现代和古代基因组的统一族谱。
A unified genealogy of modern and ancient genomes.
机构信息
Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford OX3 7LF, UK.
出版信息
Science. 2022 Feb 25;375(6583):eabi8264. doi: 10.1126/science.abi8264.
Abstract
The sequencing of modern and ancient genomes from around the world has revolutionized our understanding of human history and evolution. However, the problem of how best to characterize ancestral relationships from the totality of human genomic variation remains unsolved. Here, we address this challenge with nonparametric methods that enable us to infer a unified genealogy of modern and ancient humans. This compact representation of multiple datasets explores the challenges of missing and erroneous data and uses ancient samples to constrain and date relationships. We demonstrate the power of the method to recover relationships between individuals and populations as well as to identify descendants of ancient samples. Finally, we introduce a simple nonparametric estimator of the geographical location of ancestors that recapitulates key events in human history.
摘要
来自世界各地的现代和古代基因组的测序极大地改变了我们对人类历史和进化的理解。然而，如何从人类基因组变异的整体中最好地描述祖先关系的问题仍未解决。在这里，我们使用能够推断现代人和古代人类统一谱系的非参数方法来解决这一挑战。这种对多个数据集的紧凑表示形式探索了缺失和错误数据的挑战，并利用古代样本来约束和确定关系的时间。我们展示了该方法恢复个体和群体之间关系以及识别古代样本后代的能力。最后，我们引入了一种简单的祖先地理位置的非参数估计器，该估计器再现了人类历史上的关键事件。
相似文献
1
A unified genealogy of modern and ancient genomes.现代和古代基因组的统一族谱。
Science. 2022 Feb 25;375(6583):eabi8264. doi: 10.1126/science.abi8264.
2
Protocol for a comprehensive pipeline to study ancient human genomes.研究古代人类基因组的综合管道方案
STAR Protoc. 2024 Jun 21;5(2):102985. doi: 10.1016/j.xpro.2024.102985. Epub 2024 Apr 30.
3
Tracing the peopling of the world through genomics.通过基因组学探寻人类的全球迁徙历程。
Nature. 2017 Jan 18;541(7637):302-310. doi: 10.1038/nature21347.
4
African population history: an ancient DNA perspective.非洲人群历史：基于古 DNA 的视角。
Curr Opin Genet Dev. 2020 Jun;62:8-15. doi: 10.1016/j.gde.2020.05.008. Epub 2020 Jun 18.
5
Ancient and modern mitogenomes from Central Argentina: new insights into population continuity, temporal depth and migration in South America.阿根廷中部的古今线粒体基因组：南美洲人口连续性、时间深度和迁徙的新见解。
Hum Mol Genet. 2021 Jun 17;30(13):1200-1217. doi: 10.1093/hmg/ddab105.
6
Inferring Population Histories for Ancient Genomes Using Genome-Wide Genealogies.利用全基因组谱系推断古代基因组的种群历史。
Mol Biol Evol. 2021 Aug 23;38(9):3497-3511. doi: 10.1093/molbev/msab174.
7
Investigating population continuity with ancient DNA under a spatially explicit simulation framework.在空间明确的模拟框架下，利用古DNA研究种群连续性。
BMC Genet. 2017 Dec 15;18(1):114. doi: 10.1186/s12863-017-0575-6.
8
Dating genomic variants and shared ancestry in population-scale sequencing data.在大规模测序数据中追溯基因组变异和共同祖先。
PLoS Biol. 2020 Jan 17;18(1):e3000586. doi: 10.1371/journal.pbio.3000586. eCollection 2020 Jan.
9
Inferring whole-genome histories in large population datasets.在大型人群数据集推断全基因组历史。
Nat Genet. 2019 Sep;51(9):1330-1338. doi: 10.1038/s41588-019-0483-y. Epub 2019 Sep 2.
10
Insights into human history from the first decade of ancient human genomics.从人类基因组学研究的第一个十年看人类历史
Science. 2021 Sep 24;373(6562):1479-1484. doi: 10.1126/science.abi8202. Epub 2021 Sep 23.
引用本文的文献
1
Accelerated Bayesian inference of population size history from recombining sequence data.基于重组序列数据的群体大小历史的加速贝叶斯推断。
Nat Genet. 2025 Sep 15. doi: 10.1038/s41588-025-02323-x.
2
Robust and accurate Bayesian inference of genome-wide genealogies for hundreds of genomes.针对数百个基因组的全基因组谱系进行稳健且准确的贝叶斯推断。
Nat Genet. 2025 Sep 8. doi: 10.1038/s41588-025-02317-9.
3
The Length of Haplotype Blocks and Signals of Structural Variation in Reconstructed Genealogies.重构谱系中单体型块的长度及结构变异信号
Mol Biol Evol. 2025 Sep 1;42(9). doi: 10.1093/molbev/msaf190.
