Ancient genomics reveals tripartite origins of Japanese populations

Cooke, Niall P.; Mattiangeli, Valeria; Cassidy, Lara M.; Okazaki, Ken; Stokes, Caroline A.; Onbe, Shin; Hatakeyama, Satoshi; Machida, Katsunosuke; Kasai, Kenji; Tomioka, Naoto; Matsumoto, Akihiko; Ito, Masafumi; Kojima, Yoshitaka; Bradley, Daniel G.; Gakuhari, Takashi; Nakagome, Shigeki

doi:10.1126/sciadv.abh2419

Cited by 35 publications

(68 citation statements)

References 96 publications

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“…5). Kofun individuals, who were excavated from mainland Japan 1,300-1,400 years ago, have similar Jomon ancestry proportion of modern Japanese 13 . First, a pairwise f3 assuming the Yoruba people as an outgroup was used to test whether the allele frequencies of THC Jomon ancestry resembles that of the actual Jomon individuals (Fig.…”

Section: Resultsmentioning

confidence: 99%

Section: Fig 1 Overview Of Our Ami-based Detection Methods Of Jomon-d...mentioning

confidence: 99%

“…Phylogenetic relationships between modern Japanese, the Jomon people and continental East Asians 8,10,11,13 . Modern Japanese genomes contain a mixture of variants that occurred on each ancestral lineage of modern Japanese (Jomon and continental East Asian ancestries including "East Asians" and "Northeast Asians" in Cooke et al, 2021). The Jomon people were highly differentiated from continental East Asians, so modern Japanese genomes have Jomon-lineage specific variants (blue stars in the phylogeny) that are not found in other modern continental East Asians (Chinese, Koreans and so on); AMI is an index to distinguish Jomon-derived variants from other Japanese-specific variants based on the linkage disequilibrium status.…”

Section: Fig 1 Overview Of Our Ami-based Detection Methods Of Jomon-d...mentioning

confidence: 99%

“…5). Kofun individuals, who were excavated from mainland Japan 1,300-1,400 years ago, have similar Jomon ancestry proportion of modern Japanese 13 .…”

Section: Allele Frequencies Estimation By Jomon-derived Haplotypes Re...mentioning

confidence: 99%

“…Finally, (A) and (C) were plotted for each prefecture, while (B) was plotted for each region because data for each prefecture were not available. The estimated allele frequencies in the THC ancestries were compared with those in the 11 Jomon [9][10][11]13 , three Kofun 13 , THC 419 modern Japanese 24 and 103 Han Chinese (CHB from 1000 Genome Project) individuals 19 . In addition to the already genotyped In the pairwise f3(A, B, Yoruba (= YRI in 1000 Genomes Project)) test, we used 32,143…”

Section: Geographical Distribution Of the Jomon Allele Scorementioning

confidence: 99%

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Modern Japanese ancestry-derived variants revealed the formation process of the current Japanese regional gradations

Watanabe

Ohashi

2020

Preprint

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Modern Japanese are considered to derive from a mixture of two major ancestral populations: the indigenous Jomon people and immigrants from continental East Asia. Since most of the existing methods for detecting genetic components from ancestral populations require their genomes, ancestral genomic components in Japanese could not detected so far due to the lack of precisely sequenced ancient Jomon genomes. To overcome the difficulty, we developed a reference-free detection method using a novel summary statistic, the ancestry-marker index (AMI). We applied the AMI to modern Japanese samples from the 1000 Genomes Project and identified 208,648 ancestry-marker SNPs that were likely derived from the Jomon people (Jomon-derived SNPs). Comparing the Jomon allele score detected in this study with modern Japanese and two ancient Jomon individuals showed that the Jomon derived SNPs were detected with high accuracy by the AMI in real data, and that the Jomon derived SNPs were detected by several tens of times from a single Jomon individual by the AMI. The analysis of Jomon-derived SNPs in 10,842 modern Japanese individuals recruited from all the 47 prefectures of Japan showed that the genetic differences among the prefectures were mainly caused by differences in the admixture proportion of the Jomon people, due to the difference of population size of immigrants in the final Jomon to the Yayoi period. We also confirmed the presence of the Jomon alleles around phenotype associated SNPs characteristic of East Asians to clarify whether these phenotypes of modern Japanese were derived from the Jomon people.

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Section: Resultsmentioning

confidence: 99%

Section: Fig 1 Overview Of Our Ami-based Detection Methods Of Jomon-d...mentioning

confidence: 99%

Section: Fig 1 Overview Of Our Ami-based Detection Methods Of Jomon-d...mentioning

confidence: 99%

“…5). Kofun individuals, who were excavated from mainland Japan 1,300-1,400 years ago, have similar Jomon ancestry proportion of modern Japanese 13 .…”

Section: Allele Frequencies Estimation By Jomon-derived Haplotypes Re...mentioning

confidence: 99%

Section: Geographical Distribution Of the Jomon Allele Scorementioning

confidence: 99%

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Modern Japanese ancestry-derived variants revealed the formation process of the current Japanese regional gradations

Watanabe

Ohashi

2020

Preprint

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Genomic detection of a secondary family burial in a single jar coffin in early Medieval Korea

Lee

Jeon

Kang

et al. 2022

American Journal of Biological Anthropology

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Objectives: Family relationship is a key to understand the structure of past societies but its archeological reconstruction mostly stays circumstantial. Archaeogenetic information, especially genome-wide data, provide an objective approach to accurately reconstruct the familial relationship of ancient individuals, thus allowing a robust test of an archaeology-driven hypothesis of kinship. In this study, we applied this approach to disentangle the genetic relationship of early Medieval individuals from Korea, who were secondarily co-buried in a single jar coffin. Materials and Methods:We obtained genome-wide data of six early Medieval Korean individuals from a jar coffin. We inferred the genetic relatedness between these individuals and characterized their genetic profiles using well-established population genetics methods.Results: Congruent with the unusual pattern of multiple individuals in a single jar coffin, genome-wide analysis of these individuals shows that they form an extended family, including a couple, their two children and both paternal and maternal relatives. We show that these early Medieval Koreans have a genetic profile similar to present-day Koreans.Discussion: We show that an unusual case of the secondary multiple burial in a single jar coffin reflects family relationship among the co-buried individuals. We find both paternal and maternal relatives co-buried with the nuclear family, which may suggest a family structure with limited gender bias. We find the genetic profile of early Medieval Koreans similar to that of present-day Koreans, showing that the genetic root of the present-day Koreans goes back at least 1500 years in the Korean peninsula.

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The Discovery of Mountains: From Enigma to Exploitation

García-Ruiz,

Arnáez,

Lasanta

et al. 2024

Earth and Environmental Sciences Library

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Ancient genomics reveals tripartite origins of Japanese populations

Abstract: Ancient genomes uncover multiple migratory pulses to Japan with the spread of wet rice farming and the rise of the state.

Cited by 35 publications

References 96 publications

Modern Japanese ancestry-derived variants revealed the formation process of the current Japanese regional gradations

Modern Japanese ancestry-derived variants revealed the formation process of the current Japanese regional gradations

Genomic detection of a secondary family burial in a single jar coffin in early Medieval Korea

The Discovery of Mountains: From Enigma to Exploitation

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