Human population genomics in time and space: comparing ancient and modern genomes

描述（由申请人提供）：该项目的目标是比较古代和现代人类基因组中功能变异的模式。来自一系列时间段（公元前6300年至公元前400年，每个时间段至少有10个人）和保加利亚地点的至少50个古代人类个体的DNA将从牙齿中提取，并使用最近开发的方法进行测序，用于靶向全基因组捕获，然后进行全基因组测序。这将是第一次从一系列时间段的古代个体群体中获得基因组序列的研究。将对结果进行分析，以确定这些个体与其他古代个体和现代人群的遗传关系。此外，这些基因组中的功能变异将被检查，以检验变异的假设，包括有害突变的负荷，在过去的10,000年中，由于农业的发明所产生的人口爆炸而增加。这一假说由种群遗传学理论预测，可以用古代DNA进行最直接的检验。我将通过三个具体目标来实现这些目标：首先，我将对来自保加利亚不同地理区域和时期的50个人的牙齿进行古代DNA测序。首先对提取的DNA进行靶向全基因组捕获以富集内源性序列，并使用Illumina技术以低覆盖率对所得文库进行测序，以评估样品中的人类DNA水平。来自至少50个通过严格质量控制标准的样本的DNA将被测序， 覆盖的水平。其次，我将使用常染色体，线粒体和Y染色体变异来追踪人口的身份和运动随着时间的推移。我将确定古代个体的线粒体和Y染色体单倍群，并将它们与现代人群的单倍群进行比较。此外，我将使用全基因组测序数据来分析这些古老基因组中的常染色体变异，并与包括1，000个基因组，人口参考样本（PopRES）和人类基因组多样性小组（HGDP）在内的参考小组进行比较。最后，我将比较古代和现代人类基因组的功能变异模式。我将使用三个标准对古代和现代基因组中的变异进行分类：对氨基酸序列的影响;基于进化保守性和对蛋白质结构影响的计算方法的功能预测;以及人类疾病突变数据库中的存在。然后，我将比较古代与现代基因组中有害变异与中性变异的相对频率，以评估现代人口是否像理论预测的那样积累了不成比例的有害变异。这些分析的结果可以揭示决定现代和古代人类种群功能变异谱的人口统计学过程。!

DESCRIPTION (provided by applicant): The goal of this project is to compare patterns of functional variation in the genomes of ancient and modern human populations. DNA from at least 50 ancient human individuals from a range of time periods (6300 BC- 400 BCE, with at least 10 individuals from each time period) and locations in Bulgaria will be extracted from teeth and sequenced using a recently developed method for targeted whole-genome capture followed by whole-genome sequencing. This will be the first study to obtain genome sequences from populations of ancient individuals from a range of time periods. The results will be analyzed to determine the genetic relationships of these individuals to other ancient individuals and to modern populations. In addition, functional variation in these genomes will be examined to test the hypothesis that variation, including the load of deleterious mutations, has increased over the last 10,000 years as a result of the human population explosion produced by the invention of agriculture. This hypothesis, predicted by population genetic theory, can be most directly tested using ancient DNA. I will accomplish these goals through three specific aims: First, I will sequence ancient DNA from the teeth of 50 individuals from different geographical areas and time periods in Bulgaria. The extracted DNA will first be subjected to targeted whole-genome capture to enrich for endogenous sequences, and the resulting library will be sequenced at low coverage using Illumina technology to assess the levels of human DNA in the samples. DNA from at least 50 samples that pass strict quality control criteria will then be sequenced to higher levels of coverage. Secondly, I will use autosomal, mitochondrial, and Y-chromosomal variation to trace population identities and movements over time. I will determine the mitochondrial and Y-chromosomal haplogroups of the ancient individuals and compare them to those of modern populations. In addition, I will use the whole-genome sequencing data to analyze autosomal variation in these ancient genomes by comparing to reference panels including 1,000 Genomes, the Population Reference Sample (POPRES), and the Human Genome Diversity Panel (HGDP). Finally, I will compare patterns of functional variation in ancient and modern human genomes. I will categorize variation in ancient and modern genomes using three criteria: impact on the amino acid sequence; functional prediction by computational methods based on evolutionary conservation and effect on protein structure; and presence in databases of human disease mutations. I will then compare the relative frequency of putatively damaging vs. putatively neutral variants in the ancient vs. modern genomes to assess whether, as predicted by theory, modern-day populations have accumulated a disproportionate number of deleterious variants. The results of these analyses could shed light on the demographic processes that determined the spectrum of functional variation in modern and ancient human populations. !