Advances in Anthropology
2014. Vol.4, No.1, 7-12
Published Online February 2014 in SciRes (
Mitochondrial DNA-HVR1 Variation Reveals Genetic
Heterogeneity in Thai-Isan Peoples from the Lower Region of
Northeastern Thailand
Wibhu Kutanan1*, Suparat Srithawong1, Artittaya Kamlao2, Jatupol Kampuansai3
1Department of Biology, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand
2Forensic Science Program, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand
3Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
Email: *
Received November 12th, 2013; revised December 15th, 2013; accepted January 9th, 2014
Copyright © 2014 Wibhu Kutanan et al. This is an open access article distributed under the Creative Co mmons
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original work is properly cited. In accordance of the Creative Commons Attribution License all Copyrights ©
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The Thai-Isan are the largest ethnic group in Northeastern Thailand, who migrated from the territory of
present-day Laos around 200 years ago. There are a limited number of previous studies of mtDNA diver-
sity in Northeastern Thai populations. The present study investigates genetic variation and genetic struc-
ture in three Thai-Isan populations by analyzing mitochondrial DNA variation in hypervariable region 1.
We also evaluate genetic relationship and admixture between Thai-Isan and surrounding populations from
Northeastern Thailand, and neighboring countries. The studied Thai-Isan populations reveal genetic dif-
ferentiation from each other and from compared populations. Thai-Isan exhibit a close relationship with
surrounding populations, particularly the Lao and Khmer, reflecting extensive gene flow among them.
Admixture proportions observed in most Thai-Isan populations exhibit a higher contribution from the pa-
rental Lao than the Khmer. Different admixture patterns reflect genetic heterogeneity of Thai-Isan groups.
The lower the latitude, the higher the Khmer contribution might be associated with the ethnic constitution
of parental populations in each Thai-Isan population. More genetic data from HVR2 and coding regions,
as well as different marker systems are needed to infer population history of Thai-Isan populat ions.
Keywords: mtDNA Diversity; Genetic Relationship; Genetic Admixture; Thai-Isan; Northeastern
Isan is the term employed by Thais referring to the region
and people of Northeastern Thailand. Northeastern Thailand
geographically shares a border with Laos and Cambodia, and
lies in close proximity to Vietnam, thus, this region has sub-
stantial cultural, linguistic, and ethnic diversity. The word Isan
is derived from Isana which is the Sanskrit name of the ancient
Mon-Khmer kingdom (Bonnie Pacala & Somroay, 2010). The
Thai-Isan people refer to the predominant ethnic peoples who
are ethnically Lao but have Thai citizenship. The population of
Northeastern Thailand also comprises native Mon-Khmer
speaking groups, e.g. Khmer and Chaobon, and other Tai-
speaking groups such as the Phuthai (Keyes, 1974; Lewis,
2009). Hence, there are approximately eighteen ethnicities,
three major languages and twenty-two dialects in Northeastern
Thailand (Premsrirat, 1999). Among several ethnic affiliations,
the majority of these populations are Thai-Isan people (over 20
million inhabitants) whose regional identity is completely asso-
ciated with the Lao language (McCargo & Hongladarom,
The historical motherland of Thai-Isan peoples is in the area
of the present-day Lao People’s Democratic Republic (LPRD).
The Isan and LPRD are geographically and politically divided
by the Mekong River. Around the 9th century, before the immi-
gration from Laos, Northeastern Thailand was heavily influ-
enced by the Khmer empire in Angkor which raised several
remarkable Khmer temples and relics, especially in southern
Isan (Wongtaed, 1999; Schliesinger, 2001). After the decline of
the Khmer empire, a large Lao population was forcibly relo-
cated to the area of Isan between the mid-fourteenth and the
late-eighteenth centuries (Keyes, 1967). When the French en-
tered Indochina in the late 19th century, the Mekong was used
as a boundary between Lao people. Isan became the region on
the southern bank of the Mekong River, controlled by the state
of Siam, while the area on the north side (present-day LPRD)
was controlled by the French (Schliesinger, 2001).
