Doctoral Dissertation Research: Genomic Investigation of Ancient Pathogens and the Implications of Conquest

当人类群体第一次接触时，疾病可以通过以前未接触过的人群迅速传播。在过去，最初接触期间的疾病被认为会导致大规模死亡，并可能影响殖民企图的结果。这个博士论文项目使用古代DNA数据来检测与征服和殖民有关的病原体，并确定这些病原体是如何进化的，以及它们为什么如此致命。项目成果可以促进对殖民后果以及疾病的进化和生态的了解，其中许多疾病今天仍然难以治疗和控制。研究人员强调与后代社区和社区利益相关者的实质性合作。当地社区积极参与该项目，这项研究为这些地区的教育材料和博物馆展品做出了贡献。该项目还促进科学交流和公共宣传活动，并为本科生提供实验室培训，包括来自STEM代表性不足群体的学生。这一古老的病原体基因组学项目旨在查明在欧洲征服期间哪些特定病原体导致土著人民广泛死亡，这些疾病如何在新的环境中演变，以及不同的环境和/或文化做法可能如何导致疾病传播或死亡结果的差异。这项研究检查了来自四个不同生态和文化环境的战略选择的早期接触时代地点的大约200个人产生的数据。研究人员使用黄金标准的古代病原体基因组学方法对这些病原体的DNA进行排序，确定它们的进化树，确认它们的欧洲起源，发现它们可能如何以及何时进化成现代菌株，并检测杂交或多样化事件。在有足够数据的地方，研究人员还进行功能分析，通过特定的定义标记来识别变异，例如任何基因丢失或获得对毒力或致病性重要的基因。除了标准的高通量基因组学和生物信息学方法，这项研究还结合了历史记载、疾病生态学和考古学背景，以揭示人类历史上关键事件的更全面的视角。这一奖项反映了NSF的法定使命，并通过使用基金会的智力优势和更广泛的影响审查标准进行评估，被认为值得支持。

When human groups first come into contact, diseases can be transmitted rapidly through previously unexposed populations. In the past, diseases during initial contact are believed to have led to mass mortality and likely influenced the outcome of colonization attempts. This doctoral dissertation project uses ancient DNA data to detect pathogens associated with conquest and colonization and determine how the pathogens evolved and why they were so deadly. The project outcomes can advance knowledge about the consequences of colonization as well as the evolution and ecology of diseases, many of which are still a struggle to treat and control today. The researchers emphasize substantive collaborations with descendant communities and community stakeholders. Local communities are actively involved in the project, and the research contributes to educational materials and museum exhibits in those regions. The project also fosters science communication and public outreach activities and provides laboratory training for undergraduates, including students from underrepresented groups in STEM.This ancient pathogen genomics project aims to identify which specific pathogens were causing the widespread deaths of Indigenous people during European conquest, how these diseases evolved in a new environment, and how different environments and/or cultural practices may have led to differences in disease spread or mortality outcomes. The study examines data generated from approximately 200 individuals from four strategically selected early contact-era sites of differing ecological and cultural environments. The researchers use gold-standard ancient pathogen genomics methods to sequence the DNA of these pathogens, determine their evolutionary trees, confirm their European origin, discover how and when they may have evolved into modern-day strains, and detect hybridization or diversification events. Where there is enough data, the researchers also perform functional analyses to identify variants through specific defining markers such as any gene loss or gain important for virulence or pathogenicity. In addition to standard high-throughput genomics and bioinformatics methods, this study incorporates historical accounts, disease ecology, and archaeological contexts to uncover a more comprehensive perspective of key events in human history.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.