Strengthening global-change science by integrating aeDNA with paleoecoinformatics

Ancient environmental DNA (aeDNA) data are close to enabling insights into past global-scale biodiversity dynamics at unprecedented taxonomic extent and resolution. However, achieving this potential requires solutions that bridge bioinformatics and paleoecoinformatics. Essential needs include support for dynamic taxonomic inferences, dynamic age inferences, and precise stratigraphic depth. Moreover, aeDNA data are complex and heterogeneous, generated by dispersed researcher networks, with methods advancing rapidly. Hence, expert community governance and curation are essential to building high-value data resources. Immediate recommendations include uploading metabarcoding-based taxonomic inventories into paleoecoinformatic resources, building linkages among open bioinformatic and paleoecoinformatic data resources, harmonizing aeDNA processing workflows, and expanding community data governance. These advances will enable transformative insights into global-scale biodiversity dynamics during large environmental and anthropogenic changes

Ancient DNA from marine sediments: Precautions and considerations for seafloor coring, sample handling and data generation

The study of ancient DNA (aDNA) from sediments (sedaDNA) offers great potential for paleoclimate interpretation, and has recently been applied as a tool to characterise past marine life and environments from deep ocean sediments over geological timescales. Using sedaDNA, palaeo-communities have been detected, including prokaryotes and eukaryotes that do not fossilise, thereby revolutionising the scope of marine micropalaeontological research. However, many studies to date have not reported on the measures taken to prove the authenticity of sedaDNA-derived data from which conclusions are drawn. aDNA is highly fragmented and degraded and extremely sensitive to contamination by non-target environmental DNA. Contamination risks are particularly high on research vessels, drilling ships and platforms, where logistics and facilities do not yet allow for sterile sediment coring, and due consideration needs to be given to sample processing and analysis following aDNA guidelines. This review clarifies the use of aDNA terminology, discusses common pitfalls and highlights the urgency behind adopting new standards for marine sedaDNA research, with a focus on sampling optimisation to facilitate the incorporation of routine sedaDNA research into International Ocean Discovery Program (IODP) operations. Currently available installations aboard drilling ships and platforms are reviewed, improvements suggested, analytical approaches detailed, and the controls and documentation necessary to support the authenticity of aDNA retrieved from deep-sea sediment cores is outlined. Beyond practical considerations, concepts relevant to the study of past marine biodiversity based on sedaDNA, and the applicability of the new guidelines to the study of other contamination-susceptible environments (permafrost and outer space) are discussed.The above-named workshop was supported by the Macquarie University Marine Research Centre (MQMarine), the Department of Biological Sciences, and the Faculty of Science and Engineering, Macquarie University, North Ryde, Australia. LA was supported by the Australia and New Zealand IODP Consortium (ANZIC) 2017 Special Analytical Funding and MQMarine. MJLC was supported by Australian Research Council's (ARC) Discovery Projects DP160102587 and DP18100982 as well as by ANZIC (IODP Exp. 364 post cruise funding). LKA and SCG were supported by the ARC LIEF funding scheme LE160100067 provided to ANZIC. MO was supported by an ARC Discovery Project DP15012326. MO and AF were supported by an ARC Laureate Fellowship FL14010021 to Ian Paulsen. MS acknowledges the support of ARC Linkage Project LP160100839. JWM acknowledges the support of ARC Discovery Project DP110103668. AC is supported by ARC Laureate Fellowship (FL140100260) and LSW by ARC Future Fellowship (FT180100407), both AC and LSW are also supported by the ARC Centre of Excellence for Australian Biodiversity and Heritage (CABAH; 170100015CE). NRF was funded by the University of Adelaide RTP scholarship. FL is supported by an Early Postdoc Mobility fellowship from the Swiss National Science Foundation