Sequence capture and phylogenetic utility of genomic ultraconserved elements obtained from pinned insect specimens more than 100 years-old

Obtaining sequence data from historical museum specimens has been a growing research interest, invigorated by next-generation sequencing methods that allow inputs of highly degraded DNA. We applied a recently developed target enrichment and next-generation sequencing protocol to generate ultraconserved elements (UCEs) from 51 large carpenter bee specimens (genus Xylocopa), representing 25 species with ages ranging from 2–121 years. We measured the correlation between specimen age and DNA yield (pre- and post-library preparation DNA concentration) and several UCE sequence capture statistics (raw read count, UCE reads on target, UCE mean contig length and UCE locus count) with linear regression models. We performed piecewise regression to test for specific breakpoints in the relationship of specimen age and our DNA yield and sequence capture variables. Additionally, we reconstructed a phylogeny in order to confirm the validity of our sequence data. We recovered 6–972 UCE loci from samples with pre-library DNA concentrations ranging from 0.06–9.8 ng/µL. All investigated DNA yield and sequence capture variables were significantly but only moderately negatively correlated with specimen age. Specimens of age 20 years or less had significantly higher pre- and post-library concentrations, UCE contig lengths, and locus counts than specimens older than 20 years. We found breakpoints in our data between 21–39 years for pre- and post-library DNA concentration and UCE contig length beyond the negative effect of decreased specimen age. Our phylogenetic results confirmed the integrity of our sequences as specimens of the same species grouped together, and give preliminary insights into relationships within Xylocopa. We consider the effect of additional factors not measured in this study on our age-related sequence capture results, such as DNA fragmentation and preservation method, and discuss our phylogenetic results with regard to the promise of this UCE approach for large scale projects in insect phylogenomics using museum specimens.