古基因组揭示史前欧亚大陆现代人复杂遗传历史

doi:10.16359/j.1000-3193/AAS.2023.0010

人类学学报 ›› 2023, Vol. 42 ›› Issue (03): 412-421.doi: 10.16359/j.1000-3193/AAS.2023.0010cstr: 32091.14.j.1000-3193/AAS.2023.0010

古基因组揭示史前欧亚大陆现代人复杂遗传历史

张明¹^,²^,³(), 平婉菁²^,³, YANG Melinda Anna²^,⁴, 付巧妹²^,³()

1.中国-中亚人类与环境“一带一路”联合实验室, 文化遗产研究与保护技术教育部重点实验室, 西北大学文化遗产学院, 西安710127
2.中国科学院古脊椎动物与古人类研究所, 中国科学院脊椎动物演化与人类起源重点实验室, 北京100044
3.中国科学院生物演化与环境卓越创新中心, 北京100044
4.里士满大学生物系, 里士满VA 23173

收稿日期:2022-03-04 修回日期:2022-08-05 出版日期:2023-06-15 发布日期:2023-06-13
通讯作者: 付巧妹，研究员，主要从事古DNA研究。E-mail: fuqiaomei@ivpp.ac.cn
作者简介:张明，副教授，主要从事古DNA研究。E-mail: zhangming@nwu.edu.cn
基金资助:
中国科学院战略性先导科技专项B类(XDB26000000);国家自然科学基金杰出青年项目(41925009);国家自然科学基金青年项目(32100488)

Ancient genomes reveal the complex genetic history of Prehistoric Eurasian modern humans

ZHANG Ming¹^,²^,³(), PING Wanjing²^,³, YANG Melinda Anna²^,⁴, FU Qiaomei²^,³()

1. China-Central Asia “the Belt and Road” Joint Laboratory on Human and Environment Research, Key Laboratory of Cultural Heritage Research and Conservation, School of Culture Heritage, Northwest University, Xi’an 710127
2. Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044
3. CAS Center for Excellence in Life and Paleoenvironment, Beijing 100044
4. Department of Biology, University of Richmond, Richmond, VA 23173, USA

Received:2022-03-04 Revised:2022-08-05 Online:2023-06-15 Published:2023-06-13

摘要/Abstract

摘要：

古DNA提取与测序技术的发展，让科学家们能够利用史前现代人样本直接开展古基因组研究。古基因组研究发现，在约4万年前，欧亚大陆上至少存在着6个独立的现代人群体，其中3个群体并未对现今人群贡献基因。在距今4万年至末次盛冰期结束，欧亚大陆至少有5个具有代表性的现代人群体。末次盛冰期结束后的部分现代人群体与现今人群拥有更近的遗传关系，而部分群体则未对现今人群贡献基因。本文基于末次盛冰期前(45~19 kaBP)与末次盛冰期后(19~10 kaBP)两个重要时间段的欧亚大陆史前现代人的基因组研究，梳理欧亚现代人在时间与空间上的发展脉络，重点探究此前研究相对滞后的欧亚大陆东部地区。

关键词: 欧亚大陆, 现代人, 古DNA, 人群结构, 遗传历史

Abstract:

Significant shifts in human populations occurred several times throughout history, as populations dispersed throughout Eurasia about 50 kaBP. During the Last Glacial Maximum (LGM), global temperatures dropped sharply causing environmental deterioration and population turnover in areas. After the LGM, populations increased as the natural environment stabilized and gradually developed into today’s populations. With advancements in ancient DNA extraction and sequencing technology, it is increasingly possible to directly retrieve genome-wide data from prehistoric modern human remains. The rapid emergence of new ancient genomes provides an entirely new direction for studying modern human population structure and evolutionary history. This research on Eurasian populations spanning 45~19 kaBP (pre-LGM) and 19~10 kaBP (post-LGM) summarizes the movement and interaction of prehistoric modern human populations, focusing especially on prehistoric East Eurasia, a region that has been less well-studied genetically. Of at least six distinct populations in Eurasia, three did not contribute substantial ancestry to present-day populations: Ust’-Ishim (≈45 kaBP) from northwestern Siberia; Oase 1 (≈40 kaBP) from Romania; and Zlatý kůň (over 45 kaBP) from Czechia. One population represented by three individuals (4.6~4.3 kaBP, from Bacho Kiro Cave, Bulgaria) seemed to contribute at least a partial genetic component to later some Eurasian populations. One population represented by Tianyuan man (≈40 kaBP, from East Asia) was shown to be more similar to present-day East Asians and Native Americans than to present-day or ancient Europeans. One population represented by Kostenki 14 (≈36 kaBP, from western Siberia) and Goyet Q116-1 (≈35 kaBP, from Belgium) was more closely related to Europeans than to other Eurasians. This work also summarized five representative populations after 40 kaBP and before the end of the LGM. In East Eurasia after the LGM (or since 14 kaBP), population histories played out very differently. For instance, high genetic continuity is observed in the Amur region in the last 14 kaBP, while in the Guangxi region of southern China, an ancient population that lived 10.5 kaBP carried ancestry not represented in any present-day humans. To conclude, comparison of genome-wide ancient DNA from multiple prehistoric humans have illustrated a complex genetic history of prehistoric Eurasian modern humans. In the future, additional ancient genomes will provide more evidence and details to illuminate the complex genetic history of modern humans.

