Complex peopling history and expansion events inferred from large-scale modern and ancient Y chromosome sequences.

The origins and movements of early East Asians remain unclear due to limited ancient genomes and Y chromosome data. Here, we report a large-scale Y chromosome resource, including 1045 newly sequenced genomes from previously underrepresented groups, revealing high-resolution phylogenetic patterns in F and N1b lineages. We constructed a time-calibrated phylogeny that traces early paternal roots to diverged C/D/F lineages and indicates Paleolithic migrations from the southern Himalayas. These early movements, together with later Neolithic expansions, shaped the paternal landscape observed today. We find long-lasting bottlenecks in early F lineages and reveal inland and coastal migration routes linking South China and Southeast Asia, followed by rapid diversification during the Neolithic period associated with millet and rice farming. Distinct inland and coastal southward expansions of N1a/b hunting-gathering and farming groups, including those linked to Tibeto-Burman speakers, and demographic shifts among northern coastal populations further shaped genomic diversity. These findings provide insights into how ancient divergence and agriculture-driven expansions influenced East Asian paternal history.