Tianyuan individual represents northern ancestry basal to all East Asians. Hoabinhian hunter-gatherers provide southern ancestry related to Onge Andamanese. Modern East Asians average 40-60% Hoabinhian southern ancestry. Japanese carry 10-20% distinct Jomon ancestry linked to Australasians. Jomon lineage diverged before Tianyuan around 40,000 years ago. Northern Han Chinese have higher Tianyuan-like ancestry than southern populations. Koreans show elevated northern farmer ancestry similar to Japanese. Taiwanese Amis possess extra Basal East Asian ancestry diverging ultra-early. Hoabinhian ancestry transmits Denisovan archaic admixture to East Asians. Ancient genomes reveal no simple single-wave settlement of East Asia. East Asian populations show deep pre-Neolithic structure. Southern East Asians retain more ancient hunter-gatherer DNA than northern ones. Jomon people genetically distant from mainland East Asian farmers.