D3161: Optimizing DNA extraction of large museum specimens for phylogenomic analysis

With the advent of targeted enrichment approaches there has been renewed interest in utilizing museum specimens for phylogenomic studies. However, there exists little consensus about the best course of action for extracting DNA from large museum specimens. Large museum specimens are fraught with difficulty regarding DNA extractions due their size, fragility, and age which can result in low DNA yield. Preserving the integrity of museum specimens is also of concern as they may represent rare or extinct species. Here we test different methods for DNA extractions on large museum specimens, in order to determine the best approach for maximizing DNA yield and quality while minimizing damage to the integrity of the specimen. We tested extractions resulting from, entire bodies, those with removal of the head and thorax, removal of only the head, and finally with removal of leg alone, and removal of the leg including freezing and grinding. DNA quantity was quantified using a Qubit, with quality quantified through use of a Nanodrop and PCR amplification We attempted to control for confounding factors like taxon, age, and killing method. Ultimately, we find that method of extraction results in considerable differences in DNA yield for phylogenomic analysis.