Patterns of aDNA damage through time and environments—lessons from herbarium specimens

BACKGROUND: Herbarium collections are a vast but underutilized resource for ancient DNA research, containing over 400 million specimens with detailed metadata and spanning centuries of global biodiversity. Understanding patterns of DNA preservation in natural collections is crucial for optimizing ancient DNA studies and informing future curation practices. We analysed genomic data for 573 herbarium specimens from 6 plant species from the genera Hordeum and Oryza collected from the Americas and Eurasia over 220 years. Using standardized laboratory protocols and shotgun sequencing, we quantified DNA degradation and elucidated factors that accelerate it. RESULTS: We find significant age-dependent DNA fragmentation rates, indicating temporal degradation processes not detected in prehistoric samples. In our analysis, DNA decay rates in herbarium specimens were almost 8 times faster than in moa bones, reflecting fundamental differences in tissue composition and preservation environments. Environmental conditions at the time of specimen collection emerged as the major determinants of post-mortem damage rates, with the interaction term between temperature and genus being the dominant driver of cytosine deamination. We find no effect of sample storage on DNA damage and degradation. CONCLUSIONS: These findings provide insights into how climatic origin, preservation environment, taxonomic identity, and age influence DNA preservation while highlighting opportunities for improving institutional preservation practices. Due to standardized preservation conditions, museum collections can provide better insights into DNA damage and degradation over time than archaeological and paleontological samples.