Using sedaDNA in ecological studies
The use of sedaDNA in ecological studies is currently limited, but it is emerging as a powerful methodological framework as specialised statistical analyses are being developed (Chen & Ficetola, 2020). Techniques for the extraction, isolation and downstream analysis of ancient DNA are now so advanced that ancient sediments can be used as a genetic substrate to complement, or replace, traditional sub-fossil taxonomic identification (Pansu et al., 2015; Pérez, Liu, Hengst, & Weyrich, 2022; Slon et al., 2017; Thomas et al., 2022). Recovered sedaDNA has come from across the tree of life, including microbes, plants, and animals (Chen & Ficetola, 2020; Pansu et al., 2015; Pérez et al., 2022; Slon et al., 2017; Thomas et al., 2022; Willerslev et al., 2003).
The prospect of extracting genetic material from sediments with stable strata would allow a high-resolution temporal view of the landscape and offer new insights into ecological variation. Recent evidence from Denisova cave suggests that millimetre-scale sediment horizons can be locally stabilised over time (Massilani et al., 2022). The translocation of sedimentary strata, however, whether by climatic or biotic forces, will likely remain the primary confounding factor in sedaDNA studies (Pedersen et al., 2015). Natural variation in geology and biotic factors will mean the severity of stratum translocation will likely vary within and between sites. To address this, Massilani et al. (2022) assert that their technique of impregnating sediment samples with resin not only reduces post-sampling translocation but also allows for clearer assessment of post-depositional movement.
Viable sedaDNA was initially recovered in areas of permafrost when researchers at the University of Copenhagen successfully extracted DNA from sedimentary (dry silty) cores in Aotearoa New Zealand (Willerslev et al., 2003). They also extracted extinct moa DNA from the sand in direct contact with a moa bone. Mitochondrial DNA has been successfully recovered from a variety of species across the mid to late Pleistocene (Slon et al., 2017). Denisova cave has yielded hominin mtDNA between ~100ka to ~200ka (Slon et al., 2017; Vernot et al., 2021). More recently, shotgun sequencing of 25ka-old European sediments allowed the retrieval of genome-wide sequences from humans, wolves and bison, offering insights into the recent evolution of all three species (Gelabert et al., 2021).