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MetaDamage tool : examining post-mortem damage in sedaDNA on a metagenomic scale
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Everett, Rosie and Cribdon, Becky (2023) MetaDamage tool : examining post-mortem damage in sedaDNA on a metagenomic scale. Frontiers in Ecology and Evolution, 10 . 888421. doi:10.3389/fevo.2022.888421 ISSN 2296-701X.
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WRAP-MetaDamage-tool-examining-post-mortem-damage-in-sedaDNA-on-a-metagenomic-scale-Everett-2023.pdf - Published Version - Requires a PDF viewer. Available under License Creative Commons Attribution 4.0. Download (3156Kb) | Preview |
Official URL: http://dx.doi.org/10.3389/fevo.2022.888421
Abstract
The use of metagenomic datasets to support ancient sedimentary DNA (sedaDNA) for paleoecological reconstruction has been demonstrated to be a powerful tool to understand multi-organism responses to climatic shifts and events. Authentication remains integral to the ancient DNA discipline, and this extends to sedaDNA analysis. Furthermore, distinguishing authentic sedaDNA from contamination or modern material also allows for a better understanding of broader questions in sedaDNA research, such as formation processes, source and catchment, and post-depositional processes. Existing tools for the detection of damage signals are designed for single-taxon input, require a priori organism specification, and require a significant number of input sequences to establish a signal. It is therefore often difficult to identify an established cytosine deamination rate consistent with ancient DNA across a sediment sample. In this study, we present MetaDamage, a tool that examines cytosine deamination on a metagenomic (all organisms) scale for multiple previously undetermined taxa and can produce a damage profile based on a few hundred reads. We outline the development and testing of the MetaDamage tool using both authentic sedaDNA sequences and simulated data to demonstrate the resolution in which MetaDamage can identify deamination levels consistent with the presence of ancient DNA. The MetaDamage tool offers a method for the initial assessment of the presence of sedaDNA and a better understanding of key questions of preservation for paleoecological reconstruction.
| Item Type: | Journal Article | |||||||||
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| Subjects: | Q Science > QE Geology Q Science > QH Natural history |
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| Divisions: | Faculty of Science, Engineering and Medicine > Science > Life Sciences (2010- ) | |||||||||
| Library of Congress Subject Headings (LCSH): | Sediments (Geology) -- Analysis, DNA, Fossil, DNA, Metagenomics, Paleoecology | |||||||||
| Journal or Publication Title: | Frontiers in Ecology and Evolution | |||||||||
| Publisher: | Frontiers Media | |||||||||
| ISSN: | 2296-701X | |||||||||
| Official Date: | 24 January 2023 | |||||||||
| Dates: |
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| Volume: | 10 | |||||||||
| Number of Pages: | 15 | |||||||||
| Article Number: | 888421 | |||||||||
| DOI: | 10.3389/fevo.2022.888421 | |||||||||
| Status: | Peer Reviewed | |||||||||
| Publication Status: | Published | |||||||||
| Access rights to Published version: | Open Access (Creative Commons) | |||||||||
| Date of first compliant deposit: | 7 March 2023 | |||||||||
| Date of first compliant Open Access: | 9 March 2023 | |||||||||
| RIOXX Funder/Project Grant: |
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