Integrating multi-taxon palaeogenomes and sedimentary ancient DNA to study past ecosystem dynamics

Abstract

Ancient DNA (aDNA) has played a major role in our understanding of the past. Important advances in the sequencing and analysis of aDNA from a range of organisms have enabled a detailed understanding of processes such as past demography, introgression, domestication, adaptation and speciation. However, to date and with the notable exception of microbiomes and sediments, most aDNA studies have focused on single taxa or taxonomic groups, making the study of changes at the community level challenging. This is rather surprising because current sequencing and analytical approaches allow us to obtain and analyse aDNA from multiple source materials. When combined, these data can enable the simultaneous study of multiple taxa through space and time, and could thus provide a more comprehensive understanding of ecosystem-wide changes. It is therefore timely to develop an integrative approach to aDNA studies by combining data from multiple taxa and substrates. In this review, we discuss the various applications, associated challenges and future prospects of such an approach.

Keywords: ecosystem shifts; extinction; integrative; palaeogenomes; sedaDNA.

Figure 1.

Workflow for the integration of multi-taxon palaeogenomes and sedaDNA. Silhouettes are from PhyloPic.org. (Online version in colour.)

Figure 2.

Conceptual illustration of joint analysis of aDNA from multiple substrates. Red and black lines depict hypothetical changes in effective population size (N_e) inferred from the palaeogenomes of two distinct taxa (e.g. from a PSMC analysis). Filled bar colours represent three different ecosystem states (A–C) derived from sedaDNA. In this example, there are two distinct ecosystem state shifts. The N_e of taxon 1 is in decline prior to the ecosystem state shift from A to B. Its N_e remains stable after humans appear (dark blue line) but crashes during the shift from ecosystem state B to C. By contrast, the N_e of taxon 2 rapidly increases during the first ecosystem state shift (A–B), and again increases after the appearance of humans. The N_e of taxon 2 is unaffected by the second ecosystem state shift (B–C). Silhouettes are from PhyloPic.org. (Online version in colour.)