〇Hiroki OOTA (The University of Tokyo), Izumi NAKA (The University of Tokyo), Daisuke WAKU (Tokyo University of Agriculture), Takashi GAKUHARI (Kanazawa University), Osamu KONDO (The University of Tokyo), Soichiro MIZUSHIMA (St.Marianna University School of Medicine)
Objectives and Directions of the Study
At our laboratory, we are advancing ancient genome analysis, targeting materials such as ancient human bones, coprolites, and ancient soils. The history of research in this field traces back to the earliest genome analysis of ancient human bones, which has accumulated substantial expertise and data internationally. In contrast, the analysis of genomes from coprolites and ancient soils is relatively recent, with methodologies ranging from DNA extraction to in silico analysis still under development.
Due to established DNA extraction methods from ancient human bones, stable results can be obtained quite reliably, barring specimens where DNA is completely degraded. Research themes when analyzing ancient human bones can broadly be classified into two categories: (1) population demographic analysis and (2) kinship analysis. Within the latter category, considerations such as phylogenetic lineage, migration patterns, and detection of natural selection are encompassed. Lineage and population demographic analyses leverage classical theories in population genetics, with established methodologies. However, kinship analysis remains a significant challenge due to the instability of data analysis methods internationally, particularly with damaged ancient DNA, where analysis programs, although available, can yield inaccurate results depending on usage.
Studies targeting coprolites can be categorized into two main objectives: (3) aiming for dietary identification and (4) aiming for identification of ancient pathogens. The latter object broadly aims for paleopathological data. Coprolites retain DNA, including that of the individual who excreted them, as well as DNA from consumed food, intestinal bacteria, and viruses. Analyzing the genomic information obtained in this mixed state involves searching for and classifying species-specific nucleotide sequences, predominantly carried out computationally. However, at present, this computational analysis (in silico analysis) holds a greater number of challenges to overcome.
Similarly, while ancient soil DNA also presents numerous challenges for in silico analysis, the absolute scarcity of obtained ancient DNA poses a greater obstacle. Nonetheless, establishing a robust framework for analyzing DNA from ancient soils holds the potential for achieving objectives such as (5) reconstructing ancient environments and (6) conducting human DNA analysis in archaeological sites where ancient human bones are not found.
In our research group, we collaborate with other members of Team A02 to address these myriad challenges.