According to the historical records, biculturalism comprising
the Khmer and Thai-Isan populations existed in the lower part
of Isan, particularly spanning the provinces of Surin, Buriram,
Ubon-Ratchathani, Nakorn Ratchasima and Srisaket (Vail,
2007). Therefore, this region is of great interest to scholars
studying linguistics (Smalley, 1988; Smalley, 1994), culture,
*Corresponding author.
history (Wyatt, 1984; Khanittanan, 2001), archaeology (Welch,
1998; Talbot & Janthed, 2002), and politics (Wyatt, 1969;
McCargo & Hongladarom, 2001). However, few studies of
anthropological genetics in the southern part of Northeastern
Thailand have ever been published.
In recent years, mitochondrial DNA (mtDNA) variation has
been proven to be the most powerful genetic marker for inves-
tigating gene pools and tracing maternal genetic relatedness
(Cavalli-Sforza & Feldman, 2003; Malyarchuk et al., 2008). In
Thailand, several studies of human genetic structure and varia-
tion to infer population history and migratory routes were ex-
clusively focused in the Northern part of Thailand, while in
Isan, one of the most ethnicly diverse parts of Thailand, a li-
mited number of such studies were reported. Only Fucharoen et
al. (2001), Lertrit et al. (2008), and Boonsoda et al. (2013) re-
vealed genetic data for four populations, namely the Phutai,
Chaobon, Thai Khon Kaen, Thai Korat, and Khmer by studying
mtDNA variation. Therefore, the present study analy ses mtDNA
variation to reveal population affinity and admixture between
the Thai-Isan from the lower part of Northern Thailand and
surrounding populations reported in previous literatures.
Materials and Methods
Sample Collection and DNA Extraction
After interviewing for linguistic and personal history as well
as obtaining consent from all volunteers, buccal swabs were
collected from 134 unrelated Thai-Isan individuals belonging to
three populations from Buriram Province (Isan-Bu, n = 51),
Ubon-Ratchathani Province (Isan-Ub, n = 45) and Chaiyabhum
Province (Isan-Ch, n = 38). These provinces are located in the
lower part of Northeastern Thailand. The Khon Kaen Universi-
ty ethics committee for human research approved the research
protocol. Genomic DNA was extracted according to the manu-
facturer’s instructions (Puregene DNA Buccal Cell Kit, Qiagen).
Data of mtDNA variability of HVR-1 from surrounding popu-
lations from Northeastern Thailand (Isan-Kr, Isan-Kk, Khmer1,
Phutai, and Chaobon) as well as populations in neighboring
countries (Laos, Khmer2, Khmer3, Cham, and Kinh) from pre-
vious literature (Table 1 and Figure 1) were obtained in order
to compare population affinity admixture analyses.
mtDNA Amplification and Sequencin g
The mtDNA control region was amplified by a published
primer pair as described elsewhere (Schurr et al., 1999). PCR
products were sent for purification and the hype rva ri abl e re gi on
1 (HVR1) was sequenced by Macrogen (Seoul, Korea). Se-
quencing reactions were performed using a published set of
primers (Kampuansai et al., 2007). The sequencing results were
edited, assembled and aligned with the revised Cambridge Ref-
erence Sequence (Andrews et al., 1999) using SeqScape soft-
ware v.2.0 (Applied Biosystem, Foster City, CA). The mtDNA
Figure 1.
Geographic distribution of the studied Thai-Isan populations from the
Northeastern Thailand () and surrounding compared populations ()
from Thailand and neighboring co untries.
Table 1.
General information and genetic diversities of the studied Thai-Isan and compared populations.
