Ancient genomes from the initial Jomon period: new insights into the genetic history of the Japanese archipelago

Abstract

Starting 16000 years ago, the Neolithic lifestyle known as the Jomon culture spread across the Japanese archipelago. Although extensively studied by archaeology and physical anthropology, little is known about the genetic characteristics of the Jomon people. Here, we report the entire mitogenome and partial nuclear genome of skeletal remains from the initial Jomon period that were excavated from the Higashimyo shell midden site at Saga City, Kyushu Island, Japan. This is the first genome analysis of the initial Jomon people of Kyushu Island. These results provide important data for understanding the temporal transition and regional differences of the Jomon people. The mitochondrial DNA and Y-chromosome haplogroups were similar to those found in the previously reported later Jomon people. Moreover, comparison of three nuclear genomes from the initial to final Jomon periods indicated genetic continuity throughout the Jomon period within the Japanese archipelago with no significant evidence of admixture. This indicates that the genetic differentiation found among the Jomon people was promoted by the progression of regionalization throughout the Jomon period. Further accumulation of high-quality Jomon genome data spanning a wide range of regions and ages will clarify both intimate regional and temporal differences of the Jomon people and details of their admixture history with rice farmers, as suggested by Jomon mitochondrial genome data. The results obtained from this study provide important information for further analysis.

A genetic history of migration, diversification, and admixture in Asia

“…This finding broadly supports a core tenet of the dual structure hypothesis for the population history of Japan, wherein migrants from mainland Asia, likely through the Korean peninsula, moved to the Japanese archipelago starting 3,000 years ago, and mixed with indigenous Jōmon populations [86,95]. Adachi et al also estimated that present-day Korean and Ulchi populations in northeast Asia show 5%-8% Jōmon ancestry [64]. Furthermore, in f4-statistics, Jōmon individuals show connections to present-day Austronesians and 8,000-7,000-year-old individuals from coastal southern East Asia and Siberia [85,86].…”

“…These ancient individuals were associated with the Jōmon period of Japan, the first cultural period found in the archaeological record dating from 16,000 to 2,800 years ago. They were originally from the northern reaches of Hokkaido [83], the central and northern regions of Honshu [63,81,84,85], and the southern island of Kyushu [64]. These Jōmon individuals consistently cluster together in a PCA and show high genetic similarity to each other distinct from that found in other Asian populations; their associated ancestry is denoted here as Jōmon ancestry (Box 2, Figure 2).…”

“…In the Japanese archipelago, 7,000-3,000-year-old individuals sampled to date associated with the Jōmon culture are all closely related to each other and are associated with Jōmon ancestry. Using Treemix and f4-ratio analyses (Box 1), Adachi et al [64] found that present-day Japanese populations had 10% Jōmon ancestry. This finding broadly supports a core tenet of the dual structure hypothesis for the population history of Japan, wherein migrants from mainland Asia, likely through the Korean peninsula, moved to the Japanese archipelago starting 3,000 years ago, and mixed with indigenous Jōmon populations [86,95].…”

Preface to the special issue on the Yaponesia Genome Project

“…,Saitou and Jinam (2017), andJinam et al (2021a) is compatible with these datasets Adachi et al (2021). reported the first Jomon genome data from the Higashimyo shell midden site, Kyushu, dated c. 8000 years ago.…”

“…reported the first Jomon genome data from the Higashimyo shell midden site, Kyushu, dated c. 8000 years ago. Their principal-components analysis shows that the genome of Hokkaido Jomon people reported byKanzawa-Kiriyama et al (2019) and that of Kyushu Jomon reported byAdachi et al (2021) are very similar, suggesting striking homogeneity of the Jomon people over a long time.…”