Biology subjects

Ishiya, K.

Publications and source records attributed to Ishiya, K..

3 recordsLinked to original sources

bioRxiv2025

Towards On-Site Paleogenomics: Application and Perspective of Nanopore Sequencing with Ancient DNA

Ancient DNA (aDNA) research has greatly advanced understanding of past populations, yet progress in this field is still limited by two fundamental issues: dependence on fixed laboratory infrastructure and ethical considerations surrounding the cross-border transfer of archaeological biological specimens. In this study, we present the first successful application of Oxford Nanopore Technologies (ONT) sequencing to authentic aDNA from ancient human remains dating to the Early Jomon period. Our results demonstrate that nanopore platforms can recover characteristic postmortem damage signatures, generate genome-wide information with time-stamped sequencing data, and produce population genetic inferences consistent with Illumina short-read data. Crucially, the ONT sequencing has enabled the first demonstration of time-resolved aDNA analysis. This enables key genetic metrics, such as biological sex inference, to be determined within the first 60 minutes of sequencing. The portability and operational simplicity of ONT devices provide a practical basis for on-site paleogenomics, facilitating the generation of genomic data directly at archaeological sites, in museums, or at local research institutions. This capability is particularly significant in regions where the export of biological specimens entails administrative procedures, often spanning several months or even years. By enabling local archaeologists and anthropologists to independently generate and interpret genomic data, on-site nanopore sequencing can accelerate global research alliance, and promote equitable scientific authorship and continuing dialogue on sample sovereignty and collaborative research practices between geneticists and field researchers. Together, our findings establish nanopore sequencing as a socially sustainable and viable tool for paleogenomics, offering new pathways for the rapid, field-deployable and ethical process of archaeological remains.

genomics↗

bioRxiv2025

High-Coverage Jomon Genomes Provide Insights into Population Structure and Genetic Traits of Ancient Japanese Hunter-Gatherers

We analyzed eight high-coverage Jomon genomes spanning 9,000-2,800 years ago across the Japanese archipelago. Population genomic analyses revealed substantial genetic homogeneity across time and space reflecting post-glacial isolation, yet temporal stratification emerged: Initial Jomon (Iyai) individuals formed the earliest branch with weaker affinities to present-day Japanese. Using genomes from Todoroki and Chidorikubo sites, we estimated Jomon ancestry in mainland Japanese at [~]20%, substantially higher than previous estimates ([~]13%). Polygenic score analyses, based on the direct analysis of Jomon genomes, provided the genetic evidence for their phenotypic predispositions, including elevated BMI and metabolic trait scores, reduced immune-related scores, and larger cardiac dimensions, patterns consistent with hunter-gatherer adaptations. These ancestral genetic influences, including elevated risks for obesity and dyslipidemia, persist in present-day Japanese. Our findings demonstrate that Jomon populations maintained genetic continuity despite ecological diversity, while their greater-than-expected contribution to present-day Japanese reshapes population history models and reveals how ancient adaptations continue influencing contemporary disease susceptibility.

genomics↗

bioRxiv2024

High-coverage genome sequencing of Yayoi and Jomon individuals shed light on prehistoric human population history in East Eurasian

The migration of prehistoric humans led to intriguing interactions and changes in cultural and genetic heritage. In Eurasia, prehistoric migration and population replacement have affected present-day humans. The available high-quality genetic evidence for prehistoric migration in eastern Eurasia, particularly in the Far East, is still limited. We succeeded in obtaining low-contaminant, high-coverage genomes from middle-Yayoi (>46-fold coverage) and Initial Jomon (>67-fold coverage) individuals from mainland Japan. This study demonstrated that the Yayoi individual exhibited a genetic profile distinct from that of the indigenous Jomon population of the Japanese archipelago, suggesting that Yayoi ancestry was connected to the peopling of the Eurasian continent. Our high-coverage genome provides interesting insights into the evolution of copy number polymorphisms related to the dietary styles of ancient Japanese people. The copy number estimates of the amylase gene for the Yayoi individual were comparable to those of present-day East Asians who have diets high in starch. This suggests that the population in the middle Yayoi period may have already adapted to high-starch diets, which may have been related to paddy rice agriculture introduced from the continent. Furthermore, the individual from the initial Jomon period showed high amylase copy numbers comparable to those from modern East Eurasia, including modern Japanese. This suggests that some Jomon people may have consumed a high-starch diet then. The high-coverage whole-genome sequence also revealed differences in the demographic backgrounds of the two ancestral populations during the Yayoi and Jomon periods. Our results shed light on the prehistorical events and origins of related migrations from Eurasia at that time and their genetic background, cultural transformations, and links to modern Japanese people.

genomics↗