Reconstructing the human genetic history of mainland Southeast Asia: Insights from genome-wide data from Thailand and Laos

Thailand and Laos, located in the center of Mainland Southeast Asia (MSEA), harbor diverse ethnolinguistic groups encompassing all five language families of MSEA: Tai-Kadai (TK), Austroasiatic (AA), Sino-Tibetan (ST), Hmong-Mien (HM), and Austronesian (AN). Previous genetic studies of Thai/Lao populations have focused almost exclusively on uniparental markers and there is a paucity of genome-wide studies. We therefore generated genome-wide SNP data for 33 ethnolinguistic groups, belonging to the five MSEA language families from Thailand and Laos, and analyzed these together with data from modern Asian populations and SEA ancient samples. Overall, we find genetic structure according to language family, albeit with heterogeneity in the AA-, HM-, and ST-speaking groups, and in the hill tribes, that reflects both population interactions and genetic drift. For the TK speaking groups, we find localized genetic structure that is driven by different levels of interaction with other groups in the same geographic region. Several Thai groups exhibit admixture from South Asia, which we date to ∼600–1000 years ago, corresponding to a time of intensive international trade networks that had a major cultural impact on Thailand. An AN group from Southern Thailand shows both South Asian admixture as well as overall affinities with AA-speaking groups in the region, suggesting an impact of cultural diffusion. Overall, we provide the first detailed insights into the genetic profiles of Thai/Lao ethnolinguistic groups, which should be helpful for reconstructing human genetic history in MSEA and selecting populations for participation in ongoing whole genome sequence and biomedical studies

Identification of Close Relatives in the HUGO Pan-Asian SNP Database

The HUGO Pan-Asian SNP Consortium has recently released a genome-wide dataset, which consists of 1,719 DNA samples collected from 71 Asian populations. For studies of human population genetics such as genetic structure and migration history, this provided the most comprehensive large-scale survey of genetic variation to date in East and Southeast Asia. However, although considered in the analysis, close relatives were not clearly reported in the original paper. Here we performed a systematic analysis of genetic relationships among individuals from the Pan-Asian SNP (PASNP) database and identified 3 pairs of monozygotic twins or duplicate samples, 100 pairs of first-degree and 161 second-degree of relationships. Three standardized subsets with different levels of unrelated individuals were suggested here for future applications of the samples in most types of population-genetics studies (denoted by PASNP1716, PASNP1640 and PASNP1583 respectively) based on the relationships inferred in this study. In addition, we provided gender information for PASNP samples, which were not included in the original dataset, based on analysis of X chromosome data

Population Genetic Structure of Peninsular Malaysia Malay Sub-Ethnic Groups

Patterns of modern human population structure are helpful in understanding the history of human migration and admixture. We conducted a study on genetic structure of the Malay population in Malaysia, using 54,794 genome-wide single nucleotide polymorphism genotype data generated in four Malay sub-ethnic groups in peninsular Malaysia (Melayu Kelantan, Melayu Minang, Melayu Jawa and Melayu Bugis). To the best of our knowledge this is the first study conducted on these four Malay sub-ethnic groups and the analysis of genotype data of these four groups were compiled together with 11 other populations' genotype data from Indonesia, China, India, Africa and indigenous populations in Peninsular Malaysia obtained from the Pan-Asian SNP database. The phylogeny of populations showed that all of the four Malay sub-ethnic groups are separated into at least three different clusters. The Melayu Jawa, Melayu Bugis and Melayu Minang have a very close genetic relationship with Indonesian populations indicating a common ancestral history, while the Melayu Kelantan formed a distinct group on the tree indicating that they are genetically different from the other Malay sub-ethnic groups. We have detected genetic structuring among the Malay populations and this could possibly be accounted for by their different historical origins. Our results provide information of the genetic differentiation between these populations and a valuable insight into the origins of the Malay sub-ethnic groups in Peninsular Malaysia

Mapping human genetic diversity in Asia

Asia harbors substantial cultural and linguistic diversity, but the geographic structure of genetic variation across the continent remains enigmatic. Here we report a large-scale survey of autosomal variation from a broad geographic sample of Asian human populations. Our results show that genetic ancestry is strongly correlated with linguistic affiliations as well as geography. Most populations show relatedness within ethnic/linguistic groups, despite prevalent gene flow among populations. More than 90% of East Asian (EA) haplotypes could be found in either Southeast Asian (SEA) or Central-South Asian (CSA) populations and show clinal structure with haplotype diversity decreasing from south to north. Furthermore, 50% of EA haplotypes were found in SEA only and 5% were found in CSA only, indicating that SEA was a major geographic source of EA populations

Complete mitochondrial genomes of Thai and Lao populations indicate an ancient origin of Austroasiatic groups and demic diffusion in the spread of Tai–Kadai languages

The Tai–Kadai (TK) language family is thought to have originated in southern China and spread to Thailand and Laos, but it is not clear if TK languages spread by demic diffusion (i.e., a migration of people from southern China) or by cultural diffusion, with native Austroasiatic (AA) speakers switching to TK languages. To address this and other questions, we obtained 1234 complete mtDNA genome sequences from 51 TK and AA groups from Thailand and Laos. We find high genetic heterogeneity across the region, with 212 different haplogroups, and significant genetic differentiation among different samples from the same ethnolinguistic group. TK groups are more genetically homogeneous than AA groups, with the latter exhibiting more ancient/basal mtDNA lineages, and showing more drift effects. Modeling of demic diffusion, cultural diffusion, and admixture scenarios consistently supports the spread of TK languages by demic diffusion

