DNA POLYMORPHISMS IN NORTHERN NATIVE AMERICANS

北美原住民的 DNA 多态性

• 批准号: 2181029
• 负责人: RICHARD H WARD
• 金额: $ 24.38万
• 依托单位: UNIVERSITY OF UTAH
• 依托单位国家: 美国
• 财政年份: 1989
• 资助国家: 美国
• 起止时间: 1989-04-01 至 1996-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/2181029
• 关键词: Alaskan Native American; alleles; biochemical evolution; clinical chemistry; computer assisted sequence analysis; gene frequency; genetic markers; genetic polymorphism; haploidy; human genetic material tag; human population distribution; human population genetics; human subject; linkage mapping; mitochondrial DNA; nucleic acid sequence; polymerase chain reaction; sex chromosomes; statistics /biometry

DESCRIPTION: This a resubmission of a proposal designed to characterize the genetic structure of selected groups of Northern Native Americans with a number of questions relating to their origin and population structure. The proposal will examine genetic variation in three linguistic groups where the proposed sampling strategy is designed to be balanced with respect to characterizing intra- and interpopulation differences; this will include two tribes of the Eskimo-Aleut, three tribes of the Na-Dene, and three tribes of the Amerid. Samples from each tribe will consist of 25 mother-father-offspring trios. This will result in approximately 75 individuals per tribe and 600 individuals overall. Genetic characterizations will focus on mitochondrial genomes, Y chromosome restriction site markers, and estimates of variation in a sample of nuclear genes including 30 microsatellite loci and four-locus haplotypes at seven well characterized autosomal regions. From this data set sequence divergence within and between populations will be estimated and characterized. A number of questions will be addressed: First, it will be possible to address the hypothesis that mtDNA lineages among the Eskimo-Aleut and Na-Dene show lower sequence diversity and thus a shorter evolutionary history than the Amerid. Second, it will be asked if the distribution of Y-associated, and thus patrilinearily transmitted haplotypes are congruent with matrilinearily inherited mtDNA lineages. This will examine the potential contribution of differential migration or fertility among males and females. The congruence of mtDNA and nuclear genes, in particular presumedly neutral microsatellite loci, will be assessed. If hypotheses concerning invasion times and population structure based on mtDNA are true then nuclear genes should show concordant features, such as reduced variation in the Eskimo-Aleut and Na-Dene compared to the Amerid. Mitochondrial sequence data will be collected by directly sequencing the non-coding control region and the NAD5 (nicotamide adenine dinucleotide dehydrogenase subunit 5) region. This involves sequencing 375 bases of the non-coding control region and the first 350-360 bases of NAD5 by established PCR-based methods using solid support biotinylated primer methods. To provide information about deep splits in the mitochondrial genealogy it is also proposed to examine informative restriction sites polymorphisms in the coding regions. These mtDNA sites have already been identified in other groups. Nuclear regions will be characterized by a variety of methods, all restriction site based from either total genomic DNA, or PCR amplified fragments. These nuclear regions are already well characterized in other diverse ethnic groups, thus providing a perspective of variation. These seven regions (HLA, ApoB, ApoAI CIII/AIV, LDLR, PAH, CFTR, and HBB) also are associated with diseases and have clinical importance. Finally a highly information rich set of microsatellite "loci" will be screened. This involves generating data on 30 loci localized to chromosomes 13 and 15 and will identify 240 alleles. A number of conventional statistical analyses are proposed to estimate allele and haplotype frequencies, test for departure from Hardy-Weinberg and examine linkage disequilibrium which can also be used in the analysis of population structure. Maximum likelihood methods such as available in Felsenstein's PHYLIP package will be used to construct molecular genealogies. These will be useful not only in reconstructing lineage affinities, but also will permit identification of admixture events. Actual tests of diversity across the hierarchical design will be tested using the AMOVA technique. Traditional tests using F- statistics will also be carried out on the nuclear polymorphisms, and Mantel test will be used to test concordance of different sets of markers. Finally, the PI proposes a series of continuing collaborations to investigate specific features of the molecular evolution of mtDNA in humans, and its ability to reflect aspects of historical demography. These include evaluating how demographic fluctuations such as population size changes and geographic subdivision influence the properties of the coalescent using both analytical and computer simulation strategies.

