Structural and Protein Preservation in Fossil Whale Bones From the Pisco Formation (Middle-Upper Miocene), Peru

Abstract

Microstructural and biomolecular preservation is reported in fossils as old as the Triassic. Such preservation suggests unusual taphonomic conditions. We collected fragments of fossil whale bone from silty, tuffaceous, and diatomaceous rocks of the middle-upper Miocene portion of the Pisco Formation. The whale fossils within the region are generally well-preserved and mostly articulated, including some specimens with in situ baleen. Due to the depositional setting associated with the preservation of these fossils, they could be expected to be favorable candidates for the preservation of cellular microstructures and/or original biomolecules. To test this hypothesis, fossil whale bone fragments were subjected to microscopic analysis and EDTA-mediated demineralization to release extractable materials. Microscopy of partially demineralized fossil bones revealed quartz-permineralized osteocyte-like and vessel-like structures. Protein assay (micro-Bicinchoninic Acid Assay) of the supernatants obtained from demineralized fossils yielded 12 to 19.5 μg of protein per gram of bone. MALDI-TOF analysis of the extracted protein demonstrated the presence of approximately 5 kD molecules in one fossil sample, consistent with the presence of highly fragmented polypeptides. An LC-MS/MS analysis of the fragmentation pattern of the tryptic digest of extracted protein was performed. However, attempted protein identification was unsuccessful. Nevertheless, this study first documents the microstructural preservation with some silicification of the fossil whale bones of the Pisco Formation, and then quantifies extractable protein from these bones. It adds to the growing body of reports of microstructural and organic preservation in fossils.

Molecular Histology as a Novel Proxy for Ancient DNA and Protein Sequence Preservation

“…The presence of such exogenous minerals supports that this tibia had undergone substantial chemical alteration. Both mineral precipitants are consistent with observations from older tertiary [37][38][39] and even Mesozoic specimens 16,35,36,40,41 , and certainly precludes it from being considered a "sub-fossil". Despite the apparent chemical alteration to its molecular histology, the tibia still preserved collagen sequences identifiable via mass spectrometry 2 .…”

“…Thus, the preserved state of a fossil/subfossil'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 specimens 22,[28][29][30][31][32][33][34][35][36][37][38][39][40] . Data characterizing the molecular histology of such remains is herein hypothesized to be usable as a proxy for molecular sequence preservation.…”

Vertebrate Palaeoecology of the Pisco Formation (Miocene, Peru): Glimpses into the Ancient Humboldt Current Ecosystem

“…International interest in the Pisco Formation soared with the description of numerous marine vertebrates from the late 1970s onwards [15,16,20,46,48,50,. The richness and exceptional quality of these fossils in turn triggered attempts to quantify the overall association and investigate its taphonomy [17][18][19]31,34,88].…”

A Chemical Framework for the Preservation of Fossil Vertebrate Cells and Soft Tissues

“…Anaerobic AGE formation could provide this stabilization relatively shortly post-mortem (Vistoli et al 2013), as could sulfurization in the presence of substantial hydrogen sulfide (Damsté et al 2007;Koopmans et al 1997;McNamara et al 2016). This would account for the observation that specimens exhibiting cell and other soft tissue preservation can be recovered from anoxic depositional environments (Boskovic et al 2021;Lindgren et al 2017;Lindgren et al 2018;Lindgren et al 2011).…”

“…Combined with the generally recalcitrant nature of lipids (Briggs et al 2000;Schweitzer 2011), this could stabilize soft tissues to some extent under anoxic conditions and allow thermally/time mediated in-situ polymerization to then take place. This would potentially account for reports of soft tissues from vertebrate specimens of anoxic, marine settings (Boskovic et al 2021;Lindgren et al 2017;Lindgren et al 2018;Lindgren et al 2011). However, further exploration of the nature of such a mechanism is outside the scope of this paper.…”