AbstractMainland 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.

摘要大陆日本人被认为具有双重血统，起源于本土绳文人和来自欧亚大陆东部的移民。尽管从弥生时期到科芬时期，从大陆到日本群岛的移民仍在继续，但由于弥生时期缺乏高质量的基因组样本，我们对这些移民，特别是他们的起源的理解仍然不足，这使得对混合过程的预测复杂化。

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.

。对Doigahama弥生个体以及东亚和欧亚大陆东北部的古代和现代种群进行的全面种群遗传分析表明，Doigahama弥生个体与Kofun个体和现代大陆日本人相似，具有三个不同的遗传祖先：绳文相关，东亚相关和东北西伯利亚相关。

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.

在非日本人群中，拥有东亚血统和东北西伯利亚血统的韩国人群与Doigahama弥生个体的遗传相似程度最高。弥生个体，Kofun个体和现代日本人的混合模型分析分别支持假设绳文相关和韩国相关血统的双向混合模型。

These results suggest that between the Yayoi and Kofun periods, the majority of immigrants to the Japanese Archipelago originated primarily from the Korean Peninsula..

这些结果表明，在弥生和科芬时期，日本列岛的大多数移民主要来自朝鲜半岛。。

IntroductionThe prehistory of the Japanese Archipelago is represented by the “Jomon period”, a Neolithic period. The name “Jomon”, meaning “rope pattern”, reflects the distinctive feature of the Jomon culture, characterized by pottery with a unique pattern created using rope [1]. Although there are various opinions about the duration of the Jomon period, archeological evidence widely supports that it started approximately 16,500 years ago and persisted in isolation from the Eurasian continent for at least 10,000 years [2].

引言日本列岛的史前史以“绳文时期”为代表，这是一个新石器时代。“绳纹”这个名字的意思是“绳纹”，它反映了绳纹文化的鲜明特征，其特征是用绳纹制作的具有独特图案的陶器。虽然关于绳纹时期的持续时间有各种各样的观点，但考古学证据广泛支持绳纹时期大约在16500年前开始，并且与欧亚大陆隔离至少10000年（2）。

The main subsistence activities during the Jomon period were hunting and gathering. Rice cultivation in paddy fields was introduced to northern Kyushu, Japan, at the end of the Final Jomon period, about 3000 years ago, marking the beginning of the Yayoi period. It then gradually spread throughout Japan from the Middle to Late Yayoi period [3].There were various hypotheses to explain the history of the Japanese.

绳文时期的主要生计活动是狩猎和采集。大约3000年前，绳文末期结束时，稻田水稻种植被引入日本九州北部，标志着弥生时期的开始。然后，它从弥生中期到晚期逐渐传播到整个日本（3）。有各种假说可以解释日本人的历史。

For example, the “transformation model” posits that only culture, not people, came from the continent. The “replacement model” suggests a complete replacement of indigenous Jomon people by the Yayoi people, while the “hybridization model” proposes admixture between indigenous Jomon people and continental immigrants [4].

例如，“转型模式”假定只有文化而不是人来自非洲大陆。“替代模型”表明弥生人完全替代了土着绳文人，而“杂交模型”则提出了土着绳文人和大陆移民之间的混合。

Currently, the “dual-structure model,” one of the hybridization models proposed by Hanihara [5] based on the skeletal characteristics of ancient Jomon and Yayoi individuals, is widely accepted.Strong evidence supporting the dual-structure model has been accumulated through population genetic studies.

目前，“双重结构模型”是Hanihara（5）基于古代绳文和弥生个体的骨骼特征提出的杂交模型之一，已被广泛接受。通过种群遗传学研究积累了支持双重结构模型的有力证据。

The presence of not only the mitochondrial DNA (mtDNA) and Y chromosome haplogroups commonly found in continental East Asians, but also the mtDNA haplogroups such as N9b and M7a [6,7,8] and Y chromosome haplogroups such as D-M125 [9.

不仅存在东亚大陆常见的线粒体DNA（mtDNA）和Y染色体单倍群，还存在线粒体DNA单倍群，如N9b和M7a[6,7,8]和Y染色体单倍群，如D-M125[9]。

f-statisticsTo assess the genetic relationships between Doigahama Yayoi individual, D1604, and other East Eurasian populations, we computed f-statistics using the qp3Pop v651 program and the qpDstat v980 program in ADMIXTOOLS v7.0.2 package [63].First, we calculated f3(Mbuti; Doigahama_Yayoi, X), the outgroup f3 with Mbuti pygmy as an outgroup, where X was one of the populations in our dataset (Tables S1 and S2).

f统计量为了评估Doigahama弥生个体，D1604和其他东欧亚种群之间的遗传关系，我们使用ADMIXTOOLS v7.0.2软件包中的qp3Pop v651程序和qpDstat v980程序计算了f统计量。首先，我们计算了f3（Mbuti；Doigahama\u Yayoi，X），这是以Mbuti侏儒为外群的外群f3，其中X是我们数据集中的种群之一（表S1和S2）。

This outgroup f3 was used to identify the modern population with the closest genetic affinity to the Doigahama Yayoi sample. Then, we computed f4-statistics [64] in the form f4(Mbuti, Doigahama_Yayoi; modern Korean or modern Japanese, X) to rigorously test the hypothesis that no population surpasses modern Korean or modern Japanese populations in terms of genetic affinity with Doigahama Yayoi.

