Miss Karin Zwiep1, Dr. Tim Staples1, Dr. Juan Carlos Ortiz2, Dr. Maria del Carmen Gomez Cabrera2, Prof. Dr. Cynthia Riginos1, Prof. Dr. John Pandolfi1
1The University Of Queensland, Brisbane, Australia, 2The Australian Institute of Marine Science, Townsville, Australia
Analysis of ancient environmental DNA (aeDNA) can expand the understanding of long-term ecological patterns beyond current long-term monitoring records and the taxonomic breadth beyond organisms that fossilise. Yet, biases arising from degradation could affect ecological inferences, and reduce the confidence in ecological conclusions drawn from aeDNA datasets. A decrease in the magnitude and fragment length of recoverable DNA with increasing sediment age is common, but few studies have quantified the extent of aeDNA degradation. This is likely to be stronger in tropical environments, where high temperatures are thought to accelerate aeDNA degradation. In this study, we simulate aeDNA data and introduce different degradation and community compositional changes. In particular, we focus on the distribution of the slopes of taxonomic relative abundance over time (i.e., whether the relative abundance of a taxon is decreasing or increasing), and we show how this can be used to indicate the presence of degradation and compositional shift. We also show how this analysis is able to differentiate between the two, even when occurring simultaneously. We then compare these conceptual patterns in the simulated results to genuine 18S metabarcoding data from ten sediment cores from the Great Barrier Reef, which predominantly show patterns of degradation and no strong community shift.
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