Hybridisation capture allows DNA damage analysis of ancient marine eukaryotes

Marine sedimentary ancient DNA (sedaDNA) is increasingly used to study past ocean ecosystems, however, studies have been severely limited by the very low amounts of DNA preserved in the subseafloor, and the lack of bioinformatic tools to authenticate sedaDNA in metagenomic data. We applied a hybridisation capture baits technique to target marine eukaryote sedaDNA (specifically, phytoplankton, Phytobaits1; and harmful algal bloom taxa, HABbaits1), which resulted in up to 4- and 9-fold increases, respectively, in the relative abundance of eukaryotes compared to shotgun sequencing. We further used the new bioinformatic tool HOPS to authenticate the sedaDNA component, establishing a new proxy to assess sedaDNA authenticity, the Ancient: Default (A:D) sequences ratio, here positively correlated with subseafloor depth, and generated the first-ever DNA damage profiles of a key phytoplankton, the ubiquitous coccolithophore Emiliania huxleyi. Our study opens new options for the detailed investigation of marine eukaryotes and their evolution over geological timescales.