Population structure in Thailand

PLoS ONE 8(11): e79522. doi:10.1371/journal.pone.0079522

Insight into the Peopling of Mainland Southeast Asia from Thai Population Genetic Structure

Pongsakorn Wangkumhang et al.

There is considerable ethno-linguistic and genetic variation among human populations in Asia, although tracing the origins of this diversity is complicated by migration events. Thailand is at the center of Mainland Southeast Asia (MSEA), a region within Asia that has not been extensively studied. Genetic substructure may exist in the Thai population, since waves of migration from southern China throughout its recent history may have contributed to substantial gene flow. Autosomal SNP data were collated for 438,503 markers from 992 Thai individuals. Using the available self-reported regional origin, four Thai subpopulations genetically distinct from each other and from other Asian populations were resolved by Neighbor-Joining analysis using a 41,569 marker subset. Using an independent Principal Components-based unsupervised clustering approach, four major MSEA subpopulations were resolved in which regional bias was apparent. A major ancestry component was common to these MSEA subpopulations and distinguishes them from other Asian subpopulations. On the other hand, these MSEA subpopulations were admixed with other ancestries, in particular one shared with Chinese. Subpopulation clustering using only Thai individuals and the complete marker set resolved four subpopulations, which are distributed differently across Thailand. A Sino-Thai subpopulation was concentrated in the Central region of Thailand, although this constituted a minority in an otherwise diverse region. Among the most highly differentiated markers which distinguish the Thai subpopulations, several map to regions known to affect phenotypic traits such as skin pigmentation and susceptibility to common diseases. The subpopulation patterns elucidated have important implications for evolutionary and medical genetics. The subpopulation structure within Thailand may reflect the contributions of different migrants throughout the history of MSEA. The information will also be important for genetic association studies to account for population-structure confounding effects.

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Genetic structure in China

After my experiment on Spain, I decided to carry out a similar experiment in China, for which there is a large number of regional/ethnic sub-populations.15 clusters were inferred with 22 MDS dimensions.

The Uygur are the clear outlier population, doubtlessly due to their substantial Caucasoid admixture and geographical position in Central Asia, a region that was traditionally at the outskirts of Chinese civilization. Other Altaic speakers (both Mongolic and Tungusic) are also divergent, as are the Dai/Lahu people from the China/Thailand/Laos area.

Interestingly, the Tujia people from Central China seem to be the ones most like the Han overall, with Hmongic Miaozu/She more like the southern Han.

Craniofacial Differences Between Modern and Archaeological Asian Skeletal Populations (Ph.D. thesis)

From p. 169:

Since physical changes have been documented in these Asian populations, principal components analyses were conducted for certain variable groupings in each population to understand how crania shape were related. Based on visual inspection, ancient crania appears to be long and narrower compared to their more modern counterparts, and these tests will illustrate which portions of the crania are changing over time.

p. 181:

Since physical differences were shown to be present between the two ethnic groups, shape and size changes were calculated to understand how the crania have changed over time. Principal components analysis was calculated using transformed log variables of the dataset to determine which measurements were changing. All populations appeared to be extremely divergent from one another, resulting in unequal variancecovariance matrices. Modern Chinese individuals appear to have a shorter head than their ancient counterpart while modern Thais tend to have narrower faces and heads than their ancestral group.

p. 187:

None of the variable groupings show a close biological relationship between modern populations. However, the modern Thai population did show a closer biological relationship with the modern Chinese than with either archaeological population. One possible reason for this outcome is due to the influx of Chinese immigrants to Thailand that eventually became part of the gene pool. However, gene flow did not work in reverse with Thai people moving into China. For the most part Thai people remained ethnically Thai and Chinese people remained Chinese.

p. 197:

Modern Chinese individuals appear to have narrower and longer crania, which is opposite than expected. Ancient Chinese crania have higher cranial vaults than their modern counterparts, which contributes to their divergence. Facial variables that appear to be most divergent are ones that measure for prognathism and upper facial height. Modern Chinese individuals have longer upper facial height but are not as prognathic as their ancient counterparts.

Craniofacial Differences Between Modern and Archaeological Asian Skeletal Populations

Chan, Wing Nam Joyce

The principal objective of this study is to perform a biological distance analysis of two Asian ethnic groups to better understand environmental factors influencing cranial shape and size. Cranial shape and size are influenced by both epigenetic and genetic factors, resulting in differences in crania over time. Cranial measurements can be used as a proxy for genetic data and to understand epigenetic factors affecting crania. Therefore, craniometrics can be used to determine differences between populations.

