Through high-precision ancient human genome analysis, the origins of the Jomon and Yayoi peoples, changes in ancestral population sizes, and the fact that Jomon people also consumed starch abundantly have been clarified. Assistant Professor Koji Ishiya at the Sapiens Life Sciences, Evolution and Medicine Research Center, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, in collaboration with Associate Professor Fuzuki Mizuno at Toho University, Lecturer Jun Gojobori and Visiting Professor Li Wang (at the time of research) at the Graduate University for Advanced Studies (SOKENDAI), Senior Researcher Masahiko Kumagai at the National Agriculture and Food Research Organization (NARO), Associate Professor Yasuhiro Taniguchi at Kokugakuin University, and Director Takayuki Matsushita at the Doigahama Site Anthropological Museum, succeeded in constructing and clarifying high-precision Jomon and Yayoi genomes significantly exceeding conventional standards. The findings were published in PNAS.
Ancient human genome analysis involves collecting samples from human bones or teeth and purifying the DNA from it, attaching adapters to fragmented DNA, and then determining the DNA sequence using next-generation sequencing technology. Ancient DNA, however, is often affected by degradation over time, including fragmentation and deamination, as well as contamination from exogenous DNA originating in the surrounding soil. This challenge is particularly pronounced for ancient human remains excavated from sites on Japan's main island of Honshu, where acidic soils and the warm, humid climate accelerate DNA degradation, making it difficult to obtain well-preserved genomes with minimal missing data.
As a result, most ancient human genomes recovered from the Japanese archipelago to date have had a coverage depth of less than 1, meaning that each position in the genome was sequenced fewer than once on average. Coverage depth reflects how many times a given genomic position is read by a DNA sequencer, with higher coverage enabling more accurate estimates of genotypes, gene copy numbers, and other genetic features.
The researchers attempted to reconstruct the genomes of two ancient individuals: IY1, an Initial Jomon-period female who lived approximately 8,300 to 8,200 years ago and was excavated from the Iyai Rock Shelter Site in Naganohara, Gunma Prefecture, and DO, a Middle Yayoi-period male who lived approximately 2,306 to 2,238 years ago and was excavated from the Doigahama Site in Shimonoseki, Yamaguchi Prefecture. They successfully generated high-coverage whole-genome sequences, achieving approximately 67× coverage for IY1 and 46× coverage for DO. Contamination from exogenous DNA was also low, placing the genomes among the highest-quality ancient genome datasets produced worldwide.
Principal component analysis and ancestry clustering showed that IY1 carried ancestry components characteristic of the Jomon people that are uncommon among other East Asian populations. The analyses also confirmed that the Jomon represent a lineage that diverged relatively early from other East Asian populations and contributed genetically to the ancestry of present-day Japanese people. In contrast, DO, a Yayoi individual, was genetically closer than the Jomon to East Asian populations, including modern Japanese, and carried ancestry components commonly found in Northeast Asia.
Estimates of ancestral population size, measured as effective population size, indicated that the ancestral populations of both the Jomon and Yayoi experienced population declines during the Last Glacial Maximum. Thereafter, the ancestral Jomon population showed little evidence of substantial growth, whereas the ancestral Yayoi population underwent a gradual increase in size. This population expansion may have occurred on the Eurasian continent before the ancestors of the Yayoi migrated to the Japanese archipelago.
The high-coverage genomes obtained in this study also enabled the researchers to estimate the copy number of AMY1, the salivary amylase gene associated with starch digestion, in both the Jomon individual IY1 and the Yayoi individual DO. Both individuals were found to carry between nine and ten copies of AMY1, substantially more than reported for Neanderthals (one copy) and European hunter-gatherers (approximately five copies). Numerous plant remains, including walnuts, chestnuts, and acorns, have been recovered from the Iyai Rock Shelter Site where IY1 was excavated. These findings suggest that genetic variation associated with plant resource use may already have existed among Jomon populations before the spread of agriculture, reflecting differences in local subsistence environments.
The constructed high-precision ancient human genomes serve as an important research foundation for clarifying genetic characteristics that were difficult to evaluate with conventional data. Such characteristics include demographic dynamics of ancestral populations, structural polymorphisms including gene copy numbers, and highly polymorphic gene regions, in addition to population roots and phylogenetic relationships.
The high-quality ancient genomes generated in this study provide an important foundation for investigating genetic characteristics that have been difficult to assess using conventional datasets. Beyond clarifying population origins and evolutionary relationships, they make it possible to examine features such as ancestral population dynamics, structural variation including gene copy number differences, and highly polymorphic regions of the genome. Looking ahead, the accumulation of high-quality ancient genomes from different regions and time periods, combined with data from plant and animal remains, stable isotope analyses of diet, and reconstructions of past climates and environments, is expected to provide a more detailed understanding of how population movements, cultural change, and shifts in lifestyle have shaped human genetic diversity.
Ishiya said, "The sequencing data underlying these high-coverage genomes were enormous, amounting to roughly 300 terabytes per individual. As a result, one of our biggest challenges was improving a range of computational methods and developing techniques capable of isolating and analyzing only the DNA data from these massive datasets. At the same time, I believe those technological advances became one of our key contributions to the research."
Mizuno noted, "I participated primarily from the experimental side, but this project involving the two individuals actually began about a decade ago. Initially, we analyzed DNA from teeth and iliac bones. However, during the course of the project, reports emerged showing that DNA is often better preserved in the petrous bone. By analyzing DNA recovered from the petrous bone, we were ultimately able to obtain these results. I believe these findings reflect years of accumulated technical advances in both laboratory work and data analysis finally coming together."
Gojobori said, "We began by compiling all publicly available ancient human genome data from around the world, but determining the analytical framework took considerable time, including deciding which ancient genomes should be included for comparison. Because the conclusions can vary depending on the reference datasets selected, we approached that process with great care."
Journal Information
Publication: PNAS
Title: High-coverage ancient genomes reveal divergent population histories and prehistoric starch-related genetic variation in Japan
DOI: 10.1073/pnas.2606162123
This article has been translated by JST with permission from The Science News Ltd. (https://sci-news.co.jp/). Unauthorized reproduction of the article and photographs is prohibited.