Phylogenomic analyses from archival DNA

世界各地的博物馆收藏了数以百万计的标本，作为各个研究领域的参考。样品的策展处理通常涉及甲醛（FA）作为固定剂。虽然样品的固定和随后的保存允许保存许多形态特征，但样品的DNA被破坏，因为FA在DNA分子以及DNA和蛋白质之间引入交联，抑制了采用DNA扩增的技术，包括所有当前可用的DNA测序技术。此外，FA固定和随后的乙醇储存通过去嘌呤作用严重降解DNA，造成严重的片段化。因此，档案DNA （arcDNA）样本与古代DNA （aDNA）具有许多共同特征。在这个项目中，我们打算将目前所有关于固定样品FA特异性处理的知识与专注于捕获非常短的DNA片段（<100个碱基对）的aDNA提取方案结合起来。这些短片段必须被整合到DNA库中。最有希望的方法是从单链DNA构建文库，它可以直接测序，或者适合更具体的步骤，如杂交富集。我们的最终目标是建立一个成本和时间效率高，普遍适用的协议，以成功地从档案DNA文库中提取和靶捕获mt和系统发育信息nDNA，特别是从FA固定样本中。测试成功后，我们将重点放在深海灯笼鲨（灯笼鲨科）的博物馆样本上。这些鲨鱼完美地体现了稀有物种分子分析中出现的典型问题，这些问题在自然界中很难获得。在这里，来自博物馆样本的DNA序列信息将对分类和系统发育分析具有重要价值。

Museum collections worldwide house millions of specimens serving as references in various fields of research. The curatorial treatment of samples often involves formaldehyde (FA) as fixative. While the fixation and subsequent preservation of samples allows for the conservation of many morphological characters, the DNA of samples is damaged as FA introduces cross-links between DNA molecules as well as DNA and proteins, inhibiting techniques that employ amplification of DNA, including all currently available DNA sequencing techniques. Further, FA fixation and subsequent ethanol storage heavily degrade DNA by depurination, causing severe fragmentation. Therefore, archival DNA (arcDNA) samples share many characters with ancient DNA (aDNA). In this project, we intend to combine all current knowledge on FA specific treatments of fixed samples with aDNA extraction protocols focusing on capturing very short DNA fragments (<100 basepairs). These short fragments have to be incorporated into a DNA library. The most promising way are library constructions from single stranded DNA, which can be directly sequenced or, alternatively, are suitable for more specific steps, such as hybrid enrichment. Our ultimate goal is the establishment of a cost- and time efficient, universally applicable protocol for successful DNA extraction and target capture of mt and phylogenetically informative nDNA from archival DNA libraries, especially from FA fixed samples. After successful testing, we focus on museum samples of deep-sea lantern sharks (Etmopteridae). These sharks perfectly exemplify typical issues arising with molecular analyses of rare species, which are difficult to access in nature. Here, DNA sequence information from museum samples would be of great value for taxonomic and phylogenetic analyses.