Languagea family,
(province, country) Reference
Haplotype diversity
Nucleotide diversity
Buriram, Thailand
Present study
0.9718 (0.0109)
0.0232 (0.0122)
Isan-Ub 45 TK, TT Ubon Ratcha tha ni, T ha ila nd Present study 0.9323 (0.0283) 0.0225 (0.0119)
Isan-Ch 38 TK, TT Chaiyabhum, Thailand Present study 0.9673 (0.0172) 0.0216 (0.0115)
Khon Kaen, Thailand
Fuchareon et al. (2001)
0.9989 (0.0051)
0.0211 (0.0112)
Isan-Kr 32 TK, TT Nakorn Ratchasima, Thailand Lertrit et al. (2008) 1.0000 (0.0078) 0.0210 (0.0112)
Phutai 25 TK, TT Mukdahan, Thailand Fuchareon et al. (20 01) 0.9767 (0. 0193) 0.02 27 (0.0122)
Laos 213 TK, TT LPRD Bodner et al. (2011) 0.9918 (0.00 19) 0.0210 ( 0 .0109)
Chaobon 20 AA, MK Nakorn Ratchasima, Thailand Lertrit et al. (2007) 0.9474 (0.0300) 0.0221 (0. 0120)
Khmer 1
Surin, Thai l and
Boonsoda et al. (2013)
0.9317 (0.0324)
0.0199 (0.0106)
Khmer 2 22 AA, MK Thailand-Cambodia border Lertrit et al. (2007) 0.9913 (0.0165) 0.0169 (0.0093)
Khmer 3 31 AA, MK Cambodia Black et al. (2006) 0.9527 (0.0261) 0.0223 (0.0118)
Peng et al. (2010)
0.9912 (0.0030)
0.0235 (0.0121)
Peng et al. (2010)
0.9878 (0.0027)
0.0253 (0.0130)
aLanguage: TK: Tai-Kadai, AA: Austr o-asiatic, AS: Austronesian, TT: Tai, MK: Mon-Khmer, MP: Malayo-Polynesian.
sequences can be obtained from the corresponding author on
Statistical Analyses
The mtDNA sequences of 336 nucleotides (np 16048-16383)
were identified for polymorphic sites by DnaSP v.5.10 (Librado
& Rozas, 2009). Arlequin 3.5 program (Excoffier & Lischer,
2010) was used to calculate intrapopulation diversity: nucleo-
tide diversity (π), number of haplotype, haplotype diversity (h),
and mean number of pairwise differences (MPD). Several pa-
rameters describing demographic history were observed by
mismatch distribution and neutrality approaches. DnaSP v.5.10
software was also employed to construct the observed pairwise
differences against the expected mismatch distribution under
both constant size population and sudden population expansion
models. A raggedness index value (r) (Harpending, 1994), neu-
trality estimators, Fu’s Fs (Fu, 1997) and Tajima’s D (Tajima,
1989) data were calculated using Arlequin 3.5 program. In
order to evaluate population relationships, the same program
was employed to compute genetic distance based on pairwise
difference (Fst) and then a genetic distance matrix was plotted
in two dimensions by means of multidimensional scaling (MDS)
using the commercially available STATISTICA 7.0 (StatSoft
Software Ltd.). Admixture estimation was performed by AD-
MIX 2.0 (Dupanloup & Bertorelle, 2001), taking mutation and
molecular divergence between alleles into account (Bertorelle
& Excoffier, 1998; Dupanloup & Bertorelle, 2001).
Result and Discussion
Genetic Variation and Population Expansion of the
Studied Thai-Isan Populations
A 336 bp mtDNA-HVR1 segment between pos itions 16048 to
16383 was sequenced and compared among three studied pop-
ulations. Within 134 samples, 76 different haplotypes were
identified and defined by 92 variable positions, (Figure 2).
Among 76 haplotypes, 53 and 15 were single unique and mul-
tiple unique, respectively, while only 8 shared haplotypes were
found. Among the 8 shared haplotype, only one haplotype
(16129-16192-16223-16297) was present in all populations.
This indicates that the studied populations were differentiated.
The highest frequency of haplotype was 16093-16124-16148-
16223, which is exclusively found in the Isan-Ub populations.
The number of intrapopulation MPD were 7.5657 (Isan-Ub),
Figure 2.
