A partial nuclear genome of the Jomons who lived 3000 years ago in Fukushima, Japan

Abstract

The Jomon period of the Japanese Archipelago, characterized by cord-marked ‘jomon' potteries, has yielded abundant human skeletal remains. However, the genetic origins of the Jomon people and their relationships with modern populations have not been clarified. We determined a total of 115 million base pair nuclear genome sequences from two Jomon individuals (male and female each) from the Sanganji Shell Mound (dated 3000 years before present) with the Jomon-characteristic mitochondrial DNA haplogroup N9b, and compared these nuclear genome sequences with those of worldwide populations. We found that the Jomon population lineage is best considered to have diverged before diversification of present-day East Eurasian populations, with no evidence of gene flow events between the Jomon and other continental populations. This suggests that the Sanganji Jomon people descended from an early phase of population dispersals in East Asia. We also estimated that the modern mainland Japanese inherited <20% of Jomon peoples' genomes. Our findings, based on the first analysis of Jomon nuclear genome sequence data, firmly demonstrate that the modern mainland Japanese resulted from genetic admixture of the indigenous Jomon people and later migrants.

Jomon genome sheds light on East Asian population history

“…We found that IK002 clusters between present-day Southeast and East Asians and the Upper-Paleolithic human remain (40 kya) from Tiányuán Cave [28,33] ( Fig.1A ). Second, when using a smaller number of SNPs (41,264 SNPs) including the present-day Ainu [34] from Hokkaido ( Fig.S1 ), IK002 clusters with the Hokkaido Ainu ( Fig.S4 ), supporting previous findings that they are direct descendants of the Jomon people [14,[34][35][36][37][38][39][40][41] . Thus, the PCA plot showed that IK002 is slightly different from present-day people in East Eurasia and Japan except for the Hokkaido Ainu.…”

“…A critical challenge for ancient genome analysis in the Japanese archipelago is the inherent nature of warm and humid climate conditions, and the soils indicating strong acidity because of the volcanic islands, which generally result in poor DNA preservation [12,13] . A partial genome of a 3,000-years old Jomon individual from the east-north part of the main-island (Honshu) Japan was reported, but with very limited coverage (~ 0.03-fold) due to the poor preservation [14] . To identify the origin of the Jomon people, we sequenced a 1.85-fold genomic coverage of a 2,500-years old Jomon individual (IK002) excavated from the central part of the Japanese archipelago [15] .…”

Regional variations in the Jomon population revisited on craniofacial morphology

“…A new nuclear genomic sequence of a Sanganji Jomon (Tohoku region) specimen indicated that the Jomon people were derived from an ancestral East Eurasian population prior to the currently recognizable population diversification (Kanzawa-Kiriyama et al, 2016), as previously mentioned from an osteological point of view (Yamaguchi, 1992). Determining the geographic origins of the candidate Jomon ancestral populations is still difficult; thus, we should expand the plausible target to more ancient Pleistocene fossils as previously suggested (Yamaguchi, 1992;Mizoguchi, 2011) and attempt to recover more genetic data on relevant ancient populations.…”

Initial Movements of Modern Humans in East Eurasia

“…We have therefore proceeded to determine nuclear DNA sequences that are much larger than mtDNA. The results (Kanzawa-Kiriyama et al 2017) clearly indicate that the present-day Japanese have inherited the DNA of Jomon people, as best represented by the Ainu who are direct descendants of the Jomon. This confirms Hanihara's (1991) by ANU Press, The Australian National University, Canberra, Australia.…”