighbors,
such as the Koreans or Japanese, than to a minority living
in China.
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