Nucleotide differences in the 76 distinct haplotypes, defined by 92 polymorphic sites are shown based on a comparison with the 336-bp Revised
Cambridge Reference Sequence ranged from 16,024 - 16,383. The reference is presented below the order for polymorphic sites (16+). For the other 76
haplotypes, only differences from the Revised Cambridge Reference Sequence are indicated. The number of individuals which are found in each
haplotype is embedded in Arabic numerals on the ri ght.
7.8086 (Isan-Bu), and 7.2660 (Isan-Ch), reflected higher genetic
heterogeneity within Isan-Bu than Isan-Ub and Isan-Ch. The
interpopulation MPD, range d from 7.6749 to 7.9394, were rela-
tively high compared to previous report (Bodner et al., 2011)
reflecting genetic differentiation among them. Genetic structure
among the populations was tested for significant variation by
AMOVA (Excoffier et al., 1992). Most genetic var iation was th e
difference within populations (96.83%), whereas the rest of the
variance (3.17%) was found among populations. The AMOVA
result was significant (Fst = 0.0316; P = 0.0000), indicating a
genetic difference among Thai-Isan populations. Pairwise ge-
netic distances with significant levels (P < 0.05) were 0.0317
(Isan-Bu and Isan-Ub), 0.0298 (Isan-Bu and Isan-Ch), and
0.0336 (Isan-Ub and Isan-Ch), reflecting genetic differentiation
among present Thai-Isan populations.
Although population growth was not the primary subject of
this study, we performed Fu’s Fs and Tajima’s D to explore the
demographic history of each population. These two parameters
were used to evaluate neutrality under the null hypothesis,
which stated that if the studied populations evolve with a con-
stant effective population size, all mutations are selectively
neutral. The value of the Fu’s Fs in Isan-Bu, Isan-Ub, and Isan-
Ch was 14.22887 (P = 0.0000), 9.64724 (P = 0.0080), and
11.4357 (P = 0.0000), respectively. For the D test of Tajima,
non-significant negative values were detected (Isan-Bu =
1.48827 (P = 0.057), Isan-Ub = 1.33313 (P = 0.093), Isan-
Ch = 0.69434 (P = 0.256). The highly significant negative
Fu’s Fs and negative Tajima’s D, implied a recent bottleneck
following an expansion in the population. Another demograph-
ic parameter showed the lower raggedness index (less than 0.03)
as well as the unimodal mismatch distribution graph for these
populations (data not shown), providing congruent evidence for
population growth and expansion (Rogers & Harpending,
Genetic Comparison with Surrounding Populations
Two parameters used for estimating the genetic diversity
within Isan populations were haplotype diversity and nucleotide
diversity. The highest haplotype diversity (1.0000) was found
in Isan-Kr, the lowest in Khmer1 (0.9317), reflecting a weaker
degree of diversity in Khmer1. Studied Thai-Isan populations
showed relatively high haplotype diversity (h = from 0.9323 to
0.9718). Nucleotide diversity in studied Thai-Isan populations
(π) ranged from 0.0216 to 0.0232, similar to compared popula-
tions (Table 1).
To shed more light on genetic structure, the interpopulation
MPD which ranged from 6.7128 (Isan-Kk-Khmer2) to 9.3
(Khmer1-Chaobon), while the corrected MPD values ranged
from 0 (Laos-Kinh) to 1.9401 (Khmer1-Chaobon), indicating
genetic similarity between Laos and Kinh. Khmer1 and Chao-
bon had high MPD values comparing to all other populations,
indicating differences in genetic structure of these two popula-
tions to others. In pairwise Fst analysis among 78 comparisons,
61 (78%) were statistically significant (P < 0.05) (data not
shown). Intermediate to high Fst values with significant levels
pointed out genetic differentiation among populations. The
Khmer1, Chaobon, and Cham had significant Fst values for all
comparisons. The Isan-Kr, Khmer2 and Phutai had the top three
non-significant pairwise Fst values, indicating extensive gene
flow within these populations.
