The Impact of European Contact on Native American Evolutionary History

该奖学金项目的目的是通过分析来自美国南部的当代和古代美洲原住民的全基因组多样性模式，研究欧洲接触（EC）对美洲原住民基因组多样性的影响。许多遗传学研究调查了美洲原住民的起源和早期历史，但相对较少关注最近的进化历史以及选择，迁移和遗传漂变对美洲原住民基因组多样性的影响。然而，自从欧洲接触以来，美洲原住民经历了反复的流行病，人口崩溃和与非原住民的基因交换（混合）。如果我们要准确地重建美洲原住民的进化历史，并在其他研究中解释种群遗传结构，那么我们就必须测试这些事件是否以及如何重塑土著种群的遗传结构。此外，该项目还为西班牙裔女性博士后研究员提供研究和培训机会，以培养她在科学和学术界取得成功所需的技术和流程技能。该项目还为来自代表性不足群体的学生提供研究经验和指导，包括一些来自参与的美洲原住民社区的学生。此外，该项目制定了一个基于社区的参与性研究模式，为未来的遗传研究，它通过广泛的推广到土著community.While一些研究表明，混合和人口崩溃后，EC影响美洲原住民的遗传多样性，没有研究充分评估后EC发生的遗传变化。现有的数据集不足以达到这一目的，因为很少有研究研究检查了全基因组变异，并且分析了相对较少的前EC样本。由于这些限制，我们对美洲原住民的遗传构成或欧洲接触的遗传影响知之甚少。该项目克服了这些缺陷，有两个主要的研究目标：（1）评估前EC和当代（后EC）北美原住民的基因组多样性，（2）通过测量后EC人口崩溃，选择和混合的影响来评估EC的遗传影响。该项目使用新开发的微阵列和下一代测序技术，并实施一种新的比较方法。PI团队分析了629，443个全基因组SNP，以评估EC后人群的多样性模式。他们还分析了来自同一地理区域的前EC埋葬人群的古代DNA样本中约370，000个相同的SNP，以跟踪美洲原住民基因库随时间的变化。这项研究的重点是当代和古代人口从美国南部，EC首先发生在北美。该项目旨在产生一个前所未有的数据集，将全基因组覆盖范围与跨越广泛时间范围的人口样本相结合。有了这个数据集，它将成为可能来衡量漂移，选择和混合后EC的影响，提供了第一个全面的测试的假设，EC重塑了美洲原住民人口的遗传结构。该项目有可能改变我们对美国南部美洲原住民遗传多样性和进化历史的理解，并提高我们在疾病关联研究中解释当前人群遗传结构的能力。它还可以让我们了解社会文化变化如何影响人类基因组。

The objective of this Fellowship project is to investigate the impact of European contact (EC) on Native American genomic diversity by analyzing genome-wide diversity patterns in contemporary and ancient Native Americans from the southern US. Many genetic studies have investigated the origins and early history of Native Americans, but comparatively little attention has been given to recent evolutionary history and the impact that selection, migration, and genetic drift have had on Native American genomic diversity over the last five centuries. However, since European Contact, Native Americans have experienced repeated epidemics, demographic collapse, and genetic exchange (admixture) with non-native peoples. It is critical that we test whether and how each of these events reshaped the genetic structure of indigenous populations if we are to accurately reconstruct Native American evolutionary history and account for population genetic structure in other studies. In addition, this project provides research and training opportunities for a female Hispanic postdoctoral researcher to develop the technical and process skills necessary for her to succeed in science and in academia. The project also provides research experience and mentoring for students from underrepresented groups, including some from participating Native American communities. Additionally, this project formulates a community-based participatory research model for future genetic studies, and it integrates education and research through extensive outreach to indigenous communities.While some research suggests that admixture and the population collapse after EC influenced Native American genetic diversity, no study has fully assessed the genetic changes that occurred after EC. Existing datasets are insufficient for this purpose because few studies have examined genome-wide variation and relatively few pre-EC samples have been analyzed. Because of these limitations, we know remarkably little about the genetic makeup of Native American populations or about the genetic impact of European Contact. This project overcomes these deficiencies and has two major research goals: (1) assess the genomic diversity in pre-EC and contemporary (post-EC) Native North Americans, and (2) evaluate the genetic impact of EC by measuring the effects of post-EC demographic collapse, selection, and admixture. This project uses newly developed microarray and next-generation sequencing technologies and implement a novel comparative approach. The PI-team analyzes 629,443 genome-wide SNPs to evaluate diversity patterns in a post-EC population. They also analyze ~370,000 of the same SNPs in ancient DNA samples from pre-EC burial populations in the same geographic region to track changes in the Native American gene pool over time. This study focuses on contemporary and ancient populations from the southern US, where EC first occurred in North America. This project is designed to produce a dataset that is unprecedented in combining genome-wide coverage with population samples spanning a wide temporal range. With this dataset, it will become possible to measure the effects of drift, selection, and admixture following EC, providing the first comprehensive test of the hypothesis that EC reshaped the genetic structure of Native American populations. This project has the potential to transform our understanding of Native American genetic diversity and evolutionary history in the southern US, and improve our ability to account for current population genetic structure in disease association studies. It can also inform our understanding of how sociocultural change influences the human genome.