Data from: Phylogenomics using formalin-fixed and 100+ year old intractable natural history specimens

Museum specimens provide a wealth of information to biologists, but obtaining genetic data from formalin-fixed and fluid-preserved specimens remains challenging. While DNA sequences have been recovered from such specimens, most approaches are time-consuming and produce low data quality and quantity. Here we use a modified DNA extraction protocol combined with high-throughput sequencing to recover DNA from formalin-fixed and fluid-preserved snakes that were collected over a century ago and for which little or no modern genetic materials exist in public collections. We successfully extracted DNA and sequenced ultraconserved elements (x̄ = 2,318 loci) from 10 fluid-preserved snakes and included them in a phylogeny with modern samples. This phylogeny demonstrates the general use of such specimens in phylogenomic studies and provides evidence for the placement of enigmatic snakes, such as the rare and never-before sequenced Indian Xylophis stenorhynchus. Our study emphasizes the relevance of museum collections in modern research and simultaneously provides a protocol that may prove useful for specimens that have been previously intractable for DNA sequencing.博物馆标本为生物学家提供了丰富的研究资料，但从福尔马林固定且液体保存的标本中获取遗传数据仍存在诸多挑战。尽管已有研究从这类标本中成功获取了DNA序列，但多数方法耗时较长，且所得数据的质量与数量均欠佳。本研究采用改良的DNA提取方案结合高通量测序技术，从百年前采集、公共馆藏中几乎无现代遗传材料留存的液体保存蛇类标本中成功获取了DNA。我们从10份此类蛇类标本中成功提取DNA并完成了超保守元件（ultraconserved elements）测序，平均获得2318个基因座，并将其与现代样本一同整合入系统发育树中。该系统发育树证实了这类标本在系统发育基因组学研究中的普遍应用价值，同时为谜样蛇类的分类定位提供了实证——例如此前从未被测序的珍稀印度管蛇（Xylophis stenorhynchus）。本研究既凸显了博物馆馆藏在现代科研中的重要意义，同时也提供了一套可用于此前难以开展DNA测序的标本的实验方案，具备广泛的应用前景。