4
A genealogy-based approach for revealing ancestry-specific structures in admixed populations.一种基于系谱学的方法，用于揭示混合群体中特定祖先的结构。
Am J Hum Genet. 2025 Jul 17. doi: 10.1016/j.ajhg.2025.06.016.
5
Tsbrowse: an interactive browser for ancestral recombination graphs.Tsbrowse：一种用于祖先重组图的交互式浏览器。
Bioinformatics. 2025 Aug 2;41(8). doi: 10.1093/bioinformatics/btaf393.
6
Resolving out of Africa event for Papua New Guinean population using neural network.利用神经网络解析巴布亚新几内亚人群的“走出非洲”事件。
Nat Commun. 2025 Jul 9;16(1):6345. doi: 10.1038/s41467-025-61661-w.
7
The TMRCA of general genealogies in populations with deterministically varying size.大小确定性变化人群中一般谱系的最近共同祖先时间
Theor Popul Biol. 2025 Jul 2;165:1-9. doi: 10.1016/j.tpb.2025.06.002.
8
Recent Statistical Innovations in Human Genetics.人类遗传学领域的最新统计创新
Ann Hum Genet. 2025 Sep;89(5):241-254. doi: 10.1111/ahg.12606. Epub 2025 Jun 27.
9
The chronospatial revolution in psychology.心理学中的时空革命。
Nat Hum Behav. 2025 Jun 2. doi: 10.1038/s41562-025-02229-y.
10
Urbanization and genetic homogenization in the medieval Low Countries revealed through a ten-century paleogenomic study of the city of Sint-Truiden.通过对圣特吕登市长达十个世纪的古基因组研究揭示中世纪低地国家的城市化与基因同质化
Genome Biol. 2025 May 20;26(1):127. doi: 10.1186/s13059-025-03580-z.
本文引用的文献
1
An ancestral recombination graph of human, Neanderthal, and Denisovan genomes.人类、尼安德特人和丹尼索瓦人基因组的祖先重组图谱。
Sci Adv. 2021 Jul 16;7(29). doi: 10.1126/sciadv.abc0776. Print 2021 Jul.
2
Inferring Population Histories for Ancient Genomes Using Genome-Wide Genealogies.利用全基因组谱系推断古代基因组的种群历史。
Mol Biol Evol. 2021 Aug 23;38(9):3497-3511. doi: 10.1093/molbev/msab174.
3
Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program.美国国立卫生研究院生物医学高级研究与发展局（NHLBI）TOPMed 项目中对 53831 个不同基因组进行测序。
Nature. 2021 Feb;590(7845):290-299. doi: 10.1038/s41586-021-03205-y. Epub 2021 Feb 10.
4
Disentangling selection on genetically correlated polygenic traits via whole-genome genealogies.通过全基因组谱系解析遗传相关多基因性状的选择。
Am J Hum Genet. 2021 Feb 4;108(2):219-239. doi: 10.1016/j.ajhg.2020.12.005. Epub 2021 Jan 12.
5
Sampling bias and model choice in continuous phylogeography: Getting lost on a random walk.连续系统地理学中的抽样偏差与模型选择：在随机游走中迷失方向
PLoS Comput Biol. 2021 Jan 6;17(1):e1008561. doi: 10.1371/journal.pcbi.1008561. eCollection 2021 Jan.
6
Hotspots of Human Mutation.人类突变热点。
Trends Genet. 2021 Aug;37(8):717-729. doi: 10.1016/j.tig.2020.10.003. Epub 2020 Nov 13.
7
Evaluating genotype imputation pipeline for ultra-low coverage ancient genomes.评估超低覆盖度古基因组的基因型推断流程。
Sci Rep. 2020 Oct 29;10(1):18542. doi: 10.1038/s41598-020-75387-w.
8
Array programming with NumPy.使用 NumPy 进行数组编程。
Nature. 2020 Sep;585(7825):357-362. doi: 10.1038/s41586-020-2649-2. Epub 2020 Sep 16.
9
Mapping gene flow between ancient hominins through demography-aware inference of the ancestral recombination graph.通过对祖先重组图的具有人口统计学意识的推断，绘制古代人类之间的基因流动图谱。
PLoS Genet. 2020 Aug 6;16(8):e1008895. doi: 10.1371/journal.pgen.1008895. eCollection 2020 Aug.
10
Privacy challenges and research opportunities for genomic data sharing.基因组数据共享的隐私挑战和研究机会。
Nat Genet. 2020 Jul;52(7):646-654. doi: 10.1038/s41588-020-0651-0. Epub 2020 Jun 29.
Zotero 插件