Introduction
Reports on the successful recovery of biomolecules from vertebrate
fossils and sub-fossils (“subfossil” defined as being not fully
fossilized) have increased exponentially over the prior 2 decades.
Evidence supports the persistence of DNA sequences past
1Ma1, and protein sequences have been reported to
preserve into the Pliocene epoch (~3.5Ma) with minimal
controversy2-4. Predictive and empirical studies have
established that the potential of sequence data to persist into deep
time depends substantially on thermal setting3, 5-7 as
well as the type of biological material examined; bone, dentine, enamel,
or eggshell3, 5, 8. These advances in DNA and protein
sequence recovery have expanded the opportunity for palaeoecological and
paleoenvironmental studies to be conducted over a broader range of taxa
and geological timepoints. Data reported from such studies are used to
inform on and set conservation policy for extant wildlife populations
that are of commercial interest, at risk of extinction, potentially
invasive, at risk of low genetic diversity, etc.9-12.
Despite these advances, the ability to predict which ancient specimens
are likely to preserve molecular sequences still remains limited. A
prevailing view within the primary literature is that specimens exposed
to prolonged, elevated thermal conditions are less likely to preserve
proteins and DNA3, 5, 6, 13. As an example, permafrost
settings and late Pleistocene geologic timepoints have been shown
favorable for the preservation of molecular sequences5,
6, 8, 14, 15. Such findings have supported the use of specimen thermal
history and geologic age as proxies for molecular sequence
preservation3, 5, 6, 13. However, this observation
only holds in a general sense and to a relative degree. Other variables
affecting protein and DNA preservation include sediment
composition16-20, moisture
content17-21, and oxygen
content17-23, among others. Consequently, multiple
studies have reported differing degrees of sequence preservation even
for specimens sharing similar thermal histories and/or geologic
ages8, 13, 15, 24, 25. In such situations, thermal
setting and geologic age are rendered marginally effective as proxies.
Indeed, the complexity of variables influencing molecular sequence
preservation in vertebrate remains means that any single variable
selected for use as a proxy for sequence preservation will inevitably
have substantial limitations.
A potential solution to these limitations is to directly examine the
molecular histology of preserved subfossil/fossil tissues and cells.
Molecular histology is defined by Campbell and Pignatelli (2002) as “an
explanation of the morphological characteristics of a tissue in terms of
the molecules present and the functional interactions between
them”26. Molecular histology is how an organism’s
molecular makeup is manifested as cells and tissues, and variables
including thermal history, geologic age, sediment composition, and
others all directly affect how this molecular makeup
preserves17, 20, 27. Thus, the preserved state of a
fossil/sub-fossil’s molecular histology (which includes molecular
sequences), is representative of the combined effect of these diagenetic
variables upon its molecular sequences. Substantial precedence exists in
the scientific literature for the preservation of remnant cells and
tissues within ancient vertebrate specimens22, 28-40.
Data characterizing the molecular histology of such remains is herein
hypothesized to be usable as a proxy for molecular sequence
preservation. Correlating molecular histology with degree of sequence
preservation across specimens spanning the fossil record would advance
the use of such a proxy.
Testing this hypothesis can be accomplished using a suite of molecular
techniques capable of characterizing both the
morphological29, 32, 33, 35, 40, 41 and
chemical22, 23, 29, 31, 36, 42, 43 aspects of
molecular histology. Such data can then be used to identify connections
between a fossil’s observed molecular histology and its degree of
molecular sequence preservation. Additionally, changes in
fossil/sub-fossil molecular histology can be tracked across various
geologic ages and depositional environments to reveal potential insights
as to the role diagenetic variables play in sequence preservation.
Ultimately, the study of fossil and sub-fossil molecular histology will
introduce novel and practical methods for screening whether a given
specimen should be selected for molecular sequencing, and it will
increase understanding of how geologic age, thermal history, and other
diagenetic variables influence sequence preservation.