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极为丰富的研究资料，但从福尔马林固定及液浸保存的标本中获取遗传数据仍面临诸多挑战。尽管已有研究从此类标本中成功获取DNA序列，但多数现有方法不仅耗时漫长，且所得数据的质量与数量均不尽如人意。本研究采用改良的DNA提取方案结合高通量测序技术，从采集于一个多世纪前的福尔马林固定、液浸保存蛇类标本中回收DNA——此类标本在公共馆藏中几乎无对应的现代遗传材料可供获取。我们成功从10份液浸保存的蛇类标本中提取DNA并完成超保守元件（ultraconserved elements）测序，平均每个样本获得2318个位点（x̄ = 2,318 loci），并将这些标本与现代样本一同纳入系统发育树构建分析。该系统发育树不仅证实了此类标本在系统基因组学研究中的广泛适用性，还为疑难蛇类的分类定位提供了关键证据，例如此前从未被测序的珍稀印度狭吻箭蛇（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进行DNA测序的标本的实用实验方案。