Door 13: Expanding Sources of DNA in Museums

Diverse museum holdings offer unique and exciting potential sources of ancient DNA and other biomolecules (e.g., RNA and proteins).

As technology and methods advance, the accessibility and potential for success of ancient DNA has also increased; alongside the attainment of ancient DNA and other biolmolecules from once condemned museum holdings (i.e, formalin fixed specimens), new sources are also continually emerging. Museums are often a point of convergence for these advancements because of the diversity of assemblage types (e.g., objects, documents, individuals, etc.) they house from extended and important time periods. Two, recent articles demonstrate the expanding narratives and variety of biomolecular sources in museum collections.

From a formalin preserved specimen, Muschick et al. (2022) discuss evolutionary species designations among Antarctic notothenioid fishes, known to be one of the rare examples of adaptive radiation in a marine environment. Specifically, they investigated the mitochondrial genome of the red icefish (Channichthys rugosus), with the genus having between one and nine known species–depending on who you talk to. Using genetic analyses, a related genus (Pogonophryne) of Antarctic notothenioid fishes saw the synconization (collapsing) of many species (24 of 29) previously distinguished on minute morphological variations (Parker et al. 2022). Genetically confirming and corroborating species’ designations with morphology helps scientists to understand evolutionary relationships and mechanisms, while also helping clarify what the expected morphological and genetic variation is of the fish in their environment(s). With genetic information available for only one Channichtys species, genetic data was required for comparison, leaving the researchers to find suitable museum specimens for study. However, since most C. rugosus specimens were collected decades ago, it was common to preserve them in a formalin solution.

Causing the soft tissues to become stiff and rigid, formalin preservation produces extensive DNA degradation through shearing and crosslinking any available molecules together. This produces short fragments of DNA (and other molecules) that often get tangled with larger protein fragments. Because DNA sequencing requires linear, and often double stranded, DNA molecules, the large tangled masses crosslinking creates prevents molecular accessibility in these specimens. It wasn’t until the last decade that technological and methodological advancements have revived the previously molecularly condemned formalin-fixed specimens. With protocols optimized for formalin-fixed specimens, Muschick et al. (2022) maximized the retrieval of as many short DNA fragments as possible through de-tangling formalin-induced crosslinks and preparing single-stranded DNA molecules (a very recent breakthrough by Gansauge et al. 2017 and 2020) for sequencing.

In another article, by Rayo et al. (2022), ancient Egyptian canopic jars, found in many museum collections, also provided authentic ancient DNA. Containing mummified organs of Egyptian mummies, canopic jars are ritualistic objects that accompany individual burials. Affecting all ancient Egyptian archaeological findings, the arid deserts and relatively humid tomb chambers are known to negatively affect DNA, particularly through processes of fragmentation. Furthermore, modern contamination has also been a contributing worry to the believability of ancient DNA studies of ancient Egypt heritage. It has only been with targeted methods for short DNA fragments and data de-contamination procedures that these types of DNA studies have become more readily accepted as authentic (e.g. Neukamm et al. 2020).

Canopic jars are particularly interesting sources for ancient DNA, not only because of the widespread and longstanding fascination about ancient Egypt the world over, but also because they offer direct study of pathogens/diseases that affect organs. Because soft tissue is rarely recovered in archaeological contexts, genetic analyses of canopic jars could offer incredible medical insight into ancient Egypt. And, even more broadly, DNA analyses can confirm (or befuddle) current knowledge paradigms by confirming if the jars contain human tissue at all and identifying specific tissues present, while also potentially providing insight into ancient organ microbiome communities.

I enjoyed these articles for their recent examples of how museum collections offer unique and informative sources of ancient DNA, ever expanding the variation of DNA-containing sources. It’s exciting to think about where new molecular information will come from and the specific mechanisms and techniques that will optimize accessibility; as sources of ancient DNA and biomolecules continue to expand, so too, does the possibility of conducting more in-depth and evolutionarily interpretative investigations. Although, temperance remains necessary.

What is often a difficult reality when using museum collections is the lack of information for many holdings; without contextualizing information the information gained from DNA evidence cannot be incorporated with previous or associated knowledge about the object, individual, art, etc., thus limiting interpretive value of the study. This is not a fault of anyone in the past or single individuals; many scientific discoveries were impossible to imagine without current technology. However, the accompanying information for, or lack thereof, and types of assemblages in museums directs the types of scientific methods and questions that they may be applicable for. Indeed, molecular methodologies are not, nor considered to be, the pan-ultimate information source that can answer all scientific inquiries. While molecular data provides a wealth of information, it is the synthesis of multiple types of evidence with proper contextualization that allows for grand and meaningful scientific research.

Original articles: Muschick, M., Nikolaeva, E., Rüber, L. et al. The mitochondrial genome of the red icefish (Channichthys rugosus) casts doubt on its species status. Polar Biol 45, 1541–1552 (2022). https://doi.org/10.1007/s00300-022-03083-8; AND Rayo, E., Neukamm, J., Tomoum, N., Eppenberger, P., Breidenstein, A., Bouwman, A.S., Schuenemann, V.J. and Rühli, F.J.. Metagenomic analysis of Ancient Egyptian canopic jars. Am J Bio Anthro179(2), 307-313 (2022).

Other references: Parker, E., Dornburg, A., Struthers, C.D., Jones, C.D. and Near, T.J. Phylogenomic species delimitation dramatically reduces species diversity in an Antarctic adaptive radiation. Systematic Biology71(1), 58-77 (2021).

Gansauge, M.T., Gerber, T., Glocke, I., Korlević, P., Lippik, L., Nagel, S., Riehl, L.M., Schmidt, A. and Meyer, M.. Single-stranded DNA library preparation from highly degraded DNA using T4 DNA ligase. Nucleic acids research45(10), e79-e79 (2017).

Gansauge, M.T., Aximu-Petri, A., Nagel, S. and Meyer, M.. Manual and automated preparation of single-stranded DNA libraries for the sequencing of DNA from ancient biological remains and other sources of highly degraded DNA. Nature protocols15(8), 2279-2300 (2020).

Neukamm, J., Pfrengle, S., Molak, M., Seitz, A., Francken, M., Eppenberger, P., Avanzi, C., Reiter, E., Urban, C., Welte, B. and Stockhammer, P.W.. 2000-year-old pathogen genomes reconstructed from metagenomic analysis of Egyptian mummified individuals. BMC biology18(1), 1-18 (2020).

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