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.