Optimization of DNA extraction for insect museomics substantially increases DNA yield

Historical samples from museum and private collections can serve as a time machine, allowing us to follow changes in genetic composition through time as well as obtaining genomic data on past biodiversity. Thus, genetic data from collections (museomics) are increasingly being utilized in scientific studies. However, although several different DNA extraction techniques have been used successfully in insect museomics, direct comparisons between methods are uncommon. It is therefore unclear to what extent simple adjustments of DNA extraction protocols can increase yields. This is especially important when analysing museum specimens that are decades or even hundreds of years old with low endogenous DNA content. Here, we first compared two recommended protocols which include the widely used QIAamp DNA Micro Kit or the Monarch PCR & DNA Cleanup Kit, respectively. We found that the Monarch kit performed substantially better than the QIAamp kit in terms of yield. We then compared various lysis temperatures, the effect of non-destructive versus destructive lysis, and the relative yield from a second round of extraction using the Monarch kit. We evaluated our results both by measurements of DNA concentration and fragment length and results from low coverage whole genome sequencing. We found that a lysis temperature of 42°C performed better than either 56°C or 37°C, using a lysis time of approximately 20 h. Destructive extraction increased yield in some species, and a second round of non-destructive extraction can substantially increase total yield. Finally, we used our selected Monarch kit protocol to extract DNA from legs of 492 additional butterfly specimens (23-128 years old) and 21 small wasp specimens. We observed virtually no effects of specimen age on the amount of DNA extracted or the endogenous DNA content, while older specimens yielded slightly shorter lengths of sequenced fragments. The DNA extraction procedure worked well for specimens up to 128 years of age and we would expect this to be the case for substantially older specimens, which would enable successful DNA extraction from the vast majority of dried insects in collections.