Museum genomics has transformed the field of collections‐based research, opening up a range of new research directions for paleontological specimens as well as natural history specimens collected over the past few centuries. Recent work demonstrates that it is possible to characterize epigenetic markers such as DNA methylation in well preserved ancient tissues. This approach has not yet been tested in traditionally prepared natural history specimens such as dried bones and skins, the most common specimen types in vertebrate collections. In this study, we developed and tested methods to characterize cytosine methylation in dried skulls up to 76 years old. Using a combination of ddRAD and bisulphite treatment, we characterized patterns of cytosine methylation in two species of deer mouse (Peromyscus spp.) collected in the same region in Michigan in 1940, 2003, and 2013–2016. We successfully estimated methylation in specimens of all age groups, although older specimens yielded less data and showed greater interindividual variation in data yield than newer specimens. Global methylation estimates were reduced in the oldest specimens (76 years old) relative to the newest specimens (1–3 years old), which may reflect post‐mortem hydrolytic deamination. Methylation was reduced in promoter regions relative to gene bodies and showed greater bimodality in autosomes relative to female X chromosomes, consistent with expectations for methylation in mammalian somatic cells. Our work demonstrates the utility of historic specimens for methylation analyses, as with genomic analyses; however, studies will need to accommodate the large variance in the quantity of data produced by older specimens.

中文翻译：

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博物馆表观基因组学：表征历史博物馆标本中的胞嘧啶甲基化。

博物馆基因组学改变了以收藏为基础的研究领域，为过去几个世纪收集的古生物学标本和自然历史标本开辟了一系列新的研究方向。最近的工作表明，可以在保存完好的古代组织中表征表观遗传标记，例如 DNA 甲基化。这种方法尚未在传统制备的自然历史标本中进行测试，例如干燥的骨头和皮肤，这是脊椎动物收藏中最常见的标本类型。在这项研究中，我们开发并测试了表征 76 岁以下干颅骨中胞嘧啶甲基化的方法。使用 ddRAD 和亚硫酸氢盐处理的组合，我们表征了两种鹿鼠（Peromyscusspp.) 于 1940 年、2003 年和 2013-2016 年在密歇根州的同一地区收集。我们成功地估计了所有年龄组标本的甲基化，尽管较旧的标本产生的数据较少，并且与较新的标本相比，数据产生的个体间差异更大。相对于最新标本（1-3 年），最古老标本（76 岁）的全球甲基化估计值有所降低，这可能反映了死后水解脱氨作用。相对于基因体，启动子区域的甲基化减少，并且在常染色体中相对于女性 X 染色体显示出更大的双峰性，这与哺乳动物体细胞中甲基化的预期一致。我们的工作证明了历史样本在甲基化分析中的效用，就像基因组分析一样；然而，