Exploring the Quality of Historic DNA From Pinned Beetles

Obtaining fresh DNA samples for biodiversity studies is often challenging. Natural history collections offer an alternative way to obtain data, although the DNA from dry-preserved specimens of historical collections is typically degraded and potentially contaminated. Here, we tested three standard DNA isolation methods to obtain DNA for genomic sequencing approaches using 20 identical ethanol and dry-preserved beetle specimens. The best-performing method was applied to a larger set of fresh and historical specimens representing 74 species of the genus Trichodes and 33 species from other genera of Cleridae (Coleoptera) to assess how specimen age and the amount of isolated DNA affect DNA sequence quality measures. Unlike most previous studies, we assessed the quality of isolated DNA through fragment length analysis and whole-genome sequencing. The here used silica-column based oligo isolation protocol for short DNA fragments outperformed standard silica-column based and precipitation-based isolation methods for historical genomic DNA. Fragment length of isolated DNA slightly declined with sample age in dry-preserved specimens, whereas the amount of isolated DNA remained unaffected. Higher DNA amounts led to significantly more recovered loci and longer multiple sequence alignments with fewer gaps. Contamination levels were significantly higher in dry-preserved samples. Our findings demonstrated the suitability of commonly available DNA isolation kits for dry-preserved museum specimens for next generation sequencing without requiring dedicated cleanroom facilities or hazardous reagents. Compared to sample age, the absolute amount of isolated DNA had higher impact on sequence quality and substantial genomic sequence information could be recovered even from old dry-preserved specimens. Our results underscore the potential of historic insect specimens as a source of molecular data with easy to apply DNA isolation protocols.