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.