There was mostly a significant pairwise Fst between the stu-
died Thai-Isan populations and other compared populations,
supporting genetic differentiation of Thai-Isan populations.
MDS analysis based on the Fst matrix was performed to infer
population affinity (Figure 3). The MDS reveal that Isan-Bu,
Isan-Kk, and Isan-Kr were clustered with the Laos, Kinh, Cham,
Phutai, and Khmer2 around the axis center, showing a genetic
similarity. The Isan-Ub, Isan-Ch, Cham, and Khmer3 appear
more distant from the center of the axis, indicating some degree
of differentiation. Although Chaobon and Khmer1 were geo-
graphically closer to all Thai-Isan populations, they were sepa-
rated from the cluster at the axis center, reflecting a great ge-
netic distinction in both populations, which concordant to in-
terpopulation MPD result. Interestingly, the three Khmer
groups were genetically different. The Khmer1 from Surin
Province had greater differentiation, which could be possibly
explained by a weakly haplotype diversity as well as a low
intrapopulation MPD, indicating a loss in genetic diversity
(Hurles et al., 2002; Davis et al., 2011) due to a possible drift
effect. In Surin, Buriram, Srisaket, and Ubon Rachathani Prov-
inces, several Khmer stone sanctuaries and architectural sites
were found, indicating strong Khmer influence since at least the
time of Khmer empire (Schliesinger, 2000). Vail (2007) stated
that there are over a million speakers of Khmer language in this
region, making it probably the largest non-Tai language speak-
ing group within the borders of the Thai state. Therefore,
extensive gene flow might be observed in genetic analysis,
reflected in the Khmer2. The Khmer2 is intermediately posi-
tioned between the Khmer3 from Cambodia and other Tai-
speaking group. This result suggests genetic exchanges between
the Khmers and Thais, conforming to Lertrit et al. (2008) who
is the owner of Khmer2 data.
Genetic Admixture
In admixture analysis, two population groups were defined,
the admixed ones and the parental populations. All Thai-Isan
populations were considered as admixed populations who re-
ceived genetic elements from their putative parental sources.
Although in the current study eight neighboring populations
were employed to compare genetic relationships, based on his-
torical evidence, only three ethnic affiliations belonging to the
Khmer (Khmer1, Khmer2, and Khmer3), Chaobon, and Lao
Figure 3.
Multidimensional scaling scatter plot of studied populations based on
pairwise difference (Fst). ( the present study’s Thai-Isan populations,
surrounding co mpared populati ons).
were regarded as parental populations in admixture analysis. In
brief, the Khmer and Chaobon who speak Mon-Khmer were the
native inhabitants in lower Northeastern Thailand before the
Tai-speaking immigrants migrated en mass from Laos as a
result of political conflicts within Laos around 600 years ago
(Schliesinger, 2000; Schliesinger, 2001).
Admixture proportions reveal that the contributions of the
Lao maternal gene pool in the extant Thai-Isan populations
were varied, as shown in Figure 4. Admixture results indicated
genetic heterogeneity within Thai-Isan populations. Except for
Isan-Bu, other Thai-Isan populations received more genetic
contributions from the parental Lao (47% to 94%) than the
parental Khmer (0% to 31%) and Chaobon (3% to 13%). When
considering the Khmer contribution, the lower the latitude, the
higher the Khmer contribution was observed. The Khmer made
the highest contribution in the Isan-Bu, which was in agreement
with linguistic, historical, and archaeological evidence. Two
hypotheses describe the origin of Isan-Bu. First, the Isan-Bu
might be immigrants from Laos and after their migration they
were mixed with the native Khmer in present day Buriram
Province. The second hypothesis proposes that after the forcible
movement of the Lao people, the native Khmers in Buriram
adopted the Lao culture and language (Vail, 2006).
