Neandertal Genomics

描述(申请人提供)：人类生物学的许多方面，包括认知能力、高级语言和对常见疾病的易感性，都受到人类进化过程中最近发生的基因组序列变化的影响。尼安德特人的基因组序列将有助于识别这些事件。大多数证据表明，尼安德特人的基因组序列与50万年前的现代人谱系存在分歧。这项研究的目的是通过有针对性的方法获得尼安德特人的基因组序列，以便识别现代人特有的固定序列变化。我们的建议的目的是基于广泛的初步数据，包括从尼安德特人和洞熊遗骸中创建基因组DNA文库，产生尼安德特人的基因组序列，以及有针对性地从洞穴熊基因组库中恢复特定序列。我们将首先分析几个可用的尼安德特人样本，以确定哪些样本显示出最好的尼安德特人DNA保存，并将现代人类污染降至最低。利用这些尼安德特人的样本，我们将构建尼安德特人的元基因组文库，该文库将作为这些研究的尼安德特人基因组DNA的可再生来源，我们还将向广大研究社区提供这些DNA。我们将使用这些文库进行直接基因组选择和基于PCR的特定尼安德特人基因组克隆的搜索，重点放在基因和其他功能序列中人类-黑猩猩核苷酸替换的位置。这些方法产生的数据将被广泛用于比较人类、黑猩猩和尼安德特人的序列，并识别人类从尼安德特人分化后发生的替换。我们将通过从多个尼安德特人文库中恢复相同的序列来鉴定尼安德特人的序列。我们将通过与已知的SNPs进行比较，并对不同人类样本中的替换基因进行重新测序，排除现代人中具有多态的人-尼安德特人替换。这些研究将确定一组现代人类独有的人-黑猩猩序列差异，对人类起源、人类特有表型特征的兴起以及尼安德特人的生物学产生基本的见解。通俗摘要：人类是一个相对较新的物种，出现在最近的16万年。然而，我们生物学的许多方面，包括我们的语言，我们的推理能力，以及我们对许多疾病的易感性，都是我们独一无二的。我们希望通过将我们的基因组序列与尼安德特人或最接近但现已灭绝的近亲的基因组序列进行比较，我们将识别出我们基因组中发生的导致独特人类特征兴起的变化。

DESCRIPTION (provided by applicant): Many aspects of human biology, including cognitive abilities, advanced language, and susceptibility to common diseases, are influenced by genome sequence changes that occurred very recently in human evolution. Genomic sequence from the Neandertal, which most evidence suggests diverged from the modern human lineage -500,000 years ago, would help identify these events. The goal of this study is to obtain Neandertal genome sequences by targeted methods in order to identify fixed sequence changes unique to modern humans. The aims of our proposal are based on extensive preliminary data, including the creation of genomic DNA libraries from Neandertal and cave bear remains, the generation of Neandertal genomic sequences, and the targeted recovery of specific sequences from cave bear genomic libraries. We will first analyze several Neandertal samples available to us to identify those that show the best Neandertal DNA preservation with minimal amounts of modern human contamination. Using these Neandertal samples, we will construct Neandertal metagenomic libraries that will serve as a renewable source of Neandertal genomic DNA for these studies and which we will also make available to the research community at large. We will use these libraries in both direct genomic selection and PCR-based searches for specific Neandertal genomic clones, focusing on sites of human-chimpanzee nucleotide substitution in genes and other functional sequences. The data generated by these methods will be used in an extensive effort to compare human, chimpanzee and Neandertal sequences and identify substitutions that occurred after humans diverged from Neandertals. We will authenticate Neandertal sequences by recovering the same sequences from multiple Neandertal libraries. We will exclude human-Neandertal substitutions polymorphic in modern humans by comparison to known SNPs and by resequencing substituted loci in a diverse panel of human samples. These studies will identify a set of human-chimpanzee sequence differences that are unique to modern humans, yielding fundamental insights into human origins, the rise of human-specific phenotypic traits, and the biology of Neandertals. Lay Summary: Humans are a relatively recent species, arising in the last -160,000 years. However, many aspects of our biology, including our language, our ability to reason, and our susceptibility to many diseases, are unique to us. We hope that by comparing our genome sequence to that of the Neandertal, or closest, but now extinct relative, we will identify the changes that occurred in our genome that led to the rise of unique human traits.