Advanta
Regarding fossil/sub-fossil specimen sampling, the above described methods generally function over a scale of micrometers to nanometers (Bozzola & Russell, 1999; Ferraro et al., 2003;
Handbook of Microscopy, 2019; Marini et al., 2015; Pan & Hu, 2019; Smith & Dent, 2019; Sodhi, 2004; Thiel & Sjövall, 2011). Small samples of tens to hundreds of milligrams will suffice for any one of these molecular methods, provided care is taken during sample preparation. This limits the extent of destructive sampling necessary to study fossil/sub-fossil specimen biomolecular histology.
Particularly, this allows for minimally destructive sampling of specimens that preserve exceptional morphology; this includes articulation, fossil organs, color, amongst other examples (Brown et al., 2017; Greenwalt, Goreva, Siljeström, Rose, & Harbach, 2013; Lindgren et al., 2017; Lindgren et al., 2015; Lindgren et al., 2018; Manning et al., 2009; Yamagata et al., 2019). 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. If initial analysis of biomolecular histology suggests that a given "exceptional" specimen has limited potential for molecular sequence preservation, destructive sampling can be halted.
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 morphologically (Bertazzo et al., 2015; Cleland, Schroeter, Feranec, & Vashishth, 2016; Ngatia et al., 2019; Wiemann et al., 2018). 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 then 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 potential (Demarchi et al., 2016; Hofreiter et al., 2015; Wadsworth et al., 2017; Welker et al., 2019). Late Pleistocene and Holocene specimens from cooler regions, especially permafrost deposits, have been shown to generally possess the highest preservation potential for molecular sequence information (Hofreiter et al., 2015; Letts & Shapiro, 2012; Ngatia et al., 2019; Wadsworth & Buckley, 2014; Welker et al., 2019). However, depositional environments are influenced by other variables including moisture (Briggs, 2003; Gupta, 2014; Lennartz et al., 2020; Lindahl, 1993; Schweitzer et al., 2019) and oxygen content (Briggs, 2003; Gupta, 2014; Lindahl, 1993; Schweitzer et al., 2019; Wiemann et al., 2020; Wiemann et al., 2018), ion species present, and sediment composition (Briggs, 2003; Gupta, 2014; Lindahl, 1993; Schweitzer et al., 2019; Schweitzer et al., 2014). 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 sequences (Briggs, 2003; Briggs et al., 2000; Gupta, 2014). 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 potential (Asara et al., 2007; Rybczynski et al., 2013; Schweitzer et al., 2002; Schweitzer, Wittmeyer, et al., 2007). 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 detection (Bozzola & Russell, 1999; Ferraro et al., 2003; Handbook of Microscopy, 2019; Marini et al., 2015; Pan & Hu, 2019; Smith & Dent, 2019; Sodhi, 2004; Thiel & Sjövall, 2011), 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.
Acknowledgements
The author thanks the journal editor-in-chief Dr. Gareth Jenkins, Ph.D., the associate editor Dr. Stefan Prost, Ph.D., and the anonymous reviewer for their time and efforts invested towards improving this manuscript. The author would further like to thank both his Ph.D. advisor, Dr. Mary H. Schweitzer, Ph.D., as well as Dr. Elena R. Schroeter, Ph.D., for their feedback and comments on various drafts of this manuscript. Thank you to Dr. Christopher L. Hill for his assistance in providing and verifying information regarding specimens MOR 91.72, MOR 604, and MOR 605 used in this study. Also, thank you to Dr. Lance C. Anderson, D.O., (degree expected Spring 2024) for his feedback which helped improve the manuscript’s clarity and readability.
Additionally, several people and institutions contributed resources essential to the production of this manuscript in its finalized format. Many thanks to the Museum of the Rockies for access to specimens used in this research: MOR 604 and 605, (donated to the Paleontology Department by Jerry and Kathy Doeden) and MOR 91.72 (Cultural History Department). Thank you to Miles Carson for his assistance and support in recovering and subsequently donating specimen YG 610.2397, and thank you to the Yukon Palaeontology Program of the Yukon Government for curating and permitting access to specimen YG 610.2397. The author also acknowledges that specimen YG 610.2397 was found on and recovered from the traditional territories of the Tr’ondek Hwech’in. An additional special thanks to the donors Lynn and Susan Packard Orr, and Vance and Gayle Mullis, for funding the data collection and article processing charge for this manuscript. Finally, this work was performed in part at the Chapel Hill Analytical and Nanofabrication Laboratory, CHANL, a member of the North Carolina Research Triangle Nanotechnology Network, RTNN, which is supported by the National Science Foundation, Grant ECCS-1542015, as part of the National Nanotechnology Coordinated Infrastructure, NNCI.
Competing Interests
There are no competing interests to declare.
Data Availability Statement
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