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).