Increasing sustainability in palaeoproteomics by optimizing digestion times for large-scale archaeological bone analyses

Palaeoproteomic analysis of skeletal proteomes is used to provide taxonomic identifications for an increasing number of archaeological specimens. The success rate depends on a range of taphonomic factors and differences in the extraction protocols employed. By analyzing 12 archaeological bone specimens from two archaeological sites, we demonstrate that reducing digestion duration from 18 to 3 hours has no measurable impact on the obtained taxonomic identifications. Peptide marker recovery, COL1 sequence coverage, or proteome complexity are also not significantly impacted. Although we observe minor differences in sequence coverage and glutamine deamidation, these are not consistent across our dataset. A 6-fold reduction in digestion time reduces electricity consumption, and therefore CO2 emission intensities. We furthermore demonstrate that working in 96-well plates further reduces electricity consumption by 60%, in comparison to individual microtubes. Reducing digestion time therefore has no impact on the taxonomic identifications, while reducing the environmental impact of palaeoproteomic projects

Molecular characterization and effect of diagenesis and maturation of melanin in the fossil record

Thesis: S.M. in Geology, Geochemistry and Geobiology, Massachusetts Institute of Technology, Department of Earth, Atmospheric, and Planetary Sciences, 2019Cataloged from PDF version of thesis.Includes bibliographical references.Despite the fact that melanin is a ubiquitous pigment found in bacteria, fungi, plants and animals, little is known about its chemical preservation and distribution in the fossil record. Melanins are polymeric phenolic compounds classified into two major groups based in their chemical structures and molecular precursors: eumelanin (dark brown-black in color) and pheomelanin (orange-red in color). Both eumelanin and pheomelanin are complex highly cross-linked biopolymers, being comparable to biomolecules like chitin that are resistant to microbial degradation and diagenetic alteration thereby affording melanins the potential to maintain their integrity for millions of years. Color patterns depend on pigment composition and arrangement. Recent studies have demonstrated that melanin is one of those pigments with the high preservation potential over geologic time scales; it is found in virtually all extant organisms, from bacteria to humans.For this reason, the analysis of fossil pigments such as melanin may allow inferences about important aspects of the ecology, behavior and evolution of ancient animals. Several studies and techniques have been presented in the last couple of years that have described ways to characterize pigment patterns. These include coupled microscopic and spectroscopic methods, such as Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS), scanning electron microscope (SEM) and synchrotron X-ray techniques, used to examine the morphology and spatial distribution of pigment structures in well-preserved fossil tissues. More recently, mass spectroscopic techniques such as pyrolysis-gas chromatography-mass spectroscopy (Py-GCMS) have been applied, allowing us to determine the composition of melanin fossils through of the identification of its diagenetic products and their processes of chemical preservation.In this study, we applied Py-GCMS to understand and identify degradation products of melanin from different cephalopod taxa with different maturation histories. Additionally, we analyze fossilized soft-tissue samples from an exceptionally preserved specimen of Borealopelia markmitchelli, a heavily armored herbivorous tetrapod dinosaur, to unveil color patterns and ecology. Our preliminary results improve our understanding of soft tissue preservation and show chemical evidence to support melanin identification, as well to discern chemical features that reflect original color characteristics.by Jorsua Herrera Bethencourt.S.M. in Geology, Geochemistry and GeobiologyS.M.inGeology,GeochemistryandGeobiology Massachusetts Institute of Technology, Department of Earth, Atmospheric, and Planetary Science

An Exceptionally Preserved Three-Dimensional Armored Dinosaur Reveals Insights into Coloration and Cretaceous Predator-Prey Dynamics

Predator-prey dynamics are an important evolutionary driver of escalating predation mode and efficiency, and commensurate responses of prey. Among these strategies, camouflage is important for visual concealment, with countershading the most universally observed. Extant terrestrial herbivores free of significant predation pressure, due to large size or isolation, do not exhibit countershading. Modern predator-prey dynamics may not be directly applicable to those of the Mesozoic due to the dominance of very large, visually oriented theropod dinosaurs. Despite thyreophoran dinosaurs’ possessing extensive dermal armor, some of the most extreme examples of anti-predator structures, little direct evidence of predation on these and other dinosaur megaherbivores has been documented. Here we describe a new, exquisitely three-dimensionally preserved nodosaurid ankylosaur, Borealopelta markmitchelli gen. et sp. nov., from the Early Cretaceous of Alberta, which preserves integumentary structures as organic layers, including continuous fields of epidermal scales and intact horn sheaths capping the body armor. We identify melanin in the organic residues through mass spectroscopic analyses and observe lighter pigmentation of the large parascapular spines, consistent with display, and a pattern of countershading across the body. With an estimated body mass exceeding 1,300 kg, B. markmitchelli was much larger than modern terrestrial mammals that either are countershaded or experience significant predation pressure as adults. Presence of countershading suggests predation pressure strong enough to select for concealment in this megaherbivore despite possession of massive dorsal and lateral armor, illustrating a significant dichotomy between Mesozoic predator-prey dynamics and those of modern terrestrial systems.Suncor EnergyRoyal Tyrrell Museum Cooperating SocietyNational Geographic Society (U.S.