Population dynamics in the Japanese Archipelago since the Pleistocene revealed by the complete mitochondrial genome sequences

Genetic analysis of a Yayoi individual from the Doigahama site provides insights into the origins of immigrants to the Japanese Archipelago

Mainland Japanese have been recognized as having dual ancestry, originating from indigenous Jomon people and immigrants from continental East Eurasia. Although migration from the continent to the Japanese Archipelago continued from the Yayoi to the Kofun period, our understanding of these immigrants, particularly their origins, remains insufficient due to the lack of high-quality genome samples from the Yayoi period, complicating predictions about the admixture process. To address this, we sequenced the whole nuclear genome of a Yayoi individual from the Doigahama site in Yamaguchi prefecture, Japan. A comprehensive population genetic analysis of the Doigahama Yayoi individual, along with ancient and modern populations in East Asia and Northeastern Eurasia, revealed that the Doigahama Yayoi individual, similar to Kofun individuals and modern Mainland Japanese, had three distinct genetic ancestries: Jomon-related, East Asian-related, and Northeastern Siberian-related. Among non-Japanese populations, the Korean population, possessing both East Asian-related and Northeastern Siberian-related ancestries, exhibited the highest degree of genetic similarity to the Doigahama Yayoi individual. The analysis of admixture modeling for Yayoi individuals, Kofun individuals, and modern Japanese respectively supported a two-way admixture model assuming Jomon-related and Korean-related ancestries. These results suggest that between the Yayoi and Kofun periods, the majority of immigrants to the Japanese Archipelago originated primarily from the Korean Peninsula.

Genetic legacy of ancient hunter-gatherer Jomon in Japanese populations

The tripartite ancestral structure is a recently proposed model for the genetic origin of modern Japanese, comprising indigenous Jomon hunter-gatherers and two additional continental ancestors from Northeast Asia and East Asia. To investigate the impact of the tripartite structure on genetic and phenotypic variation today, we conducted biobank-scale analyses by merging Biobank Japan (BBJ; n = 171,287) with ancient Japanese and Eurasian genomes (n = 22). We demonstrate the applicability of the tripartite model to Japanese populations throughout the archipelago, with an extremely strong correlation between Jomon ancestry and genomic variation among individuals. We also find that the genetic legacy of Jomon ancestry underlies an elevated body mass index (BMI). Genome-wide association analysis with rigorous adjustments for geographical and ancestral substructures identifies 132 variants that are informative for predicting individual Jomon ancestry. This prediction model is validated using independent Japanese cohorts (Nagahama cohort, n = 2993; the second cohort of BBJ, n = 72,695). We further confirm the phenotypic association between Jomon ancestry and BMI using East Asian individuals from UK Biobank (n = 2286). Our extensive analysis of ancient and modern genomes, involving over 250,000 participants, provides valuable insights into the genetic legacy of ancient hunter-gatherers in contemporary populations.

High prevalence of m.1555A > G in patients with hearing loss in the Baikal Lake region of Russia as a result of founder effect

Mitochondrial forms account approximately 1-2% of all nonsyndromic cases of hearing loss (HL). One of the most common causative variants of mtDNA is the m.1555A > G variant of the MT-RNR1 gene (OMIM 561000). Currently the detection of the m.1555A > G variant of the MT-RNR1 gene is not included in all research protocols. In this study this variant was screened among 165 patients with HL from the Republic of Buryatia, located in the Baikal Lake region of Russia. In our study, the total contribution of the m.1555A > G variant to the etiology of HL was 12.7% (21/165), while the update global prevalence of this variant is 1.8% (863/47,328). The m.1555A > G variant was notably more prevalent in Buryat (20.2%) than in Russian patients (1.3%). Mitogenome analysis in 14 unrelated Buryat families carrying the m.1555A > G variant revealed a predominant lineage: in 13 families, a cluster affiliated with sub-haplogroup A5b (92.9%) was identified, while one family had the D5a2a1 lineage (7.1%). In a Russian family with the m.1555A > G variant the lineage affiliated with sub-haplogroup F1a1d was found. Considering that more than 90% of Buryat families with the m.1555A > G variant belong to the single maternal lineage cluster we conclude that high prevalence of this variant in patients with HL in the Baikal Lake region can be attributed to a founder effect.

