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.博物馆标本可为生物学家提供海量研究数据支撑，但从福尔马林固定（formalin-fixed）与液浸保存（fluid-preserved）的标本中获取遗传数据仍颇具挑战。尽管已有从这类标本中回收DNA序列的先例，但绝大多数方法耗时冗长，且所得数据的质量与产出量均偏低。本研究采用改良的DNA提取方案结合高通量测序（high-throughput sequencing）技术，从百余年前采集、公共馆藏中几乎无对应现代遗传材料留存的液浸保存蛇类标本中成功回收DNA。我们从10件液浸保存蛇类标本中成功提取DNA并完成超保守元件（ultraconserved elements）测序，平均获得2318个基因座（loci）的序列，并将这些标本与现代样本一同纳入系统发育分析。此次系统发育分析验证了这类标本在系统基因组学（phylogenomic）研究中的通用适用性，并为谜样蛇类的分类定位提供了关键证据——例如此前从未被测序的稀有印度狭吻林蛇（Xylophis stenorhynchus）。本研究既凸显了博物馆馆藏在现代科研中的核心价值，同时也为此前难以完成DNA测序的标本提供了一套切实可行的实验方案。