古丹尼索瓦人个体的高覆盖度基因组序列。
A high-coverage genome sequence from an archaic Denisovan individual.
机构信息
Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany.
出版信息
Science. 2012 Oct 12;338(6104):222-6. doi: 10.1126/science.1224344. Epub 2012 Aug 30.
Abstract
We present a DNA library preparation method that has allowed us to reconstruct a high-coverage (30×) genome sequence of a Denisovan, an extinct relative of Neandertals. The quality of this genome allows a direct estimation of Denisovan heterozygosity indicating that genetic diversity in these archaic hominins was extremely low. It also allows tentative dating of the specimen on the basis of "missing evolution" in its genome, detailed measurements of Denisovan and Neandertal admixture into present-day human populations, and the generation of a near-complete catalog of genetic changes that swept to high frequency in modern humans since their divergence from Denisovans.
摘要
我们提出了一种 DNA 文库制备方法，使我们能够重建一个高覆盖率（30×）的丹尼索瓦人基因组序列，丹尼索瓦人是尼安德特人的灭绝亲属。该基因组的质量允许直接估计丹尼索瓦人的杂合度，表明这些古老人类的遗传多样性极低。它还允许根据其基因组中的“缺失进化”、对丹尼索瓦人和尼安德特人混合到现代人类中的详细测量，以及生成一个近乎完整的遗传变化目录来对标本进行暂定日期，这些遗传变化自与丹尼索瓦人分化以来在现代人中高频出现。
相似文献
1
A high-coverage genome sequence from an archaic Denisovan individual.古丹尼索瓦人个体的高覆盖度基因组序列。
Science. 2012 Oct 12;338(6104):222-6. doi: 10.1126/science.1224344. Epub 2012 Aug 30.
2
Excavating Neandertal and Denisovan DNA from the genomes of Melanesian individuals.从美拉尼西亚人的基因组中挖掘尼安德特人和丹尼索瓦人的DNA。
Science. 2016 Apr 8;352(6282):235-9. doi: 10.1126/science.aad9416. Epub 2016 Mar 17.
3
Early history of Neanderthals and Denisovans.尼安德特人和丹尼索瓦人的早期历史。
Proc Natl Acad Sci U S A. 2017 Sep 12;114(37):9859-9863. doi: 10.1073/pnas.1706426114. Epub 2017 Aug 7.
4
Chromosomal Rearrangements as Barriers to Genetic Homogenization between Archaic and Modern Humans.染色体重排作为古代人类与现代人类之间基因同质化的障碍。
Mol Biol Evol. 2015 Dec;32(12):3064-78. doi: 10.1093/molbev/msv204. Epub 2015 Sep 23.
5
Insights into hominin phenotypic and dietary evolution from ancient DNA sequence data.从古代DNA序列数据洞察古人类表型和饮食进化。
J Hum Evol. 2015 Feb;79:55-63. doi: 10.1016/j.jhevol.2014.10.018. Epub 2015 Jan 3.
6
Analysis of Human Sequence Data Reveals Two Pulses of Archaic Denisovan Admixture.人类序列数据分析揭示了两次古丹尼索瓦人基因混合。
Cell. 2018 Mar 22;173(1):53-61.e9. doi: 10.1016/j.cell.2018.02.031. Epub 2018 Mar 15.
7
Identification of African-Specific Admixture between Modern and Archaic Humans.鉴定现代人与古人类之间的非洲特有混合
Am J Hum Genet. 2019 Dec 5;105(6):1254-1261. doi: 10.1016/j.ajhg.2019.11.005.
8
Multiple Deeply Divergent Denisovan Ancestries in Papuans.巴布亚人群中存在多个深度分化的丹尼索瓦人血统。
Cell. 2019 May 2;177(4):1010-1021.e32. doi: 10.1016/j.cell.2019.02.035. Epub 2019 Apr 11.
9
ABO Genetic Variation in Neanderthals and Denisovans.尼安德特人和丹尼索瓦人 ABO 基因变异。
Mol Biol Evol. 2021 Jul 29;38(8):3373-3382. doi: 10.1093/molbev/msab109.
10
Deleterious variants in genes regulating mammalian reproduction in Neanderthals, Denisovans and extant humans.在尼安德特人、丹尼索瓦人和现存人类中，调控哺乳动物生殖的基因中的有害变异。
Hum Reprod. 2021 Feb 18;36(3):734-755. doi: 10.1093/humrep/deaa347.
引用本文的文献
1
The AADR Visualizer: An ArcGIS Online Visualizer for ancient human DNA from the Allen Ancient DNA Resource.美国牙科研究协会可视化工具：一种用于来自艾伦古代DNA资源的古代人类DNA的ArcGIS在线可视化工具。
Bioinformatics. 2025 Aug 18;5(1). doi: 10.1093/bioadv/vbaf199.
