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.
