Phylogenomic analyses from archival DNA

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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.