Abstract
Advances in ancient DNA research have transformed our understanding of human evolution, admixture-driven adaptation, and genetic underpinnings of traits. However, the evolutionary dynamics of Paleolithic and Neolithic East Asian remain fragmented. This review synthesizes 160,000 years of population interactions, highlighting three waves of archaic introgression and extensive population admixtures. We examine how ancestral lineages and agricultural innovations shaped East Asian populations, while migrations and admixture events linked to shifting subsistence strategies contributed to genomic and phenotypic diversity. Adaptive signatures from ancient genomes further elucidate the underpinnings of high-altitude adaptation, pigmentation, and morphological traits, offering new insights into human evolutionary biology. GRAPHICAL ABSTRACT: [Image: see text] SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-025-03859-1.