Ancient DNA helps researchers elucidate the structure of a prehistoric Southeast Asian community

Deciduous and evergreen forests dominate the limestone karst formations of the northwestern highlands of Thailand. A large number of caves and rock shelters dot the mountains.

In more than 40 caves in Mae Hong Son province, large wooden coffins mounted on stilts can be found, dating from between 2,300 and 1,000 years ago. During the Iron Age period, each of these coffins measuring up to several meters long was made from a single teak tree and features exquisite carvings of geometric, animal or human shapes on the handles from both ends.

This archaeological assemblage has been studied for more than two decades by members of the Prehistoric Population and Cultural Dynamics of the Pang Mapha Highlands project, led by Professor Rasmi Shoocongdej, Department of Archeology, Faculty of Archeology, University of Silpakorn.

“Our research examines the relationship between humans and their environment in the seasonal tropics. A crucial aspect is the exploration of the social structure of these prehistoric communities, as well as the explanation of their connections with other pre-Neolithic groups, neolithic and post-Neolithic in this region,” says Shoocongdej, an archaeologist and lead author of the study.

To understand the genetic profile of Log Coffin-associated communities and the connections between individuals buried in different caves, an interdisciplinary team of German and Thai researchers analyzed the DNA of 33 ancient individuals from five Log Coffin sites. Genomes recovered from ancient individuals enable the first detailed study of the structure of a prehistoric Southeast Asian community. The article is published in the journal Natural communications.

“This project illustrates how ancient DNA can contribute to our understanding of past communities, their daily lives and their interregional connections,” says first author Selina Carlhoff, a researcher in the Department of Archaeogenetics at the Max Planck Institute for Research. ‘evolution. Anthropology.

Complex genetic landscape in post-Neolithic mainland Southeast Asia

DNA preservation conditions in tropical regions are difficult and limit genetic studies of ancient Southeast Asian populations. Most studies were limited to single individuals or small groups representing a country and time period, and identified only general patterns, such as the genetic admixture of farmers in the Yangtze River valley in southern China. China, with the local gene pool associated with Hòabìnhian hunter-gatherers during the pre. -Neolithic.

The present study identifies two distinct farmer-associated ancestries in individuals associated with Log Coffin: one linked to the Yangtze River Valley and another to the Yellow River Valley of China.

While previously published individuals from Myanmar, Laos, and Vietnam also carry ancestry linked to the Yellow River, it was absent in Bronze and Iron Age individuals from Ban Chiang, northeastern Thailand . These genetic differences reflect cultural differences between the two regions, such as mortuary practices and diet, and point to distinct spheres of influence and links to distinct initial migration routes during the Neolithic period.

“Our results contribute to the emerging picture of a complex genetic landscape in post-Neolithic mainland Southeast Asia; however, this study provides positive genetic results from samples collected from highland limestone caves from northwest Thailand. Future studies on outdoor samples “Archaeological sites in the lowlands look promising. If possible, they can provide additional information about the genetic history of mainland Southeast Asia,” says Wibhu Kutanan, a scientist at Naresuan University, Thailand, involved in designing the study.

Detailed analyzes of uniparental markers, which may reveal the sex-specific demographic histories of Log Coffin-associated groups, will be provided in a future study. Further archaeogenetic studies in collaboration with local researchers, as well as new modeling and dating techniques for mixtures, will better inform developing models and allow direct connections to archaeological discoveries and hypotheses.

First community-level analysis in Southeast Asian archeology

On a local scale, the study provided the first community-based analysis of Southeast Asian archaeology. To study relationships between individuals, the authors used identical genetic regions in two individuals, because they were inherited from a common ancestor.

The analysis of so-called IBD (identical by descent) blocks helps trace complex biological relatedness patterns within a site and between regions – and has until now not been applied in archaeogenetic studies of the South East Asia.

The study identified close genetic relatives buried in the same cave system, such as parents and children or grandparents and grandchildren. This group of closely related individuals was more distantly connected to all other individuals buried at the site.

Although this suggests selection of burial site with consideration of genetic relatedness, the more distant genetic relationships between Log Coffin sites, a low level of inbreeding, as well as high mitochondrial diversity and low diversity at the genome scale suggest that the groups associated with Log Coffin were rather large and consistently connected to each other across different river valleys.

“This result is very significant, since wooden coffins were also used in other archaeological cultures throughout Southeast Asia. Comparing kinship patterns and cross-regional genetic connections would be a fascinating future collaborative project that could potentially explain cultural dynamics and population interactions within Southeast Asia and other regions,” says Shoocongdej.