Regarding fossil/sub-fossil specimen sampling, the above described methods generally function over a scale of micrometers to nanometers
78, 79, 85, 95, 96, 104, 105, 112. Small samples of tens to hundreds of milligrams will suffice for any one of these molecular methods, provided care is taken during sample preparation. Particularly, this allows for minimally destructive sampling of specimens that preserve exceptional morphology; this includes articulation, fossil organs, color, amongst other examples
36-38, 113-116. Examination of specimen biomolecular histology is hypothesized to yield insight into the general preservational state of such specimens at the molecular level. This would inform on whether future destructive molecular analyses, including sequencing, are justified for such morphologically exceptional specimens.
Furthermore, several recent studies have demonstrated isolated, disarticulate remains, even those stored for extended periods in museum collections, can often be used in molecular analyses in place of exceptionally preserved specimens that are more informative morphologically16, 29, 117, 118. The potential use of such specimens would improve stewardship of fossil and sub-fossil resources. Studying the biomolecular histology of such morphologically unexceptional specimens is hypothesized to further advance understanding on which geologic timepoints and depositional environments are most likely to harbor fossils/sub-fossils preserving ancient sequences. Advancing such knowledge, in this way, would help limit the unnecessary sampling of more morphologically exceptional fossil/sub-fossil specimens that are otherwise unlikely to preserve sequence-able biomolecules at the molecular level, based on their diagenetic history.
Conclusion
Thermal setting and geologic age have been commonly used as proxies for predicting molecular sequence preservation potential3, 5, 6, 15. Late Pleistocene and Holocene specimens from cooler regions, especially permafrost deposits, have been shown to generally possess the highest preservation potential for molecular sequence information5, 6, 10, 16, 17. However, depositional environments are influenced by other variables including moisture18, 20-22, 25 and oxygen content18, 20-22, 29, 30, ion species present, and sediment composition18, 20-23. These confounding variables limit the usefulness of thermal setting and geologic age as proxies outside of a broad scale.
Direct analysis of fossil and sub-fossil biomolecular histology is a potential answer to this limitation. The biomolecular histology of a specimen’s preserved cells and tissues reflects the cumulative effects of environmental variables upon its constituent biomolecules, including DNA and protein sequences20, 22, 34. Observed degradation of cell and tissue biomolecular histology is hypothesized to correlate with constituent biomolecules having undergone degradation. This agrees with the limited data in the primary literature on the correlation of biomolecular histology with sequence preservation potential2, 40, 63, 91. Thus, the preserved state of fossil/sub-fossil biomolecular histology is predicted to be an accurate proxy for molecular sequence preservation. A potential limitation to this approach is that some aspects of biomolecular histology may be beyond resolution or limit of detection for current molecular methods. However, modern molecular instrumentation regularly functions on the micro- and nanoscale in terms of resolution and limit of detection78, 79, 85, 95, 96, 104, 105, 112, thus minimizing this limitation as a potential obstacle. The use of fossil/sub-fossil biomolecular histology as a proxy for sequence preservation has potential to elucidate why ancient specimens of some formations and timepoints preserve sequences while others do not; such understanding would facilitate the selection of ancient specimens for use in future ancient DNA and paleoproteomic studies.
Competing Interests
There are no competing interests to declare.
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