Sequence capture phylogenomics of historical ethanol-preserved museum specimens: unlocking the rest of the vault. Opiliones

Natural history collections play a crucial role in biodiversity research and museum specimens are increasingly being incorporated into modern genetics-based studies. Sequence capture methods have proven incredibly useful for phylogenomics providing the additional ability to sequence historical museum specimens with highly degraded DNA, which until recently have been deemed less valuable for genetic work. The successful sequencing of ultraconserved elements (UCEs) from historical museum specimens has been demonstrated on multiple tissue types including dried bird skins, formalin-fixed squamates, and pinned insects. However, no study has thoroughly demonstrated this approach for historical ethanol-preserved museum specimens. Alongside sequencing of fresh specimens preserved in >95% ethanol and kept at -80 ºC, we used extraction techniques specifically designed for degraded DNA coupled with modified sequence capture protocols to sequence UCEs from standard museum specimens preserved in 70–80% ethanol and kept at room temperature, the standard for such ethanol-preserved museum collections. Across 35 fresh and 15 museum samples of the arachnid order Opiliones, an average of 345 UCE loci were included in phylogenomic matrices, with museum samples ranging from 6–495 loci. We successfully demonstrate the inclusion of ethanol-preserved museum species in modern sequence capture phylogenomic studies, show potential for species and population-level variation from these data, and successfully recover multiple loci from off-target reads traditionally sequenced in multi-locus studies including mitochondrial loci and nuclear rRNA loci. The methods detailed in this study will allow researchers to potentially acquire genetic data from millions of ethanol-preserved museum specimens held in collections worldwide.