After the late-Paleolithic period in the Japanese archipelago, the Jomon culture starts around 15,000 years ago, and the Yayoi culture took place of it around 3,000 years ago. The former is a culture by the indigenous people who have hunting-gathering life style, whereas the latter is a culture of large-scale rice cultivation that would be brought by immigrants (and their descendants) from the East Asian continent. Many of previous studies based on skeletal remains have described that the Jomon people have been morphologically homogeneous for more than 10,000 years. The dual structure model for peopling history of modern Japanese has been proposed; according to the model, the Jomon and the immigrants have gradually admixed since the Yayoi period, and the modern main-island Japanese have been formed at last. Our recent study based on computer simulation using genome-wide SNP data from modern Chinese and Hokkaido Ainu, however, has estimated that the admixture between the Jomon and the immigrants occurred 5~6,000 years ago that is twice older than the estimates based on the archaeological evidences, suggesting a possibility of gene flow from the East Asian continent before the Yayoi culture starts.
To resolve the discrepancy, we organized a research team of the Jomon genome sequencing, including physical anthropologists, physiological anthropologists, archaeologists, and researchers of statistics, genomics, and population genetics. We conducted prescreening for the Jomon specimens excavated from various sites by using the next generation sequencer (NGS). The states of preservation of DNAs from the specimens in the Japanese archipelago were commonly even worse than those in Europe and America, because of acid soils, and warm and high humid climate. But, a couple of specimens showed more than 1.0% mapping ratio. Here we present the results of preliminary analyses, and discuss about feasibility of the deep sequencing of Jomon.