THE ANALYSIS OF ANCIENT DNA: FROM MITOCHONDRIA TO PATHOGENS

Ancient DNA (aDNA) is arguably one of the most difficult science fields to work in due to the constant battle against contamination and degradation; however, it is also one of the most rewarding. aDNA researchers have consistently garnered interest the world over with their findings and sparking the curiosity of many who wish to know more about who we are as Homo sapiens. Mitochondrial DNA (mtDNA) and pathogen DNA were used in this dissertation to understand more about where populations came from, how they moved, and what their environment was like through the identification of their maternally inherited mtDNA and pathogens. This is a synthesis of my work and collaboration with other researchers both in lab and at the computer to add more data to the story of humankind

Reconstruction of ancient microbial genomes from the human gut

Loss of gut microbial diversity in industrial populations is associated with chronic diseases, underscoring the importance of studying our ancestral gut microbiome. However, relatively little is known about the composition of pre-industrial gut microbiomes. Here we performed a large-scale de novo assembly of microbial genomes from palaeofaeces. From eight authenticated human palaeofaeces samples (1,000–2,000 years old) with well-preserved DNA from southwestern USA and Mexico, we reconstructed 498 medium- and high-quality microbial genomes. Among the 181 genomes with the strongest evidence of being ancient and of human gut origin, 39% represent previously undescribed species-level genome bins. Tip dating suggests an approximate diversification timeline for the key human symbiont Methanobrevibacter smithii. In comparison to 789 present-day human gut microbiome samples from eight countries, the palaeofaeces samples are more similar to non-industrialized than industrialized human gut microbiomes. Functional profiling of the palaeofaeces samples reveals a markedly lower abundance of antibiotic-resistance and mucin-degrading genes, as well as enrichment of mobile genetic elements relative to industrial gut microbiomes. This study facilitates the discovery and characterization of previously undescribed gut microorganisms from ancient microbiomes and the investigation of the evolutionary history of the human gut microbiota through genome reconstruction from palaeofaeces

The Forgotten Epidemic: Identification of MTBC in the Neolithic Trypillia of Verteba Cave, Ukraine

Microorganisms have plagued humankind for millennia and frequently participate in an evolutionary arms race against their hosts. Diseases from various microorganisms have crippled entire countries or led to massive population declines in recent history. However, much is unknown about epidemiology in ancient times. My project will be the first comprehensive paleoepidemiological approach to understand disease across populations in Europe during the Neolithic era (7000-1700BC). The Neolithic was one of the most profound transformations in human history, both culturally and biologically. Massive migrations, formations of the earliest settlements in Europe, and introduction of agriculture and pastoralism led to new environments for humans, domesticates, and microorganisms. By analyzing over 1000 genomes from across Europe, I will be able to identify certain pathogens in specific populations. This data will be coupled with archaeology and linguistics data to begin tracing the group’s movements to understand the disease dynamics and how disease started and spread. Eventually, a broad picture will be painted of the entire ancient history of disease on the European continent. This research will provide understanding of largescale disease progression and its many variables including cultural subsistence, population migration, and pathogen evolution. Conclusions from this research can be used as case studies for current or future disease outbreaks and the genetic information obtained from pathogens can potentially be used to identify ways around resistant strains, such as the modern Tuberculosis resistant strains