A Matrilineal Genetic Perspective of Hanging Coffin Custom in Southern China and Northern Thailand

Malaria resistance-related biological adaptation and complex evolutionary footprints inferred from one integrative Tai-Kadai-related genomic resource

Pathogen‒host adaptative interactions and complex population demographical processes, including admixture, drift, and Darwen selection, have considerably shaped the Neolithic-to-Modern Western Eurasian population structure and genetic susceptibility to modern human diseases. However, the genetic footprints of evolutionary events in East Asia remain unknown due to the underrepresentation of genomic diversity and the design of large-scale population studies. We reported one aggregated database of genome-wide SNP variations from 796 Tai-Kadai (TK) genomes, including that of Bouyei first reported here, to explore the genetic history, population structure, and biological adaptative features of TK people from southern China and Southeast Asia. We found geography-related population substructure among TK people using the state-of-the-art population genetic structure reconstruction techniques based on the allele frequency spectrum and haplotype-resolved phased fragments. We found that the northern TK people from Guizhou harbored one TK-dominant ancestry maximized in the Bouyei people, and the southern TK people from Thailand were more influenced by Southeast Asians and indigenous people. We reconstructed fitted admixture models and demographic graphs, which showed that TK people received gene flow from ancient southern rice farmer-related lineages related to the Hmong-Mien and Austroasiatic people and from northern millet farmers associated with the Sino-Tibetan people. Biological adaptation focused on our identified unique TK lineages related to Bouyei, which showed many adaptive signatures conferring Malaria resistance and low-rate lipid metabolism. Further gene enrichment, the allele frequency distribution of derived alleles, and their correlation with the incidence of Malaria further confirmed that CR1 played an essential role in the resistance of Malaria in the ancient "Baiyue" tribes.

Genomic portrait and relatedness patterns of the Iron Age Log Coffin culture in northwestern Thailand

The Iron Age of highland Pang Mapha, northwestern Thailand, is characterised by a mortuary practice known as Log Coffin culture. Dating between 2300 and 1000 years ago, large coffins carved from individual teak trees have been discovered in over 40 caves and rock shelters. While previous studies focussed on the cultural development of the Log Coffin-associated sites, the origins of the practice, connections with other wooden coffin-using groups in Southeast Asia, and social structure within the region remain understudied. Here, we present genome-wide data from 33 individuals from five Log Coffin culture sites to study genetic ancestry profiles and genetic interconnectedness. The Log Coffin-associated genomes can be modelled as an admixture between Hòabìnhian hunter-gatherer-, Yangtze River farmer-, and Yellow River farmer-related ancestry. This indicates different influence spheres from Bronze and Iron Age individuals from northeastern Thailand as reflected by cultural practices. Our analyses also identify close genetic relationships within the sites and more distant connections between sites in the same and different river valleys. In combination with high mitochondrial haplogroup diversity and genome-wide homogeneity, the Log Coffin-associated groups from northwestern Thailand seem to have been a large, well-connected community, where genetic relatedness played a significant role in the mortuary ritual.

Phylogenetic evidence reveals early Kra-Dai divergence and dispersal in the late Holocene

Studying language evolution brings a crucial perspective to bear on questions of human prehistory. As the most linguistically diverse region on earth, East and Southeast Asia have witnessed extensive sociocultural and ethnic contacts among different language communities. Especially, the Kra-Dai language family exhibits tremendous socio-cultural importance in these regions. Due to limited historical accounts, however, there are several controversies on their linguistic relatedness, ambiguities regarding the divergence time, and uncertainties on the dispersal patterns. To address these issues, here we apply Bayesian phylogenetic methods to analyze the largest lexical dataset containing 646 cognate sets compiled for 100 Kra-Dai languages. Our dated phylogenetic tree showed their initial divergence occurring approximately 4000 years BP. Phylogeographic results supported the early Kra-Dai language dispersal from the Guangxi-Guangdong area of South China towards Mainland Southeast Asia. Coupled with genetic, archaeological, paleoecologic, and paleoclimatic data, we demonstrated that the Kra-Dai language diversification could have coincided with their demic diffusion and agricultural spread shaped by the global climate change in the late Holocene. The interdisciplinary alignments shed light on reconstructing the prehistory of Kra-Dai languages and provide an indispensable piece of the puzzle for further studying prehistoric human activities in East and Southeast Asia.