The highest Chaobon influences were found in Isan-Kr and
Isan-Ub. As earlier described in Lertrit et al. (2008) who stu-
died the ethnography of Chaobon, the Chaobon were found
only in Thailand and scattered among different villages in the
areas of Nakorn Ratchasima, Chaiyabhum, and Petchaboon
Provinces. Because of shared geographic location in Nakorn
Ratchasima Province between Chaobon and Isan-Kr, albeit
limited by cultural difference, gene flow might explain the
slight genetic contribution from parental sources to an admixed
one. In addition, the Chaobon’s contribution to Isan-Ub from
Ubon Rachathani Province is questionable because no evidence
indicated the existence of Chaobon in Ubon Ratchathani. It
might suggest that this fraction derived from other native
Mon-Khmer inhabitants in Ubon Ratchathani who shared an-
cestors with the Chaobon, like the Bru and the Suay.
In the area of Chaiyabhum Province, both Tai-Kadai speak-
ing people and Chaobon were inhabitants, therefore, our ex-
pectation was a relative Chaobon contribution to the Isan-Ch
maternal gene pool, but the data rejected our prediction. Only a
Figure 4.
Pie diagrams showing the distribution of Laos (white), Khmer (black)
and Chaobon (grey) contributing to the Thai-Is an populations.
few Chaobon fractions (6.2%) were found. This suggests that
Chaobon in Chaiyabhum and Nakorn Ratchasima provinces
were genetically different groups, thus, in the future more ge-
netic data from Chaobon in Chaiyabhum will be useful to eva-
luate the complete genetic structure in Thai-Isan populations.
Moreover, no Khmer influence was detected in Isan-Ch. Most
of the genetic composition within Isan-Ch is contributed by the
Laos parental source.
However, it should be cautioned that the Lao samples in
LPRD from Bodner et al. (2011) which were used as parental
populations were multi-ethnic in origin and from across the
country, and there is no data of ethnic or linguistic affiliation of
each sample. Because of an extensively ethnic diversity as de-
scribed in Bodner et al. (2011), the contribution from parental
Lao in LPRD to the admixed Thai-Isan populations might not
be purely from the Tai-Kadai speaking Lao, but the Mon-
Khmer and Hmong-Mien Laos could also be the sources.
The current study based on mitochondrial DNA variation in
HVR1 regions of Thai-Isan populations from the lower part of
Northeastern Thailand shows high levels of genetic diversity
and differentiation. The significant difference among Thai-Isan
populations might be shaped by different levels of admixture
from putative distinct parental populations. The estimation of
admixture suggests that Thai-Isan populations were genetically
influenced by parental Lao and Khmer populations. This result
shows that Thai-Isan people from Northeastern Thailand and
Lao people from the LPDR previously had genetic similarity,
but after the mass migration period, the people from Laos were
mixed with the Khmer and vice versa. The possible promotion
of speedy admixture between two linguistically and culturally
different ethnicities was the process of Thaification, which is
the policy that was proposed by the Thai government in the 20th
century for the purpose of de-emphasizing the Laos and Khmer
origins of people in Northeastern Thailand (Winichakul, 2000).
After that time, all people in this region began referring to
themselves as “Thai-Isan. Therefore, either the Thaification
process, geographic proximity or both factors are important in
determining genetic structure of the current Thai-Isan popula-
tions as well as the native Khmer. Heterogeneity of admixture
patterns might be associated with the ethnic constitution of
parental populations in each area. To shed more light on ad-
mixture analysis, more genetic information of various ethnic
affiliations in Northeastern Thailand as well as the Laos sam-
ples descended from Laos Lan Xang is required. Since this
study solely examines mitochondrial DNA in HVR1 region, a
larger reading frame such as HVR2 and coding region, as well
as paternal markers is needed to help understand the complex
migration and population history of Thai-Isan populations.
Acknowledgemen ts
The authors wish to thank all volunteers and village chiefs
for their participation in sample collections. We also thank Dr.
Alvin Yoshinaga for valuable comments and suggestions on the
manuscript. This research was funded by Khon Kaen Universi-
ty, Thailand (Grant No. 563802).
Declaration of Interest
The authors report no declarations of interest.
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