A Comparative Survey of Historical DNA Degradation From Vertebrate Museum Specimens: Unexpected Utility of Fluid-Preserved Specimens.

Advances in museomics have expanded from dry and skeletal specimens to now include fluid-preserved material as a source of DNA. However, our understanding of patterns of DNA degradation across specimens and tissue types remains limited, hindering justification for targeting optimal DNA sources from museum voucher specimens. Here we quantify DNA quality across taxonomic groups (amphibians, squamates, and birds) and tissue types to benchmark DNA yield, fragmentation, endogenous content, and DNA damage in fluid-preserved specimens versus more commonly used sources (frozen tissues, dried skins, and skeletons). Our tests showed that fluid-preserved material had smaller fragments, decreased endogenous content, and increased deamination with age, indicative of extensive degradation over even short timescales. Unexpectedly, formalin-fixed fluid-preserved specimens did not show clear declines in DNA yield or fragment length with specimen age, suggesting formalin fixation initially fragments DNA but may partly decouple subsequent fragment-length patterns from specimen age. DNA yield, fragment size, and endogenous content across tissue types in fluid-preserved specimens showed both time- and tissue-type dependent patterns. DNA from liver had the highest quality metrics in younger specimens but performed worse in the oldest specimens. In older specimens, the optimal tissue types included skin, muscle or bone across taxonomic groups. However, substantial variation between individual specimens of the same preparation type and age indicated that collection history also influences DNA degradation. Our comparative analyses reinforce earlier findings that fluid-preserved specimens of all ages are viable DNA sources. We use these findings to refine DNA sampling strategies for incorporating fluid-preserved voucher specimens into museomic research.