The sedimentary ancient DNA workflow

Abstract

Sedimentary ancient DNA (sedaDNA) is continuing to revolutionise our understanding of past biological and geological processes by retrieving and analysing the ancient DNA preserved in lake, cave, open terrestrial, midden, permafrozen, and marine environments (Crump, 2021). The study of sedaDNA began in the late 1990s (Coolen and Overmann, 1998) with the first reports of extinct animal sedaDNA in 2003 (Hofreiter et al., 2003; Willerslev et al., 2003). Since then, it has been shown that sedaDNA can be recovered at high resolution from recent (10¹-10² year-old) (e.g., Capo et al., 2017) through to deep-time (10⁵-10⁶ year-old) sediments from a vast diversity of environments (Crump et al., 2021; Zavala et al., 2021; Armbrecht et al., 2022; Kjær et al., 2022). Unlike traditional palaeoenvironmental and palaeoecological proxies, sedaDNA is unique in that it is derived from any type of organism that was present in the local area and that may contain population-level information. This latter characteristic means that, unlike any other comparable proxy, sedaDNA can be used for evolutionary analyses (Gelabert et al., 2021; Lammers et al., 2021; Pedersen et al., 2021; Vernot et al., 2021). <p>

<p>The advent of next-generation sequencing (NGS) provided massively enlarged, yet economically feasible, dataset sizes and increased analytical sensitivity that has allowed the field to flourish by generating robust datasets in which contamination can be detected and controlled, and hypotheses can be tested. Coupled with ongoing methodological innovations in both molecular data generation and bioinformatics analysis techniques, NGS has driven the exponential growth in sedaDNA research over the past two decades. <p>

<p>In this chapter, we present an overview of the state-of-the-art for the sedaDNA workflow. We do not present detailed methodologies and descriptions, as these have been published elsewhere (e.g., Armbrecht et al., 2019; Capo et al., 2021 and references therein). For each step in the workflow, from ethical considerations during experimental design to environmental and evolutionary inferences, we instead outline the general rationale for conducting the step, a brief overview of the approach and methods involved, pros and cons, key pitfalls, and how the current state-of-the-art is likely to develop in the near future. Importantly, we highlight that molecular and bioinformatic methods (i.e., steps presented from section ‘DNA extraction’ onwards) are still developing due to the relative infancy of the field.