Mitogenomes from Thailand offer insights into maternal genetic history of mainland South-East Asia

Open access New insights from Thailand into the maternal genetic history of Mainland Southeast Asia, by Kutanan et al. Eur. J. Hum. Genet. (2018) 26:898–911

Abstract (emphasis mine):

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.

south-east-asian-thailand
Map showing sample locations and haplogroup distributions. Blue stars indicate the 22 presently studied populations (Tai-Kadai, Austroasiatic, and Sino-Tibetan groups) while red and green circles represent Tai-Kadai and Austroasiatic populations from the previous study [7]. Population abbreviations are in Supplementary Table S1

Interesting excerpts:

Finally, we used simulations to test hypotheses concerning the genetic relationships of groups belonging to different language families. We found that Starosta’s model [11] provided the best fit to the mtDNA data; however, Sagart’s model [9, 10] was also highly supported. These two models both postulate a close linguistic affinity between TK and AN. Although genetic relatedness between TK and AN groups has been previously studied [7, 46, 47], to our knowledge this is the first study to use demographic simulations to select the best-fitting model. Our results support the genetic relatedness of TK and AN groups, which might reflect a postulated shared ancestry among the proto-Austronesian populations of coastal East Asia [48].

Specifically, the best-fitting model suggests that after separation of the prehistoric TK from AN stocks around 5–6 kya in Southeast China, the TK spread southward throughout MSEA around 1–2 kya by a demic diffusion process, accompanied by population growth but with at most minor admixture with the autochthonous AA groups. Meanwhile, the prehistorical AN ancestors entered Taiwan and dispersed southward throughout ISEA, with these two expansions later meeting in western ISEA. The lack of mtDNA haplogroups associated with the expansion out of Taiwan in our Thai/Lao samples has two possible explanations: either the Out of Taiwan expansion did not reach MSEA (at least, in the area of present-day Thailand and Laos); or, if the prehistoric AN migrated through this area, their mtDNA lineages do not survive in modern Thai/Lao populations. Ancient DNA studies in MSEA would further clarify this issue. Moreover, although mtDNA analyses are informative in elucidating genetic perspectives in geographically and linguistically related populations, they have an obvious limitation in that they only provide insights into the maternal history of populations. Future studies of Y chromosomal and genome-wide data will provide further insights into the genetic history of Thai/Lao populations and the role of factors such as post-marital residence patterns and migration in shaping the genetic structure of the region.

Starosta’s chapter referred to in the paper is Proto-East Asian and the origin and dispersal of the languages of East and Southeast Asia and the Pacific.

Related:

Ancient genomes document multiple waves of migration in south-east Asian prehistory

southeast-asia-reich

Open access preprint at bioRxiv Ancient genomes document multiple waves of migration in Southeast Asian prehistory, by Lipson, Cheronet, Mallick, et al. (2018).

Abstract (emphasis mine):

Southeast Asia is home to rich human genetic and linguistic diversity, but the details of past population movements in the region are not well known. Here, we report genome-wide ancient DNA data from thirteen Southeast Asian individuals spanning from the Neolithic period through the Iron Age (4100-1700 years ago). Early agriculturalists from Man Bac in Vietnam possessed a mixture of East Asian (southern Chinese farmer) and deeply diverged eastern Eurasian (hunter-gatherer) ancestry characteristic of Austroasiatic speakers, with similar ancestry as far south as Indonesia providing evidence for an expansive initial spread of Austroasiatic languages. In a striking parallel with Europe, later sites from across the region show closer connections to present-day majority groups, reflecting a second major influx of migrants by the time of the Bronze Age.

south-east-asian-admixture-graph
Schematics of admixture graph results. (A) Wider phylogenetic context. (B) Details of the Austroasiatic clade. Branch lengths are not to scale, and the order of the two events on the Nicobarese lineage in (B) is not well determined (Supplementary Text).

Featured image, from the article: “Overview of samples. (A) Locations and dates of ancient individuals. Overlapping positions are shifted slightly for visibility. (B) PCA with East and Southeast Asians. We projected the ancient samples onto axes computed using the present-day populations (with the exception of Mlabri, who were projected instead due to their large population-speci c drift). Present-day colors indicate language family affiliation: green, Austroasiatic; blue, Austronesian; orange, Hmong-Mien; black, Sino-Tibetan; magenta, Tai-Kadai.”

See also:

Two more studies on the genetic history of East Asia: Han Chinese and Thailand

chinese-eurasian-drift

A comprehensive map of genetic variation in the world’s largest ethnic group – Han Chinese, by Charleston et al. (2017).

It is believed – based on uniparental markers from modern and ancient DNA samples and array-based genome-wide data – that Han Chinese originated in the Central Plain region of China during prehistoric times, expanding with agriculture and technology northward and southward, to become the largest Chinese ethnic group.

Abstract:

As are most non-European populations around the globe, the Han Chinese are relatively understudied in population and medical genetics studies. From low-coverage whole-genome sequencing of 11,670 Han Chinese women we present a catalog of 25,057,223 variants, including 548,401 novel variants that are seen at least 10 times in our dataset. Individuals from our study come from 19 out of 22 provinces across China, allowing us to study population structure, genetic ancestry, and local adaptation in Han Chinese. We identify previously unrecognized population structure along the East-West axis of China and report unique signals of admixture across geographical space, such as European influences among the Northwestern provinces of China. Finally, we identified a number of highly differentiated loci, indicative of local adaptation in the Han Chinese. In particular, we detected extreme differentiation among the Han Chinese at MTHFR, ADH7, and FADS loci, suggesting that these loci may not be specifically selected in Tibetan and Inuit populations as previously suggested. On the other hand, we find that Neandertal ancestry does not vary significantly across the provinces, consistent with admixture prior to the dispersal of modern Han Chinese. Furthermore, contrary to a previous report, Neandertal ancestry does not explain a significant amount of heritability in depression. Our findings provide the largest genetic data set so far made available for Han Chinese and provide insights into the history and population structure of the world’s largest ethnic group.

Using Shanghai individuals as representatives, shared drift between Chinese and ancient humans are computed by calculating the outgroup f3 statistics of the form f3(Mbuty;X, Y), with ancient individuals separated into approximately Palaeolithic, Mesolithic, Neolithic , and Chalcolithic-Medieval times. it is found that modern Chinese individuals show greater shared drift with pre-Neolithic hunter-gatherers rather than Neolithic farmers (Featured image from the article).

EDIT (17/7/2017): Davidski at Eurogenes shares an interesting view on this kind of results:

These sorts of estimates always look way off. And I doubt that it’s largely the result of the Silk Road, which linked China to the Near East and Mediterranean rather than to Northern Europe. More likely it reflects gene flow from the Pontic-Caspian steppe in Eastern Europe during the Bronze and Iron ages, via the Afanasievo, Andronovo, and other closely related steppe peoples


New insights from Thailand into the maternal genetic history of Mainland Southeast Asia, by Kutanan et al. (2017)

Abstract:

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 1,234 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 sequences 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 extension and expansion of TK people through MSEA, although there is also some support for an admixture model. 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.