古DNA捕获新技术与中国南方早期人群遗传研究新格局

doi:10.16359/j.cnki.cn11-1963/q.2020.0059

人类学学报 ›› 2020, Vol. 39 ›› Issue (04): 680-694.doi: 10.16359/j.cnki.cn11-1963/q.2020.0059

古DNA捕获新技术与中国南方早期人群遗传研究新格局

王恬怡¹^,²^,³(), 赵东月¹^,^*(), 张明²^,³^,⁴, 乔诗雨²^,³^,⁴, 杨帆⁵, 万杨⁵, 杨若薇²^,³, 曹鹏²^,³, 刘峰²^,³, 付巧妹²^,³^,⁴^,^*()

1.西北大学文化遗产学院,西安 710000
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.中国科学院大学, 北京 100049
5.云南省文物考古研究所,昆明 650118

收稿日期:2020-07-27 修回日期:2020-10-10 出版日期:2020-11-15 发布日期:2020-11-06
通讯作者: 赵东月,付巧妹
作者简介:王恬怡（1996-）,女,云南个旧人,西北大学文化遗产学院硕士研究生,主要从事古DNA研究。Email:wangty130@foxmail.com。
基金资助:
国家自然科学基金(91731303);国家自然科学基金(41925009);国家自然科学基金(41672021);国家自然科学基金(41630102)

Ancient DNA capture techniques and genetic study progress of early southern China populations

WANG Tianyi¹^,²^,³(), ZHAO Dongyue¹^,^*(), ZHANG Ming²^,³^,⁴, QIAO Shiyu²^,³^,⁴, YANG Fan⁵, WAN Yang⁵, YANG Ruowei²^,³, CAO Peng²^,³, LIU Feng²^,³, FU Qiaomei²^,³^,⁴^,^*()

1. College of Cultural Heritage, Northwest University, Xi’an 710000
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.University of Chinese Academy of Sciences, Beijing 100049
5. Yunnan Institute of Cultural Relics and Archaeology, Kunming 650118

Received:2020-07-27 Revised:2020-10-10 Online:2020-11-15 Published:2020-11-06
Contact: ZHAO Dongyue,FU Qiaomei

摘要/Abstract

摘要：

古DNA捕获技术目前已获得极大的发展,能够从骨骼和环境沉积物等多种材料中获取到目的DNA片段,而且对于保存环境较差的低纬度地区,同样能够获取有效的内源DNA片段,极大地丰富了古DNA研究的材料来源。本文围绕这一新技术开展总结和讨论,主要分为两个方面：1）总结并介绍该技术应用前景;2）应用这一技术打开了中国南方早期人群研究的新局面,梳理该新技术的应用对史前中国南方人群古基因组研究所获得的新认识,并对中国南方早期人群古基因组深入分析;另外,利用古DNA捕获技术成功获取云南3446~3180 BP的大阴洞遗址4例高质量线粒体基因组信息,并开展了人群遗传历史的研究。

关键词: 古DNA, 捕获, 中国南方, 古基因组, 大阴洞遗址

Abstract:

Substantial development of the ancient DNA capture techniques allows for obtaining DNA from a wide range of materials, including bone and environmental sediments. Moreover, effective endogenous DNA fragments are also obtainable from low-latitude regions with poor preservation conditions, greatly enriching the material sources for ancient DNA research. This paper summarizes and discusses this new technology in two main aspects: 1) it summarizes and presents the potential application of this technology; and 2) it reviews the knowledge gained from the application of this new technology to the study of ancient genomes. Specifically, this paper focuses on the study of ancient genomes from southern China and covers three points. First, we reveal the new insights gained from the study of ancient genomes. Second, we provide an in-depth analysis of the differences among ancient genomes of early populations in southern China. Third, we discuss the use of ancient DNA capture technology in successfully obtaining high quality mitochondrial genomic information from four individuals (3446-3180 cal BP) of Dayin Cave site in Yunnan Province.

Key words: Ancient DNA, Capture technique, Southern China, Ancient Genome, Dayin Cave

中图分类号:

Q986

王恬怡, 赵东月, 张明, 乔诗雨, 杨帆, 万杨, 杨若薇, 曹鹏, 刘峰, 付巧妹. 古DNA捕获新技术与中国南方早期人群遗传研究新格局[J]. 人类学学报, 2020, 39(04): 680-694.

