Abstract
Museum genomics is one of the most influential fields in modern collections-based research. Recently, these methods have been extended to study epigenetic markers in ancient DNA. Previous work has focused on well-preserved ancient tissues; here, we develop and test epigenomic methods for traditionally preserved natural history specimens (dried skulls) up to 76 years old. We used a combination of ddRAD and bisulfite treatment to characterize genome-wide patterns of cytosine methylation in two species of deer mice (Peromyscus spp.). We were able to describe methylation in specimens from all age groups, and global methylation did not vary due to specimen age. Locus methylation was bimodally distributed and was reduced in promoter regions and heightened in gene bodies, consistent with expectations for in vivo methylation in mammals. Global methylation estimates for the two species were within the expected range for mammals but at the lower end, suggesting that estimates may have been depressed due to the choice of reference genome. The quantity of data varied more across older specimens. For example, although most specimens in the oldest group (76 yo) yielded few cytosines, two specimens performed as well as modern specimens sequenced in the same library. Our work demonstrates the utility of historic specimens for methylation analyses, as with genomic analyses; however, such studies will need to accommodate the large variance among individuals in the quantity of data produced by historic samples, either by screening specimens for DNA quantity and quality prior to library construction or by expanding sampling to allow for a higher failure rate. We suggest that analyses requiring fewer specimens overall, such as differential methylation analyses, may be the most successful. Museum epigenomics datasets can be used to describe methylation in historic populations or shifts in methylation over time; here we present comparative data tracking methylation patterns in deer mice collected over the past 76 years over the course of an ecological range expansion.
