The study analyzes the complete Y-chromosome sequences of 345 Japanese men to reconstruct the population history of Japan during the Jomon period (14,500-2,300 years ago). Clade 1, a unique Y-DNA lineage (haplogroup D1b) that is present only in Japanese men and absent in mainland Asians, has been identified. It accounts for 35.4% of modern Japanese from the main island, and simulations indicate that about 70% of Jomon men belonged to this group. Bayesian Skyline Plot plots have shown an increase in the number of clade 1 men since the beginning of the Jomon period, followed by a significant population decline around 3,200 years ago - coinciding with a cooling of the climate and lowering of sea levels. This may have caused food shortages in hunter-gatherer Jomon communities. After the beginning of the Yayoi period (2,300 years ago), when newcomers from the mainland introduced rice cultivation, the population began to recover. Contrastingly, no such demographic collapse was observed in the descendants of Yayoi immigrants (clade 3, haplogroup O2). The study confirms the "dual structure" model, which assumes a mix of indigenous Yomon and Yayoi immigrants as the source of the modern Japanese population. The results provide genetic evidence of a demographic crisis in the late Yomon period and its recovery through the transition to agriculture. In addition, analysis of mitochondrial DNA (inherited in the female line) did not reveal a distinct clade, which may suggest a different demographic history for women.