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

Abstract

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.