Cultural variation impacts paternal and maternal genetic lineages of the Hmong-Mien and Sino-Tibetan groups from Thailand

The Hmong-Mien (HM) and Sino-Tibetan (ST) speaking groups are known as hill tribes in Thailand; they were the subject of the first studies to show an impact of patrilocality vs. matrilocality on patterns of mitochondrial (mt) DNA vs. male-specific portion of the Y chromosome (MSY) variation. However, HM and ST groups have not been studied in as much detail as other Thai groups; here we report and analyze 234 partial MSY sequences (∼2.3 mB) and 416 complete mtDNA sequences from 14 populations that, when combined with our previous published data, provides the largest dataset yet for the hill tribes. We find a striking difference between Hmong and IuMien (Mien-speaking) groups: the Hmong are genetically different from both the IuMien and all other Thai groups, whereas the IuMien are genetically more similar to other linguistic groups than to the Hmong. In general, we find less of an impact of patrilocality vs. matrilocality on patterns of mtDNA vs. MSY variation than previous studies. However, there is a dramatic difference in the frequency of MSY and mtDNA lineages of Northeast Asian (NEA) origin vs. Southeast Asian (SEA) origin in HM vs. ST groups: HM groups have high frequencies of NEA MSY lineages but lower frequencies of NEA mtDNA lineages, while ST groups show the opposite. A potential explanation is that the ancestors of Thai HM groups were patrilocal, while the ancestors of Thai ST groups were matrilocal. Overall, these results attest to the impact of cultural practices on patterns of mtDNA vs. MSY variation

Close genetic relationship between central Thai and Mon people in Thailand revealed by autosomal microsatellites

Central Thailand is home to diverse populations with the central Thai constituting the major group, while the Mon, who migrated from southern Myanmar, are sparsely distributed within the region. A total of 338 individuals of eight central Thai (246 samples) and three Mon populations (92 samples) were newly genotyped. When combined with our previously published Mon data, this provides a total of 139 Mon samples. We found genetic similarity between the central Thai and Mon and weak sub-structuring among Thais from central, northern, and northeastern Thailand. The forensic parameter results show high discrimination values which are appropriate for forensic personal identification and paternity testing in both the central Thai and Mon; the probabilities of excluding paternity are 0.999999112 and 0.999999031, respectively, and the combined discrimination power is 0.9999999999999999999999 in both groups. This regional allelic frequency on forensic microsatellites may serve as a useful reference for further forensic investigations in both Thailand and Myanmar

Contrasting paternal and maternal genetic histories of Thai and Lao populations

The human demographic history of Mainland Southeast Asia (MSEA) has not been well-studied; in particular there have been very few sequence-based studies of variation in the male-specific portions of the Y chromosome (MSY). Here, we report new MSY sequences of ∼2.3 mB from 914 males, and combine these with previous data for a total of 928 MSY sequences belonging to 59 populations from Thailand and Laos who speak languages belonging to three major MSEA families: Austroasiatic (AA), Tai-Kadai (TK) and Sino-Tibetan (ST). Among the 92 MSY haplogroups, two main MSY lineages (O1b1a1a* (O-M95*) and O2a* (O-M324*)) contribute substantially to the paternal genetic makeup of Thailand and Laos. We also analyse complete mtDNA genome sequences published previously from the same groups, and find contrasting pattern of male and female genetic variation and demographic expansions, especially for the hill tribes, Mon, and some major Thai groups. In particular, we detect an effect of post-marital residence pattern on genetic diversity in patrilocal vs. matrilocal groups. Additionally, both male and female demographic expansions were observed during the early Mesolithic (∼10 kya), with two later major male-specific expansions during the Neolithic period (∼4-5 kya) and the Bronze/Iron Age (∼2.0-2.5 kya). These two later expansions are characteristic of the modern AA and TK groups, respectively, consistent with recent ancient DNA studies. We simulate MSY data based on three demographic models (continuous migration, demic diffusion and cultural diffusion) of major Thai groups and find different results from mtDNA simulations, supporting contrasting male and female genetic histories

New insights from Thailand into the maternal genetic history of Mainland Southeast Asia

Tai-Kadai (TK) is one of the major language families in Mainland Southeast Asia (MSEA), with a concentration in the area of Thailand and Laos. Our previous study of 1234 mtDNA genome sequences supported a demic diffusion scenario in the spread of TK languages from southern China to Laos as well as northern and northeastern Thailand. Here we add an additional 560 mtDNA genomes from 22 groups, with a focus on the TK-speaking central Thai people and the Sino-Tibetan speaking Karen. We find extensive diversity, including 62 haplogroups not reported previously from this region. Demic diffusion is still a preferable scenario for central Thais, emphasizing the expansion of TK people through MSEA, although there is also some support for gene flow between central Thai and native Austroasiatic speaking Mon and Khmer. We also tested competing models concerning the genetic relationships of groups from the major MSEA languages, and found support for an ancestral relationship of TK and Austronesian-speaking groups