Ancient and modern Chinese and Thai skeletal populations were used for this biological distance analysis. The ancient Chinese population is from northern China at Anyang dating to the Shang Dynasty (1600BC-1046BC) while its modern counterpart is located in Hong Kong dating from 1977-1983. Individuals from both populations are thought to have belonged to the Han ethnic group and are possibly biologically related. Both Thai populations are located in northeastern Thailand, known as the Isaan region. The ancient Thai population from the Ban Chiang site is dated through the Pre-metal to Iron Age periods (2000 B.C.- 200 A.D.) while the modern population dates from 1970s to present. Data were collected on crania at 29 anthropologically accepted measurements to explore epigenetic and biological relationships between modern and ancient populations. Data were subjected to multiple multivariate statistical tests to understand causative agents for change and differences between populations.

These results suggest that modern and ancient Thai and Chinese populations have markedly different crania, especially in shape. However, correlated factors could not be identified in this study, primarily due to lack of historical data. Geographical, temporal, and climate variables such as temperature were tested against measures of biological distance with little to no correlation discovered. Interestingly, modern and ancient Chinese populations displayed the closest biological affinity, possibly due to similar environments and lack of genetic changes. Ban Chiang individuals were the most biologically distant from other populations, indicating possible genetic differences not yet understood. These genetic differences could indicate either that Ban Chiang individuals are not recently ancestral to the modern Thai population or a mass migration movement into northeast Thailand had occurred.

These results are interpreted to indicate that environmental factors have played a large role in altering cranial shape in these two ethnically Asian populations since genetic alteration in the areas has not been documented. Environmental factors have caused isometric changes in cranial shape as crania have become distinct from their ancestral counterparts. Cultural changes, such as diet shifts and modernization, are possible causative agents for these changes witnessed in these populations.

The findings of this study contribute to our understanding of human cranial variation for these two Asian groups, and to broader discussions of epigenetic and genetic relationships in the expression of cranial morphology. This research also contributes to the discussions of how biological distance in the crania has been influenced by epigenetic factors and ultimately how the peopling of modern Asia occurred.

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Tai and Mon-Khmer of northern Thailand

BMC Genetics 2011, 12:56doi:10.1186/1471-2156-12-56

Genetic structure of the Mon-Khmer speaking groups and their affinity to the neighbouring Tai populations in Northern Thailand

Wibhu Kutanan et al.

Background
The Mon-Khmer speaking peoples inhabited northern Thailand before the arrival of the Tai speaking people from southern China in the thirteenth century A.D. Historical and anthropological evidence suggests a close relationship between the Mon-Khmer groups and the present day majority northern Thai groups. In this study, mitochondrial and Y-chromosomal DNA polymorphisms in more than 800 volunteers from eight Mon-Khmer and ten Tai speaking populations were investigated to estimate the degree of genetic divergence between these major linguistic groups and their internal structure.

Results
A large fraction of genetic variation is observed within populations (about 80% and 90 % for mtDNA and the Y-chromosome, respectively). The genetic divergence between populations is much higher in Mon-Khmer than in Tai speaking groups, especially at the paternally inherited markers. The two major linguistic groups are genetically distinct, but only for a marginal fraction (1 to 2 %) of the total genetic variation. Genetic distances between populations correlate with their linguistic differences, whereas the geographic distance does not explain the genetic divergence pattern.

Conclusions
The Mon-Khmer speaking populations in northern Thailand exhibited the genetic divergence among each other and also when compared to Tai speaking peoples. The different drift effects and the post-marital residence patterns between the two linguistic groups are the explanation for a small but significant fraction of the genetic variation pattern within and between them.

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Ancient mtDNA from Southeast Asia

American Journal of Physical Anthropology

Genetic history of Southeast Asian populations as revealed by ancient and modern human mitochondrial DNA analysis

Patcharee Lertrit et al.

Abstract

The 360 base-pair fragment in HVS-1 of the mitochondrial genome were determined from ancient human remains excavated at Noen U-loke and Ban Lum-Khao, two Bronze and Iron Age archaeological sites in Northeastern Thailand, radio-carbon dated to circa 3,500-1,500 years BP and 3,200-2,400 years BP, respectively. These two neighboring populations were parts of early agricultural communities prevailing in northeastern Thailand from the fourth millennium BP onwards. The nucleotide sequences of these ancient samples were compared with the sequences of modern samples from various ethnic populations of East and Southeast Asia, encompassing four major linguistic affiliations (Altaic, Sino-Tibetan, Tai-Kadai, and Austroasiatic), to investigate the genetic relationships and history among them. The two ancient samples were most closely related to each other, and next most closely related to the Chao-Bon, an Austroasiatic-speaking group living near the archaeological sites, suggesting that the genetic continuum may have persisted since prehistoric times in situ among the native, perhaps Austroasiatic-speaking population. Tai-Kadai groups formed close affinities among themselves, with a tendency to be more closely related to other Southeast Asian populations than to populations from further north. The Tai-Kadai groups were relatively distant from all groups that have presumably been in Southeast Asia for longer-that is, the two ancient groups and the Austroasiatic-speaking groups, with the exception of the Khmer group. This finding is compatible with the known history of the Thais: their late arrival in Southeast Asia from southern China after the 10th-11th century AD, followed by a period of subjugation under the Khmers.

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