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

博士论文研究：古代病原体的基因组研究和征服的影响

• 批准号: 2141920
• 负责人: Lars Fehren-Schmitz
• 金额: $ 3万
• 依托单位: University of California-Santa Cruz
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-04-15 至 2025-03-31
• 项目状态: 未结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2141920&HistoricalAwards=false
• 关键词: Doctoral; Dissertation; Research; Genomic; Investigation

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.

当人类群体首次接触时，疾病可以通过以前未接触的人群迅速传播。过去，人们认为初次接触期间的疾病导致了大规模死亡，并可能影响殖民化尝试的结果。这个博士论文项目使用古老的DNA数据来检测与征服和殖民有关的病原体，并确定病原体是如何进化的，以及为什么它们如此致命。该项目的成果可以促进对殖民化后果以及疾病演变和生态学的了解，其中许多疾病今天仍然难以治疗和控制。研究人员强调与后裔社区和社区利益攸关方的实质性合作。当地社区积极参与该项目，研究有助于这些地区的教育材料和博物馆展览。该项目还促进科学传播和公共宣传活动，并为本科生提供实验室培训，包括STEM中代表性不足的群体的学生。这个古老的病原体基因组学项目旨在确定哪些特定病原体在欧洲征服期间导致土著人的广泛死亡，这些疾病如何在新环境中演变，以及不同的环境和/或文化习俗如何导致疾病传播或死亡率结果的差异。该研究分析了来自四个战略性选择的早期接触时代不同生态和文化环境的遗址的大约200个个体的数据。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进行测序，确定它们的进化树，确认它们的欧洲起源，发现它们如何以及何时进化成现代菌株，并检测杂交或多样化事件。在有足够数据的情况下，研究人员还进行功能分析，通过特定的定义标记来识别变体，例如对毒力或致病性重要的任何基因丢失或获得。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视角。该奖项反映了NSF的法定使命，并被认为值得通过使用基金会的知识价值和更广泛的影响审查标准进行评估来支持。