Paleoproteomics of Mesozoic Dinosaurs and Other Mesozoic Fossils

Abstract

Mary Higby Schweitzer would like to dedicate this review to Rune Martinson, a brave warrior in the fight against cancer who left us far too soon.Molecular studies have contributed greatly to our understanding of evolutionary processes that act upon virtually every aspect of living organisms. However, these studies are limited with regard to extinct organisms, particularly those from the Mesozoic because fossils pose unique challenges to molecular workflows, and because prevailing wisdom suggests no endogenous molecular components can persist into deep time. Here, the power and potential of a molecular approach to Mesozoic fossils is discussed. Molecular methods that have been applied to Mesozoic fossils-including iconic, non-avian dinosaurs-and the challenges inherent in such analyses, are compared and evaluated. Taphonomic processes resulting in the transition of living organisms from the biosphere into the fossil record are reviewed, and the possible effects of taphonomic alteration on downstream analyses that can be problematic for very old material (e.g., molecular modifications, limitations of on comparative databases) are addressed. Molecular studies applied to ancient remains are placed in historical context, and past and current studies are evaluated with respect to producing phylogenetically and/or evolutionarily significant data. Finally, some criteria for assessing the presence of endogenous biomolecules in very ancient fossil remains are suggested as a starting framework for such studies.

Genome-centric resolution of novel microbial lineages in an excavated Centrosaurus dinosaur fossil bone from the Late Cretaceous of North America

“…Keywords: Centrosaurus fossil bone, Diagenesis, Rare Actinobacteria, Halotolerant bacteria, Late Cretaceous, Uncultured microbial lineages Background Persistence of endogenous organic remains such as DNA and proteins in Mesozoic dinosaurs has long been deemed unlikely due to their lability and gradual breakdown through deep time and diagenesis [1][2][3]. However, a series of groundbreaking studies has proposed through structural observations, immunohistochemistry, proteomics and in situ microspectroscopic methods [4][5][6][7][8][9][10][11] that endogenous organics such as collagens, blood vessels, erythrocytes and osteocytes appear to be organically preserved in various dinosaur fossils with relatively limited alteration. The reports of collagen peptides from Mesozoic dinosaur fossils are often viewed as particularly exciting in paleontology as they, if genuine, could dramatically enhance our understanding of the evolutionary biology of extinct organisms through deep time [5].…”

“…However, a series of groundbreaking studies has proposed through structural observations, immunohistochemistry, proteomics and in situ microspectroscopic methods [4][5][6][7][8][9][10][11] that endogenous organics such as collagens, blood vessels, erythrocytes and osteocytes appear to be organically preserved in various dinosaur fossils with relatively limited alteration. The reports of collagen peptides from Mesozoic dinosaur fossils are often viewed as particularly exciting in paleontology as they, if genuine, could dramatically enhance our understanding of the evolutionary biology of extinct organisms through deep time [5]. Despite the increasing number of reports about the preservation of endogenous biocomponents in dinosaur fossils over the last decade, their existence remains controversial due to concerns about exogenous contamination from microbial biofilms [12] and other sources associated with analytical procedures [13][14][15], and to the difficulty in reasonably explaining the mechanisms for their exceptional preservation [5].…”

“…The reports of collagen peptides from Mesozoic dinosaur fossils are often viewed as particularly exciting in paleontology as they, if genuine, could dramatically enhance our understanding of the evolutionary biology of extinct organisms through deep time [5]. Despite the increasing number of reports about the preservation of endogenous biocomponents in dinosaur fossils over the last decade, their existence remains controversial due to concerns about exogenous contamination from microbial biofilms [12] and other sources associated with analytical procedures [13][14][15], and to the difficulty in reasonably explaining the mechanisms for their exceptional preservation [5].…”

“…The complete pathway for the tricarboxylic acid cycle was identified in 32 MAGs. By contrast, only 14 MAGs Since purported endogenous organics such as collagens and osteocytes have been discovered in various Mesozoic dinosaurs [4][5][6][7][8][9][10], we screened all MAGs for their potential to degrade collagens. Microbial collagenases were detected in 5 MAGs (Dino_bin7, Dino_ bin12, Dino_13, Dino_bin35, and Dino_bin44) affiliated with Actinobacteria and Acidobacteria (Fig.…”

Ambiguity coding allows accurate inference of evolutionary parameters from alignments in an aggregated state-space

“…A more speculative and potentially intriguing application would be estimating selection or structural information from ancient protein sequences. Proteins can persist for longer in the environment than DNA under certain conditions [36][37][38], enabling phylogenetic inferences to be made based on substantially older specimens such as dinosaurs [39,40]. Our methods permit the use of a mixture of all available DNA and protein sequences to maximise signal, extending analyses that are normally only possible with DNA sequences to incorporate additional data sources.…”