MetaDamage Tool: Examining post-mortem damage in sedaDNA on a metagenomic scale

Abstract

Authentication of ancient sedimentary DNA (sedaDNA) remains central to the interpretation of the proxy for wider understanding of palaeoecological archives. Distinguishing between in-situ, endogenous sedaDNA from that of contamination or modern material also allows for a wider understanding of taphonomy in the deposition and post-depositional process in the formation of the sedaDNA archive. At current, tools for authentication are reliant on single-taxon input and require a significant number of input sequences to identify an established cytosine deamination rate consistent with ancient DNA. We present the MetaDamage tool: a tool that examines cytosine deamination on a metagenomic scale. In this paper we outline the process of and testing of the MetaDamage tool using both authentic sedaDNA sequences and simulated data in order to demonstrate the resolution in which MetaDamage can observe deamination levels consistent with the presence of ancient DNA. The MetaDamage tool offers a method for initial assessment of the presence of ancient sedaDNA and provides a method for a wider understanding of key questions of preservation for palaeoecological reconstruction.