Molecular Clock Dating of Ancient Environmental DNA Reveals Damage Beyond Deamination

Ancient environmental DNA (aeDNA) from permafrost, lake, cave, and marine sediments provides a rich source of genetic data that captures broad perspectives of past biodiversity. Accurate dating is crucial for discovering ecologically relevant patterns from aeDNA, and molecular clock dating would allow for sample ages to be estimated from the recovered genetic material itself instead of the geological components. However, the fragmented and damaged nature of short-read ancient DNA (aDNA) from multiple taxonomic sources poses significant challenges and has limited this dating approach for aeDNA. Here we developed ratePlacer, a phylogeny-based method for analyzing aeDNA that can combine information from many short reads in a sample while accounting for DNA damage to provide maximum likelihood estimates of sample ages. Simulations demonstrate that ratePlacer accurately dates samples even under the fragmented, damaged conditions characteristic of aeDNA and outperforms Bayesian tip-dating approaches for taxonomically mixed samples commonly found in aeDNA. Yet age estimates from re-dating Kap København varied across taxa, highlighting the difficulty of molecular clock dating in aeDNA. This dating also revealed elevated $G\to T$ and $C\to A$ mismatches consistent with oxidative damage. These patterns reveal aDNA damage beyond deamination and that remains understudied, suggesting that aeDNA should be carefully evaluated in genomic and evolutionary analyses. The new dating method, ratePlacer, extends molecular clock dating of aDNA from single-specimen to pooled environmental DNA data, where traditional methods struggle.