Molecular Histology as a Potential Proxy for Ancient Sequence Preservation
The number of specimens reported to preserve molecular sequences decreases substantially beyond geologic ages of ~0.13-0.24Ma and ~0.8-1.0Ma for DNA and proteins respectively5, 8, 44-48. This is excluding specimens of permafrost settings and some cave deposits as these settings often confer exceptional preservation potential for molecular sequences5, 14, 49-53. The decrease in reported sequences from specimens exceeding these timepoints suggests substantial diagenetic alteration occurs to fossil/sub-fossil biomolecules over these timeframes. The extent of this diagenetic alteration is such that in many cases molecular sequences are degraded beyond the limit of detection of commonly used sequencing protocols. Still, molecular sequences, particularly protein sequences, have been reported from a few non-cave/permafrost specimens with geologic ages exceeding these thresholds2-4, 34, 54-57. A study on a Pliocene camel tibia from Ellesmere Island, Yukon, Canada, for example, managed to recover type-1 collagen peptides2, 4; in addition to two Mesozoic dinosaur specimens34, 55-57, these are the only pre-Pleistocene bones currently reported to harbor sequence-able proteins. Two other camels from Miocene and Pliocene formations of Nebraska were analyzed in the Ellesmere Island tibia study yet failed to yield detectable peptide sequences2, 4. This begs the question of why some specimens like the exceptional Ellesmere Island tibia preserve protein and/or DNA sequence information while many other pre/early and even mid-Pleistocene specimens do not.
The prevailing view in the paleogenomic and paleoproteomic literature would be that the greater thermal exposure of the temperate Nebraska specimens facilitated protein degradation relative to the Ellesmere Island tibia3, 5, 6, 13. A warmer thermal setting accelerates the rate of diagenetic reactions affecting molecular histology, including molecular sequences3, 58. Advanced geologic age expands the temporal period over which these reactions have to progress and accumulate18, 58. Hence, a lower geologic age along with a cooler thermal setting is hypothesized to inhibit the extent of such diagenetic reactions and limit molecular sequence degradation. This and the degree materials such as bone, dentine, enamel, eggshell, and others resist degradation3, 5, 8, 59 are often cited as key variables explaining examples of exceptional sequence preservation.
Indeed, a fossil or sub-fossil’s thermal setting/history and geological age are generally used as proxies for predicting sequence preservation potential3, 5, 6, 13. However, even ancient specimens from similar timepoints and depositional environments are known to display great variation in sequence preservation8, 13, 15, 24, 25, 60, 61. In a study of 118 Xenarthrans from temperate to tropical locales, 6 specimens from the Santa Clara formation (~8.5-128Ka) of Camet Norte, Buenos Aires, Argentina, were analyzed. Of these, 2 specimens out of 6 demonstrated substantial evidence of protein preservation61. In this case, geologic age and thermal setting would be rendered relatively inaccurate as proxies since all specimens came from the same formation and would be expected to share a similar thermal history, yet not all preserve sequence information to a similar degree. Furthermore, a 2017 study by Mackie et al. examined the dental calculus of 21 Roman-era H. sapiens specimens from 3 European burial sites using LC-MS/MS sequencing. Reported sequence preservation varied widely between specimens and was unattributable to any specific variables60. These differences in preservation likely result from other variables including differences in composition16-20, moisture content17-21, and oxygen17-23content of burial sediments, among others. The complex range of variables potentially affecting sequence preservation supports that factors beyond geologic age and thermal history are responsible for specimens demonstrating exceptional sequence preservation. This limits the usefulness of any single diagenetic variable, such as geologic age or thermal history, as a proxy for DNA and protein sequence preservation.
A proposed solution to this limitation is to directly use fossil/sub-fossil molecular histology as a proxy for molecular sequence preservation. Molecular histology is the underlying basis for why diagenetic variables such as thermal history and geologic age can be used as proxies, in any capacity, for predicting sequence preservation. The cumulative effects of diagenetic variables are reflected in the preservational condition of a fossil or sub-fossil’s molecular histology17, 20, 27. Directly studying molecular histology and correlating it with degree of sequence preservation bypasses the need to study any one of these variables individually. Thus molecular histology is hypothesized to be usable as an accurate proxy for molecular sequence preservation. Yet little empirical research exists to this point that has observed how molecular histology of fossil and sub-fossil specimens varies with degree of sequence preservation.