The first maternal genetic study of hunter-gatherers from Vietnam

The current limitation of ancient DNA data from Vietnam led to the controversy surrounding the prehistory of people in this region. The combination of high heat and humidity damaged ancient bones that challenged the study of human evolution, especially when using DNA as study materials. So far, only 4 k years of history have been recorded despite the 65 k years of history of anatomically modern human occupations in Vietnam. Here we report, to our knowledge, the oldest mitogenomes of two hunter-gatherers from Vietnam. We extracted DNA from the femurs of two individuals aged 6.2 k cal BP from the Con Co Ngua (CCN) site in Thanh Hoa, Vietnam. This archeological site is the largest cemetery of the hunter-gatherer population in Southeast Asia (SEA) that was discovered, but their genetics have not been explored until the present. We indicated that the CCN haplotype belongs to a rare haplogroup that was not detected in any present-day Vietnamese individuals. Further matrilineal analysis on CCN mitogenomes showed a close relationship with ancient farmers and present-day populations in SEA. The mitogenomes of hunter-gatherers from Vietnam debate the "two layers" model of peopling history in SEA and provide an alternative solution for studying challenging ancient human samples from Vietnam.

Extensive genetic admixture between Tai-Kadai-speaking people and their neighbours in the northeastern region of the Yungui Plateau inferred from genome-wide variations

BACKGROUND

Yungui Plateau in Southwest China is characterized by multi-language and multi-ethnic communities and is one of the regions with the wealthiest ethnolinguistic, cultural and genetic diversity in East Asia. There are numerous Tai-Kadai (TK)-speaking populations, but their detailed evolutionary history and biological adaptations are still unclear.

RESULTS

Here, we genotyped genome-wide SNP data of 77 unrelated TK-speaking Zhuang and Dong individuals from the Yungui Plateau and explored their detailed admixture history and adaptive features using clustering patterns, allele frequency differentiation and sharing haplotype patterns. TK-speaking Zhuang and Dong people in Guizhou are closely related to geographically close TK and Hmong-Mien (HM)-speaking populations. Besides, we identified that Guizhou TK-speaking people have a close genetic relationship with Austronesian (AN)-speaking Atayal and Paiwan people, which is supported by the common origin of the ancient Baiyue tribe. We additionally found subtle genetic differences among the newly studied TK people and previously reported Dais via the fine-scale genetic substructure analysis based on the shared haplotype chunks. Finally, we identified specific selection candidate signatures associated with several essential human immune systems and neurological disorders, which could provide evolutionary evidence for the allele frequency distribution pattern of genetic risk loci.

CONCLUSIONS

Our comprehensive genetic characterization of TK people suggested the strong genetic affinity within TK groups and extensive gene flow with geographically close HM and Han people. We also provided genetic evidence that supported the common origin hypothesis of TK and AN people. The best-fitted admixture models further suggested that ancestral sources from northern millet farmers and southern inland and coastal people contributed to the formation of the gene pool of the Zhuang and Dong people.

Fine-Scale Population Admixture Landscape of Tai–Kadai-Speaking Maonan in Southwest China Inferred From Genome-Wide SNP Data

Guizhou Province harbors extensive ethnolinguistic and cultural diversity with Sino-Tibetan-, Hmong–Mien-, and Tai–Kadai-speaking populations. However, previous genetic analyses mainly focused on the genetic admixture history of the former two linguistic groups. The admixture history of Tai–Kadai-speaking populations in Guizhou needed to be characterized further. Thus, we genotyped genome-wide SNP data from 41 Tai–Kadai-speaking Maonan people and made a comprehensive population genetic analysis to explore their genetic origin and admixture history based on the pattern of the sharing alleles and haplotypes. We found a genetic affinity among geographically different Tai–Kadai-speaking populations, especially for Guizhou Maonan people and reference Maonan from Guangxi. Furthermore, formal tests based on the f₃/f₄-statistics further identified an adjacent connection between Maonan and geographically adjacent Hmong–Mien and Sino-Tibetan people, which was consistent with their historically documented shared material culture (Zhang et al., iScience, 2020, 23, 101032). Fitted qpAdm-based two-way admixture models with ancestral sources from northern and southern East Asians demonstrated that Maonan people were an admixed population with primary ancestry related to Guangxi historical people and a minor proportion of ancestry from Northeast Asians, consistent with their linguistically supported southern China origin. Here, we presented the landscape of genetic structure and diversity of Maonan people and a simple demographic model for their evolutionary process. Further whole-genome-sequence–based projects can be presented with more detailed information about the population history and adaptative history of the Guizhou Maonan people.