Recovery and Analysis of Ancient Nuclear DNA

描述（由申请人提供）：哺乳动物基因组注释的比较方法依赖于来自现有分类群的序列来识别功能保守的元素和谱系特异性序列变化。然而，这种分析将受益于来自灭绝物种的古老DNA序列。由于微生物污染和古代DNA的降解等技术障碍，以前的古代DNA研究依赖于线粒体而不是基因组DNA。本提案概述了一种通过开发构建、测序和分析小插入古代核DNA文库的方法来克服这些障碍的方法。这些方法将使用丰富的洞穴熊古代DNA进行改进，然后扩展到尼安德特人的基因组DNA。对一个试点洞穴熊库的分析表明，使用这些方法可以恢复古代的DNA序列。洞穴熊基因组序列将用于评估洞穴熊和现代熊物种的系统发育与线粒体DNA获得。我们的合作者将提供古代DNA，然后我们将构建尼安德特人的古代DNA文库，并恢复尼安德特人与人类特征（如语言）有关的快速进化的人类基因的同源物。

DESCRIPTION (provided by applicant): Comparative approaches for the annotation of mammalian genomes rely on sequences from extant taxa to identify functionally conserved elements and lineage-specific sequence changes. However, such analyses would benefit from ancient DNA sequence from extinct species. Previous ancient DNA studies have relied on mitochondrial rather than genomic DNA due to technical hurdles such as microbial contamination and degradation of ancient DNAs. This proposal outlines a way to surmount these hurdles through the development of methods for the construction, sequencing and analysis of small-insert ancient nuclear DNA libraries. These methods will be refined using abundant cave bear ancient DNA and then extended to Neandertal genomic DNA. Analysis of a pilot cave bear library indicates that ancient DNA sequences can be recovered using these methods. Cave bear genomic sequence will be used to assess the phylogeny of cave bear and modern bear species obtained with mitochondrial DNA. With our collaborators, who will provide ancient DNAs, we will then construct Neandertal ancient DNA libraries and recover Neandertal orthologs of rapidly evolving human genes involved in human traits such as language.