Bioarchaeological study of ancient Teotihuacans based on complete mitochondrial genome sequences and diet isotopes

BACKGROUND

The Teotihuacan civilisation was the largest one in ancient Mesoamerica. The Teotihuacan city was born in the north-eastern Basin of Mexico around the second century BC, reached its peak in the fourth century AD, and had cultural influence throughout Mesoamerica. At its peak, the size of the city reached more than 20 km2, and the total population is estimated to have increased from 100,000 to 200,000. However, knowledge of the genetic background of the Teotihuacan people is still limited.

AIM

We aimed to determine the mitogenome sequences of the Teotihuacan human remains and compare the ancient and present Mesoamericans. In addition, we aimed to identify the food habits of ancient Teotihuacans.

SUBJECTS AND METHODS

We determined the mitogenome sequences of human remains dated to 250-636 cal AD using target enrichment-coupled next generation sequencing. We also performed stable isotope analysis.

RESULTS

We successfully obtained nearly full-length sequences newly unearthed from a civilian dwelling in the Teotihuacan site. Teotihuacan mitochondrial DNA was classified into the haplogroups in present and ancient Mesoamericans. In addition, Teotihuacan individuals had a diet dependent on C4 plants such as maize.

CONCLUSION

Genetic diversity varied among the Teotihuacans.

Starch granules from human teeth: New clues on the Epi-Jomon diet

This study examined starch granules from the dental calculus of specimens from the Epi-Jomon (Zoku-Jomon in Japanese, ca. 350 BCE–350 CE) period in Japan for taxonomic identification of plant food items and the reconstruction of human socioeconomic practices. Dental calculus was extracted from 21 individuals across six Epi-Jomon sites in Hokkaido. Moreover, 12 starch granules and starch clusters were recovered from nine individuals. The morphologies of the extracted starch granules were then classified into five types: elliptical, angular circular, polygonal, pentagonal, and damaged. Morphometric analysis indicated that a small portion of these starch granules may have derived from acorns, nuts, and bulb or tuber plants, with one starch granule supposedly from rice. Although extracted starch granules are poor predictors of food diversity at the individual level, the results can identify potential food sources of the surveyed population. This is the first study to determine how well plant microremains in dental calculus reflect a plant diet in the Epi-Jomon population. The starch granules discovered at the surveyed sites provide essential information about the utilization of plant species and cultural contacts in Hokkaido during this period. This is of great significance in reconstructing the Epi-Jomon subsistence patterns in Hokkaido and exploring cultural interactions between hunting-gathering-fishing and agrarian societies.

Northeastern Asian and Jomon-related genetic structure in the Three Kingdoms period of Gimhae, Korea

The genetic history of prehistoric and protohistoric Korean populations is not well understood because only a small number of ancient genomes are available. Here, we report the first paleogenomic data from the Korean Three Kingdoms period, a crucial point in the cultural and historic formation of Korea. These data comprise eight shotgun-sequenced genomes from ancient Korea (0.7×-6.1× coverage). They were derived from two archeological sites in Gimhae: the Yuha-ri shell mound and the Daesung-dong tumuli, the latter being the most important funerary complex of the Gaya confederacy. All individuals are from between the 4th and 5th century CE and are best modeled as an admixture between a northern China Bronze Age genetic source and a source of Jomon-related ancestry that shares similarities with the present-day genomes from Japan. The observed substructure and proportion of Jomon-related ancestry suggest the presence of two genetic groups within the population and diversity among the Gaya population. We could not correlate the genomic differences between these two groups with either social status or sex. All the ancient individuals' genomic profiles, including phenotypically relevant SNPs associated with hair and eye color, facial morphology, and myopia, imply strong genetic and phenotypic continuity with modern Koreans for the last 1,700 years.