Density separation for optimised aDNA yields

Density separation is a process routinely used to segregate minerals, organic matter, and even microplastics, from soils and sediments. Here we apply density separation to archaeological bone powders prior to DNA extraction to increase endogenous DNA recovery relative to a standard control extraction of the same powders. Using non-toxic heavy liquid solutions we separated powders from the petrous bones of 10 individuals of similar archaeological preservation into 8 density intervals (2.15 to 2.45 g/cm3, in 0.05 increments). We found that the 2.30-2.35 and 2.35-2.40 g/cm3 intervals yielded up to 5.28-fold more endogenous unique DNA than the corresponding standard extraction (and up to 8.53-fold before duplicate read removal), while maintaining signals of ancient DNA authenticity and increasing library complexity. Although small 0.05 g/cm3 intervals may maximally optimise yields, a single separation to remove materials with a density above 2.40 g/cm3 yielded up to 2.57-fold more endogenous DNA on average, which may enable the simultaneous separation of samples that vary in preservation or in the type of material analysed. While requiring no new ancient DNA lab equipment and fewer than 30 minutes of extra lab work, the implementation of density separation prior to DNA extraction can substantially boost endogenous DNA yields and increase library complexity. Although subsequent studies are required, we present theoretical and practical foundations that may prove useful when applied to other ancient DNA substrates such as teeth, other bones, and sediments.