Mitochondrial DNA analysis of the human skeletons excavated from the Shomyoji shell midden site, Kanagawa, Japan

Abstract

Recent studies have revealed that the Jomon people are considerably genetically different from any other population, including modern-day Japanese. This gives rise to an intriguing question: when after the Jomon era did this drastic change of genetic features occur? The Shomyoji shell midden site in Kanagawa, Japan can provide some clues to address this question. The skeletons buried at this site include some that are more recent than the Jomon-era skeletons with whom they are almost contiguously buried. We tested the genetic continuity of the Shomyoji shell midden people by analyzing mitochondrial DNA (mtDNA). Our results show that the mtDNA haplogroups of the Kofun and Heian skeletons vastly differ from those of the Jomon skeletons. This finding implies that the genetic conversion of the Japanese people may have occurred during or before the Kofun era, at least at the Shomyoji site. To confirm this hypothesis, nuclear genome analysis of the Shomyoji people is considered promising.

Crop cultivation of Middle Yayoi culture communities (fourth century bce–first century ce) in the Kanto region, eastern Japan, inferred from a radiocarbon-dated archaeobotanical record

“…During the Yayoi period (tenth/fourth century bce-250 ce) Japan underwent some of the most fundamental cultural changes in its prehistory. Despite long-term debates about its drivers, it seems most likely that these changes were mainly associated with immigration from the East Asian mainland (Shinoda 2004;Lee and Hasegawa 2011;Steinhaus and Kaner 2016;Takahashi et al 2019). The substantial population growth and increasing social inequality during the Yayoi period are linked with a fully agricultural lifestyle, which, except in Okinawa and Hokkaido, spread over the Japanese archipelago marking the termination of the preceding Jomon period (Ishikawa 2014).…”

Heian-period human skeletal remains from the Shomyoji shell midden in Yokohama City, Kanagawa Prefecture

“…These results suggest that SK1 was influenced by the Yayoi or subsequent immigrant populations. Furthermore, this scenario is supported by a recent study on the mtDNA of Shomyoji population, showing that SK1's haplogroup is vastly differ- ent from those of the Jomon skeletons (Takahashi et al, 2019).…”

“…An excavation conducted in 2017 yielded more than 26 human skeletal remains from various periods. The breakdown of these materials is as follows: 22 from the late Jomon, two from the final Jomon (1300-500 BC), one from the Kofun (third to seventh centuries AD), and one from the Heian (AD 794-1185) (Takahashi et al, 2019).…”

Peopling the Americas: Not “Out of Japan”

“…Haplogroups M7a, G1b, and D4h2 have also been identified (Adachi, Shinoda, and Izuho 2015, table 28.3;Kanzawa-Kiriyama et al 2013, appendix 1). Limited sampling of a small number of human remains from Honshu further expands this list to D4b2, as well as additional haplotypes of N9b and M7a (Adachi et al 2013;Kanzawa-Kiriyama et al 2013;Mizuno et al 2020;Takahashi et al 2019). Of particular interest for this discussion is macro-haplogroup D4, which is widely distributed and diversified across Asia.…”