Paleogenomics retraces the ancient population history of Southwestern East Asia for the past 12 000 years.

Southwestern East Asia, a key intersection linking southern East Asia, Southeast Asia, and the Tibetan Plateau, is a crucial area for the study of early human migrations. However, ancient DNA studies in the eastern part of the region, particularly in Guizhou, are still lacking. We present the first genomic study of Guizhou populations from a time period spanning 12 000 years, including five Guizhou individuals older than 10 000 years. Combined with published Guangxi and Yunnan samples, we reveal a complex genetic history of human populations in southwestern East Asia from the Paleolithic to the Early Neolithic periods. Paleolithic populations were marked by heterogeneous distribution patterns of the recently described basal East Asian Xingyi_EN ancestry admixed with ancestry present in northern East Asia. By the Bronze Age, this enigmatic basal ancestry was no longer detectable in the region. Beginning 1200 years ago, genetic interactions between Guizhou and Guangxi populations intensified following language-specific patterns. Overall, our results clarify the complex population dynamics of southwestern East Asia over the past 12 000 years.