该外群f3用于鉴定与Doigahama弥生样本具有最接近遗传亲和力的现代种群。然后，我们以f4（Mbuti，Doigahama\u Yayoi；现代韩国人或现代日本人，X）的形式计算f4统计量，以严格检验没有人口在与Doigahama Yayoi的遗传亲和力方面超过现代韩国人或现代日本人的假设。

In these analyses, Z value, the deviation of the f-statistic from zero in units of the standard error, was also calculated.Additionally, we computed f4(Mbuti, Doigahama_Yayoi; Jomon1, Jomon2) to investigate the Jomon subpopulation demonstrating exceptionally high genetic affinity with the Doigahama Yayoi individual.

在这些分析中，还计算了Z值，即以标准误差为单位的f统计量与零的偏差。此外，我们计算了f4（Mbuti，Doigahama\u Yayoi；Jomon1，Jomon2），以研究绳文亚群与Doigahama Yayoi个体表现出异常高的遗传亲和力。

The Jomon1 and Jomon2 subpopulations were selected from those listed in Table S2.Admixture modelingWe consolidated the data from seven Jomon populations explained in Table S2 into a unified group labeled “Jomon” for our admixture modeling analysis. We assessed the compatibility of the admixture model and estimated the admixture ratio of Doigahama Yayoi using the qpF4ratio v400 program in the ADMIXTOOLS v7.0.2 package [63].

Jomon1和Jomon2亚群选自表S2中列出的亚群。混合建模我们将表S2中解释的七个绳纹种群的数据合并为一个统一的标记为“绳纹”的组，用于我们的混合建模分析。我们评估了混合物模型的相容性，并使用ADMIXTOOLS v7.0.2软件包（63）中的qpF4ratio v400程序估算了Doigahama-Yayoi的混合比。

We configured French as outgroup “o”. We tested the admixture models for both ancient and modern Japanese (“x”) with potential East Eurasian gene flow sources (“b”) and Jomon sources (“c”). Detailed explanations of the assumed model are prov.

我们将法语配置为外群“o”。。对假设模型的详细解释是prov。

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Download referencesAcknowledgementsThis work was supported partly by grants from JSPS KAKENHI (Grant Number 19H05737 to FM; 20H05822, 21H04358, 23K14279, and 24H01589 to KI; 23H04838 to IN; 21H04983 to SU; 18H02514, 19H05341, 21H00336, 21H04779, 21H04983, 22H00421, 23H04840 to JO) and AMED (Grant Number JP20km0405211 to JO).FundingOpen Access funding provided by The University of Tokyo.Author informationAuthors and AffiliationsDepartment of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, JapanJonghyun Kim, Koji Ishiya, Mami Kamio, Izumi Naka, Shintaroh Ueda & Jun OhashiDepartment of Legal Medicine, Toho University School of Medicine, Tokyo, 143-8540, JapanFuzuki Mizuno, Michiko Hayashi, Kunihiko Kurosaki & Shintaroh UedaThe Doigahama Site Anthropological Museum, Yamaguchi, 759-6121, JapanTakayuki Matsushita & Masami MatsushitaMedical Genome Center, National Research Institute for Child Health and Development, Tokyo, 157-8535, JapanSaki AotoAuthorsJonghyun KimView author publicationsYou can also search for this author in.

下载参考文献致谢这项工作得到了JSPS KAKENHI（授予FM的授权号19H05737；授予KI的授权号20H058221H04358223K14279和24H01589；授予IN的授权号23H04838；授予SU的授权号21H04983；授予JO的授权号18H02514、19H05341、21H00336、21H04779、21H04983、22H00421、23H04840）和AMED（授予JO的授权号JP20km0405211）的部分支持。资金东京大学提供的开放获取资金。作者信息作者和所属机构东京大学科学研究生院生物科学系，东京，113-0033，日本正玄金，石屋小二，妈咪神户，Izumi Naka，上田信太郎和大岛纯俊日本东洋大学医学院法律医学系，东京，143-8540，日本水津美子，林美子，黑坂国彦和上田信太郎日本国立研究院人类博物馆，山口，759-6121，日本松下和松下正美医学基因组中心东京儿童健康与发展研究所，157-8535，JapanSaki AotoAuthorsJonghyun KimView作者出版物您也可以在中搜索这位作者。

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Reprints and permissionsAbout this articleCite this articleKim, J., Mizuno, F., Matsushita, T. et al. Genetic analysis of a Yayoi individual from the Doigahama site provides insights into the origins of immigrants to the Japanese Archipelago.

转载和许可本文引用本文Kim，J.，Mizuno，F.，Matsushita，T。等人。对来自Doigahama遗址的弥生个体的遗传分析提供了对日本列岛移民起源的见解。

J Hum Genet (2024). https://doi.org/10.1038/s10038-024-01295-wDownload citationReceived: 31 May 2024Revised: 09 September 2024Accepted: 09 September 2024Published: 15 October 2024DOI: https://doi.org/10.1038/s10038-024-01295-wShare this articleAnyone you share the following link with will be able to read this content:Get shareable linkSorry, a shareable link is not currently available for this article.Copy to clipboard.

J Hum Genet（2024）。https://doi.org/10.1038/s10038-024-01295-wDownload引文收到日期：2024年5月31日修订日期：2024年9月9日接受日期：2024年9月9日发布日期：2024年10月15日OI：https://doi.org/10.1038/s10038-024-01295-wShare本文与您共享以下链接的任何人都可以阅读此内容：获取可共享链接对不起，本文目前没有可共享的链接。复制到剪贴板。

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