2
Ancient microbial DNA and proteins preserve in concretions covering human remains.古代微生物的DNA和蛋白质保存在覆盖人类遗骸的结核中。
iScience. 2025 Jul 23;28(8):113182. doi: 10.1016/j.isci.2025.113182. eCollection 2025 Aug 15.
3
Human-specific gene expansions contribute to brain evolution.人类特有的基因扩增促进大脑进化。
Cell. 2025 Jul 18. doi: 10.1016/j.cell.2025.06.037.
4
A global map for introgressed structural variation and selection in humans.人类渐渗结构变异与选择的全球图谱。
bioRxiv. 2025 Jun 24:2025.06.24.661368. doi: 10.1101/2025.06.24.661368.
5
Brain-derived neurotrophic factor gene polymorphism rs6265 and elite athlete status in four independent populations.脑源性神经营养因子基因多态性rs6265与四个独立人群中的精英运动员身份
Biol Sport. 2025 Jan 20;42(3):69-77. doi: 10.5114/biolsport.2025.146786. eCollection 2025 Jul.
6
Muscle AMP deaminase activity was lower in Neandertals than in modern humans.尼安德特人的肌肉AMP脱氨酶活性低于现代人类。
Nat Commun. 2025 Jul 10;16(1):6371. doi: 10.1038/s41467-025-61605-4.
7
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.
8
Whole-genome ancestry of an Old Kingdom Egyptian.一位古王国时期埃及人的全基因组血统。
Nature. 2025 Jul 2. doi: 10.1038/s41586-025-09195-5.
9
A genome from ancient Egypt.一份来自古埃及的基因组。
Nature. 2025 Jul 2. doi: 10.1038/d41586-025-02036-5.
10
50,000 years of evolutionary history of India: Impact on health and disease variation.印度五万年的进化史：对健康与疾病差异的影响。
Cell. 2025 Jun 26;188(13):3389-3404.e6. doi: 10.1016/j.cell.2025.04.027.
本文引用的文献
1
ABRUPT CLINE FOR SEX CHROMOSOMES IN A HYBRID ZONE BETWEEN TWO SPECIES OF MICE.两种小鼠杂交区域内性染色体的突然渐变群
Evolution. 1992 Aug;46(4):1146-1163. doi: 10.1111/j.1558-5646.1992.tb00625.x.
2
Inference of population splits and mixtures from genome-wide allele frequency data.从全基因组等位基因频率数据推断种群分裂和混合。
PLoS Genet. 2012;8(11):e1002967. doi: 10.1371/journal.pgen.1002967. Epub 2012 Nov 15.
3
The bonobo genome compared with the chimpanzee and human genomes.倭黑猩猩基因组与黑猩猩和人类基因组比较。
Nature. 2012 Jun 28;486(7404):527-31. doi: 10.1038/nature11128.
4
The status of Homo heidelbergensis (Schoetensack 1908).海德堡人（舍滕斯扎克 1908 年）的现状。
Evol Anthropol. 2012 May;21(3):101-7. doi: 10.1002/evan.21311.
5
Temporal patterns of nucleotide misincorporations and DNA fragmentation in ancient DNA.古 DNA 中核苷酸错配和 DNA 片段化的时间模式。
PLoS One. 2012;7(3):e34131. doi: 10.1371/journal.pone.0034131. Epub 2012 Mar 30.
6
Predicting Homo pigmentation phenotype through genomic data: from Neanderthal to James Watson.通过基因组数据预测人类肤色表型：从尼安德特人到詹姆斯·沃森。
Am J Hum Biol. 2012 Sep-Oct;24(5):705-9. doi: 10.1002/ajhb.22263. Epub 2012 Mar 12.
7
Insights into hominid evolution from the gorilla genome sequence.从大猩猩基因组序列中洞察人类进化。
Nature. 2012 Mar 7;483(7388):169-75. doi: 10.1038/nature10842.
8
Contrasting properties of gene-specific regulatory, coding, and copy number mutations in Saccharomyces cerevisiae: frequency, effects, and dominance.酿酒酵母中基因特异性调控、编码和拷贝数突变的对比特性：频率、效应和显性。
PLoS Genet. 2012 Feb;8(2):e1002497. doi: 10.1371/journal.pgen.1002497. Epub 2012 Feb 9.
9
Length and GC-biases during sequencing library amplification: a comparison of various polymerase-buffer systems with ancient and modern DNA sequencing libraries.测序文库扩增过程中的长度和 GC 偏倚：各种聚合酶-缓冲系统与古老和现代 DNA 测序文库的比较。
Biotechniques. 2012 Feb;52(2):87-94. doi: 10.2144/000113809.
10
Cost-effective, high-throughput DNA sequencing libraries for multiplexed target capture.经济高效、高通量的用于多重靶标捕获的 DNA 测序文库。
Genome Res. 2012 May;22(5):939-46. doi: 10.1101/gr.128124.111. Epub 2012 Jan 20.
Zotero 插件