Hot air balloons drift over ancient temples at sunrise in Bagan, Myanmar. (Photo: CFP)
A decade-long international research project has revealed how geography, not language, shaped the genetic make-up of people across mainland Southeast Asia (MSEA).
Published in Nature on May 14, the study was led by the Kunming Institute of Zoology (KIZ) under the Chinese Academy of Sciences, with contributions from 34 research teams across six Southeast Asian countries, including Thailand and Cambodia.
It is the most comprehensive genomic study of the region to date—and the first to systematically map the genetic structure, history, and environmental adaptation of MSEA populations.
The region, spanning modern-day Myanmar, Thailand, Vietnam, Laos, Cambodia, and peninsular Malaysia, has long been a cultural and linguistic crossroads. However, in global genetic research, it has remained largely overlooked. Of more than 670,000 full human genome samples sequenced worldwide, only 1.57 percent are from Southeast Asia.
To help close this gap, researchers sequenced the genomes of 3,023 individuals from 30 communities across six countries and five major language families. The resulting database, known as SEA3K, includes over 80 million short DNA variants, more than 20 million of which are new to science in the context of Southeast Asia, along with nearly 100,000 structural mutations.
They found that the strongest driver of genetic difference was geography, not language. Populations tended to cluster genetically according to where they lived, rather than which language family they belonged to. This suggests that physical barriers like mountains, rivers, and jungles played a much larger role in shaping genetic diversity than cultural or linguistic shifts.
"Language can be shaped by many complex forces like migration and assimilation, but our genomes often tell a much older and more stable story," said Su Bing, a lead researcher from the KIZ.
The study also identified four main ancestral lineages that contributed to modern Southeast Asians. One was an ancient genetic signature unique to Southeast Asia's earliest inhabitants, still found today among Indigenous communities in Cambodia and the Andaman Islands. Another came from early farmers migrating southward from southern China during the Neolithic period.
A third had links to later waves of movement from southwestern China. The last component was a more widely dispersed, ancient lineage shared with populations in Bengal and across the Indo-China Peninsula.
These findings confirm that Southeast Asia played a central role in early human migration across the continent. The region, including parts of southwestern China, may have been one of the first areas modern humans reached when entering East Asia, Su said.
While farming populations brought new genes and technologies, they had less impact on the Indigenous groups, whose unique genetic traits remain relatively preserved. Past research had already suggested that prehistoric groups from southern China migrated into Southeast Asia thousands of years ago, reshaping the region's genetic landscape long before modern immigration.
The study also sheds light on how these populations adapted to the tropics over tens of thousands of years. Using a genetic scan for signs of natural selection, researchers found 44 regions in the genome that appear to have helped people cope with the region's intense heat, humidity, and dense rainforests.
Among the genes under strong selection were those linked to skin pigmentation (to block UV radiation), resistance to insect bites, and hair texture (with curly hair aiding heat dissipation).
The study also found that while Southeast Asians and African rainforest dwellers both adapted to similar environments, the genetic solutions were very different—evidence of distinct evolutionary paths to the same challenges.
"This kind of dataset is incredibly valuable," said Fu Qiaomei, a researcher at the Institute of Vertebrate Paleontology and Paleoanthropology under the Chinese Academy of Sciences in Beijing, who was not involved in the study. She noted that not only does the research provide a much clearer picture of Southeast Asian populations, but it also helps us understand the range of ways humans have adapted to their environments.
Building on this work, the team has already launched a second phase of the project—SEA10K—which aims to sequence 10,000 high-quality genomes from across the entire Southeast Asian region. The goal is to develop the most detailed genomic map of the area to date.
As researchers dig deeper into the DNA of the region's diverse populations, they hope to answer some of the most fundamental questions about who we are—and where we came from.
Reporter | Liu Xiaodi
Editor | Yuan Zixiang, James, Shen He
