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The nature of Neanderthal introgression revealed by 27,566 Icelandic genomes

机译：Neanderthal introgression的性质揭示了27,566次冰岛基因组

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摘要

Analysis of Icelandic genomes reveals chromosome fragments of Neanderthal and Denisovan origin, the latter of which occurred through Denisovan gene flow either into ancestors of the Neanderthals or directly into humans.Human evolutionary history is rich with the interbreeding of divergent populations. Most humans outside of Africa trace about 2% of their genomes to admixture from Neanderthals, which occurred 50-60 thousand years ago(1). Here we examine the effect of this event using 14.4 million putative archaic chromosome fragments that were detected in fully phased whole-genome sequences from 27,566 Icelanders, corresponding to a range of 56,388-112,709 unique archaic fragments that cover 38.0-48.2% of the callable genome. On the basis of the similarity with known archaic genomes, we assign 84.5% of fragments to an Altai or Vindija Neanderthal origin and 3.3% to Denisovan origin; 12.2% of fragments are of unknown origin. We find that Icelanders have more Denisovan-like fragments than expected through incomplete lineage sorting. This is best explained by Denisovan gene flow, either into ancestors of the introgressing Neanderthals or directly into humans. A within-individual, paired comparison of archaic fragments with syntenic non-archaic fragments revealed that, although the overall rate of mutation was similar in humans and Neanderthals during the 500 thousand years that their lineages were separate, there were differences in the relative frequencies of mutation types-perhaps due to different generation intervals for males and females. Finally, we assessed 271 phenotypes, report 5 associations driven by variants in archaic fragments and show that the majority of previously reported associations are better explained by non-archaic variants.
机译：冰岛基因组的分析显示尼安德特人和丹尼诺州的染色体片段，其中后者通过Deanisovan基因流入Neanderthals的祖先或直接进入人类。人类进化历史与分歧群体的杂交丰富。大多数人在非洲以外的大多数人追溯到其中约2％的基因组给尼安德特人的混合物，这发生了50-60千年前（1）。在这里，我们使用1440万推定的古代染色体片段来检查该事件的效果，该染色体片段在27,566型冰冰的完全序列的全基因组序列中检测到，对应于56,388-112,709个独特的古代片段，涵盖可调用基因组的38.0-48.2％ 。在与已知的古代基因组的相似之处，我们将84.5％的碎片分配给阿尔泰或维德基尼安德氏植物的碎片，3.3％到Denisovan起源; 12.2％的片段是未知的。我们发现，通过不完全的谱系排序，冰岛冰剑就会有比预期更多的denisovan样片。最好通过Denisovan基因流入肠道肠道或直接进入人类的祖先来解释。具有同期非古代碎片的古代碎片的个体的对比较显示，尽管在50万年的人类和尼安德特人中突变的总体速率相似，但它们的谱系是分开的，但相对频率存在差异突变类型 - 可能是由于男性和女性的不同一代间隔。最后，我们评估了271个表型，报告了由古代碎片中变体驱动的第5个关联，并表明，由于非古代变体，最好解释出的大多数先前报告的关联。

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  • 来源
    《Nature》 |2020年第7810期|78-83|共6页
  • 作者

    Skov Laurits; Coll Macia Moises; Sveinbjoernsson Gardar; Mafessoni Fabrizio; Lucotte Elise A.; Einarsdottir Margret S.; Jonsson Hakon; Halldorsson Bjarni; Gudbjartsson Daniel F.; Helgason Agnar; Schierup Mikkel Heide; Stefansson Kari;

  • 作者单位

    Aarhus Univ Bioinformat Res Ctr Aarhus Denmark|Max Planck Inst Evolutionary Anthropol Leipzig Germany;

    Aarhus Univ Bioinformat Res Ctr Aarhus Denmark;

    Amgen Inc deCODE Genet Reykjavik Iceland;

    Max Planck Inst Evolutionary Anthropol Leipzig Germany;

    Aarhus Univ Bioinformat Res Ctr Aarhus Denmark;

    Amgen Inc deCODE Genet Reykjavik Iceland;

    Amgen Inc deCODE Genet Reykjavik Iceland;

    Amgen Inc deCODE Genet Reykjavik Iceland|Reykjavik Univ Sch Sci & Engn Reykjavik Iceland;

    Amgen Inc deCODE Genet Reykjavik Iceland;

    Amgen Inc deCODE Genet Reykjavik Iceland|Univ Iceland Dept Anthropol Reykjavik Iceland;

    Aarhus Univ Bioinformat Res Ctr Aarhus Denmark;

    Amgen Inc deCODE Genet Reykjavik Iceland|Univ Iceland Fac Med Sch Hlth Sci Reykjavik Iceland;

  • 收录信息 美国《科学引文索引》(SCI);美国《工程索引》(EI);美国《生物学医学文摘》(MEDLINE);美国《化学文摘》(CA);
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