描述：这是重新提交的提案，旨在描述 选定的北美洲原住民群体的遗传结构 与他们的起源和人口有关的一些问题 结构。该提案将检查三个方面的遗传变异 所提出的抽样策略旨在 在描述群体内和群体间的特征方面保持平衡 差异；这将包括两个爱斯基摩-阿留申部落、三个 纳德尼部落和美洲人的三个部落。每个样本 部落将由 25 个母亲、父亲、后代三人组组成。这将 结果每个部落大约有 75 个人，每个部落大约有 600 个人 全面的。遗传特征将集中于线粒体基因组， Y 染色体限制性位点标记和变异估计 核基因样本，包括30个微卫星位点和4个位点 七个特征明确的常染色体区域的单倍型。 从该数据集可以看出群体内部和群体之间的序列差异 将被估计和表征。将会提出一些问题 解决：首先，可以解决以下假设： 爱斯基摩-阿留申人和 Na-Dene 之间的 mtDNA 谱系显示出较低的序列 多样性，因此进化历史比美洲人更短。 其次，会询问Y的分布是否相关，从而 父系传递的单倍型与母系传递的单倍型一致 遗传线粒体DNA谱系。这将检查潜在的贡献 男性和女性之间的迁移或生育能力差异。这 mtDNA 和核基因的一致性，特别是假定中性的 将评估微卫星位点。如果有关假设 那么基于 mtDNA 的入侵时间和种群结构是真实的 核基因应表现出一致的特征，例如变异减少 爱斯基摩-阿留申人和纳-德内人与美洲人相比。 线粒体序列数据将通过直接测序来收集 非编码控制区和 NAD5（烟酰胺腺嘌呤二核苷酸） 脱氢酶亚基5)区域。这涉及对 375 个碱基进行测序 非编码控制区和 NAD5 的前 350-360 个碱基 使用固相生物素化引物建立基于 PCR 的方法 方法。提供有关线粒体深度分裂的信息 谱系学还建议检查信息限制位点 编码区的多态性。这些线粒体DNA位点已经 在其他组中已被识别。核区域将被表征 通过多种方法，所有限制位点均基于任一总 基因组 DNA 或 PCR 扩增片段。这些核区是 在其他不同种族群体中已经得到了很好的表征，因此 提供变化的视角。这七个区域（HLA、ApoB、 ApoAI CIII/AIV、LDLR、PAH、CFTR 和 HBB）也与 疾病并具有重要的临床意义。最后来个信息量很大的 将筛选丰富的微卫星“位点”。这涉及到 生成位于 13 号和 15 号染色体的 30 个基因座的数据，并将 鉴定出 240 个等位基因。 提出了许多传统的统计分析来估计 等位基因和单倍型频率，测试是否偏离 Hardy-Weinberg 并检查连锁不平衡，也可用于 人口结构分析。最大似然法，例如 Felsenstein 的 PHYLIP 包中提供的将用于构建 分子谱系。这些不仅有助于重建 血统亲缘关系，但也将允许识别混合物 事件。跨层次设计的多样性的实际测试将 使用 AMOVA 技术进行测试。使用 F- 的传统测试 还将对核多态性进行统计， Mantel 测试将用于测试不同组的一致性 标记。 最后，PI 提出了一系列持续合作的建议 研究 mtDNA 分子进化的具体特征 人类及其反映历史人口统计各个方面的能力。 其中包括评估人口等人口波动如何 规模变化和地理细分会影响其属性 使用分析和计算机模拟策略进行合并。