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.

馆藏标本为生物学家提供了海量研究信息，但从福尔马林固定液保存标本中获取遗传数据仍存在诸多挑战。尽管已有研究者从这类标本中成功获取DNA序列，但绝大多数方法耗时漫长，且所得数据的质量与数量均不理想。本研究采用改良后的DNA提取方案结合高通量测序技术，从一批百年前采集的福尔马林固定液保存蛇类标本中成功回收DNA——这类标本在公共馆藏中几乎不存在现代遗传物质。我们从10份液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，随后将这些标本与现代样本一同纳入系统发育分析。此次构建的系统发育树证明了这类标本在系统发育基因组学研究中的通用适用性，并为神秘蛇类的分类定位提供了关键证据，例如此前从未被测序过的珍稀印度狭吻筒蛇（Xylophis stenorhynchus）。本研究既凸显了馆藏标本在现代科研中的重要价值，同时也为此前难以进行DNA测序的标本提供了一套可行的实验方案。