Collaborative Research: Strengthening Global Biodiversity Research by Building Informatics Capacity for Ancient Environmental DNA

Ancient environmental DNA (aeDNA) is transforming the scientific study of past biodiversity dynamics and the effects of past climate change and intensifying human land use. aeDNA methods permit the detection of past species by recovering ancient fragments of DNA from sediments and matching these fragments to genetic libraries of known species. Because many species preserve poorly and are thus invisible to traditional paleontological approaches, aeDNA is enabling the study of past biodiversity dynamics at an unprecedented combination of taxonomic extent and resolution; in principle the entire tree of life can be studied. aeDNA so far has been at an early stage of research, focusing on methodological refinements and discoveries at individual sites. As the number of aeDNA research teams and records rapidly grows worldwide, the next-stage scientific opportunity is to integrate these many records and thereby study biodiversity responses to past environmental change at regional to global scales. Achieving this global synthesis requires building both the advanced data platforms that can support aeDNA data sharing and the community of experts who will provide and curate this data. This award will enable the next generation of global-scale biodiversity research at unprecedented taxonomic resolution, coverage, and temporal extent, powered by 1) the integration of aeDNA data into a linked open ecosystem of paleoecological and bioinformatic resources and 2) building a closely interlinked social infrastructure that ensures high data quality, social trust, and alignment of informatics development with scientific priorities. To achieve this data integration, the data schema, curatorial systems, and data-sharing systems of the Neotoma Paleoecology Database will be extended to support aeDNA data and metadata. Linking services will be built between Neotoma and standard bioinformatic resources (NCBI/EMBL, GBIF, ORCID), so that aeDNA-based taxonomic inferences are provenanced back to standard authorities and can be regenerated as reference databases improve. To build social infrastructure and a data governance system, the project establishes a Council of aeDNA Stewards and holds annual workshops to advance data governance and metadata norms. Multiple training workshops are held for early career aeDNA researchers and virtual workshops employ a platform-agnostic Docker-based system to minimize barriers to access. Protocols and recommendations will be published in Protocols.io and peer-reviewed journals. The project develops multiple venues for engaging with high-school, college-level, and graduate-level students interested in learning more about how aeDNA can be used to study life’s responses to past environmental change.