Key words: Eurasia, modern human, Ancient DNA, Population structure, Genetic history

中图分类号:

Q987

张明, 平婉菁, YANG Melinda Anna, 付巧妹. 古基因组揭示史前欧亚大陆现代人复杂遗传历史[J]. 人类学学报, 2023, 42(03): 412-421.

ZHANG Ming, PING Wanjing, YANG Melinda Anna, FU Qiaomei. Ancient genomes reveal the complex genetic history of Prehistoric Eurasian modern humans[J]. Acta Anthropologica Sinica, 2023, 42(03): 412-421.

图/表 1

图1 45~10 kaBP欧亚大陆人群示意图 A）阶段1 Period I（45~19 kaBP）；B）阶段2 Period II（19~10 kaBP）：AE，以Kostenki 14为代表的古欧洲人群相关的遗传成分ancestry related to Ancient Europeans (represent by Kostenki 14)；BE，与未经取样的古欧亚人群相关且在现今欧洲人群、部分古代和现今中东人群中可找到的遗传成分ancestry related to an unsampled population known as Basal Eurasians and found in small numbers in ancient and present-day populations of the Near East and in present-day Europeans；ANS，以Yana为代表的古西伯利亚北部人群相关的遗传成分ancestry related to ancient North Siberians (represent by Yana); ANE, ancestry related to ancient North Eurasians (represent by Mal’ta-1 and Afontova Gora-3)；ANE，以Mal’ta-1和Afontova Gora-3为代表的古北欧亚人群相关的遗传成分；BEA，以田园洞人和AR33K为代表的基础东亚人相关的遗传成分；BA，以La368为代表的古代东南亚狩猎采集人群相关祖源成分；AEA，东亚古北方人群和东亚古南方人群分离前的亚洲人群；ANEA，以AR14K、扁扁洞、Devil’s Gate等个体为代表的东亚古北方人群；ASEA，以奇和洞、亮岛个体为代表的东亚古南方人群；AGX，以隆林个体为代表的古广西人群。图1A中的紫色代表田园洞人和Goyet Q116-1个体相联系的成分。虚线区域是指该遗传成分源自根据遗传数据所推测的人群状态，但未发现这一时期的古代样本。各颜色大致显示为某代表区域之间或之内的遗传成分组合，且颜色梯度显示为不同人群之间可能存在的遗传联系（如基因流）。

Fig.1 Schematic of Populations in Eurasia from 45 to 10 kaBP AE, ; BE, ; ANS, ; BEA, ancestry related to Basal East Asians (represent by Tianyuan and AR33K); BA, ancestry related to Basal Asians (represented by La368); AEA, ancestry related to Ancient East Asians; ANEA, ancestry related to Ancient Northern East Asians (represented by AR14K, Bianbian, Devil’s Gate, etc); ASEA, ancestry related to Ancient Southern East Asians (represented by Qihe and Liangdao); AGX, ancestry related to Ancient Guangxi population (represented by Longlin). The purple color in Fig.1A shows the connection between Tianyuan and Goyet Q116-1. Broken lines indicate no ancient genetic samples have been found for a population with the inferred ancestry. Colors loosely indicate genetic groupings between or within a region, with color gradients showing the connections (i.e., gene flow) that may exist between different ancient populations.

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古基因组揭示史前欧亚大陆现代人复杂遗传历史

Ancient genomes reveal the complex genetic history of Prehistoric Eurasian modern humans

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