WANG Tianyi, ZHAO Dongyue, ZHANG Ming, QIAO Shiyu, YANG Fan, WAN Yang, YANG Ruowei, CAO Peng, LIU Feng, FU Qiaomei. Ancient DNA capture techniques and genetic study progress of early southern China populations[J]. Acta Anthropologica Sinica, 2020, 39(04): 680-694.

图/表 6

图1 杂交捕获方法流程图

Fig.1 Overview of the capture-on-beads method

图2 中国南方已发表的古DNA样本信息不同颜色表示所发表古DNA数据的类型：红色表示核基因组数据,蓝色表示线粒体基因组数据。不同形状代表了不同的年代：圆形表示个体碳测年在距今7500年以前,三角形表示距今7500到4000年之间的个体,菱形表示距今4000年到距今1000年的个体,正方形表示距今1000年以内的个体。括号中的数字代表样本数量。

Fig.2 Information on published ancient DNA samples in southern China Red indicates the data is the nuclear genome, blue indicates it’s the mitochondrial genome. The different symbol means different time periods. The sample sizes of sequenced individuals are put in the brackets.

图3 f4-statistics分析图。蓝色表示f4（Mbuti,X;Qihe,Liangdao1）,橙色表示f4（Mbuti,X;Qihe,Liangdao2）,每个点的数值对应人群计算所得的f4值,浅色线段表示误差线即f4±std.err。f4-statistics具有显著性的结果（|Z|>3）圆点加了黑色边缘。若f4值小于零,即f4（Mbuti,X;Qihe,Liangdao1/Liangdao2）<0,表示该人群相较于两个亮岛人与奇和洞人的遗传关系更近,大于零则反之。样本名称后为样本距今年代

Fig.3 The result of f4(Mbuti, X; Qihe, Liangdao1/Liangdao2), where X is various ancient populations from East Eurasia. The blue indicates the results of f4(Mbuti, X; Qihe, Liangdao1). The orange indicates the results of f4(Mbuti, X; Qihe, Liangdao2). Circle with black edge are significant results with |Z|>3. If the f4-value lesser than 0, suggesting the “X” population is closer to Qihe than Liangdao. The number after the sample name is the date before present.

图4 大阴洞地理信息以及线粒体基因组分析结果 A) 大阴洞遗址地理位置location of Dayin Cave site;B) 大阴洞个体相关单倍群分布直方图histogram of haplogroup distributions;C) 基于单倍群频率的主成分分析图PCA analysis based on the haplogroup frequency;D) 共享单倍群值热图heatmap of haplogroup sharing calculation。图中大阴洞古代个体以a.DYD表示,括号中的数字表示本研究中该人群样本的数量。

Fig.4 Geographic information and mtDNA genome analyses of Dayin Cave The ancient individuals of Dayin Cave are represented by “a.DYD”, and each number in the bracket shows the sample size from the population in this study.

表1 大阴洞样本信息

Tab.1 Information of the Dayin Cave samples

样本Sample ID	取样部位 Skeletal Element	线粒体DNA 平均覆盖度 Mean Coverage of mtDNA	平均污染度% Contamination of mtDNA%	污染度% （95%置信区间） Contamination% (95%CI)	单倍型 Haplotype	¹⁴C校正年代 Calibrated years (cal BP)
2017GDM10	指骨	108.23	2.0	0.9-4.1	R+16189	3446-3326
2017GDM6:R1	距骨	226.34	1.6	0.8-2.4	R9c1b1	3360-3180
2017GDM1	距骨	217.98	1.1	0.5-2.1	R30	3367-3213
2017GDM7:R1	指骨	308.30	1.9	1.2-2.7	B4c1b2a	3444-3249
2017GDM12*	尺骨	10.13	10.7	6.6-16.7	H+195	3386-3237

图5 大阴洞个体所属单倍型网络结构图 A) R+16189单倍型网络结构图network of R+16189;B) R9c1b1单倍型网络结构图network of R9c1b1;C) R30单倍型网络结构图network of R30;D) B4单倍型网络结构图network of B4。箭头指出大阴洞个体以及与大阴洞个体所属单倍型相关的人群。

Fig.5 Haplotype networks of individuals from Dayin Cave Black arrows indicate the Dayin Cave individuals and the populations associated with haplotypes which Dayin Cave individuals belong to.

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古DNA捕获新技术与中国南方早期人群遗传研究新格局

Ancient DNA capture techniques and genetic study progress of early southern China populations

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