Mineralized soft-tissue structure and chemistry in a mummified hadrosaur from the Hell Creek Formation, North Dakota (USA)

An evaluation of the effect of hydrofluoric acid (HF) treatment on keratins

Hydrofluoric acid (HF) is commonly used in geological and paleontological research to extract organic fossils for morphological and chemical studies. However, during HF treatment, organic matter can also be altered, which raises concerns that HF-treated organic matter may not be representative of the original organic matter. To provide reference data for protein studies on fossils, herein, we use Fourier transform infrared (FTIR) spectroscopy to investigate the effect of HF (21.3 M) treatment on keratins, with treatment durations ranging from 2 to 48 h. Results show that the FTIR spectra of HF-treated samples are overall similar to that of the untreated sample, while curve fitting shows that HF treatment has led to alteration of the secondary structure in all the HF-treated samples and the effect is time-dependent. The 2- and 4-h treatment mainly reduced the content of the random coils, α-helix, and intermolecular β-sheet. From 8h onwards, the content of random coils greatly increased at the expense of other structures. Our results imply that for protein detection in fossils using FTIR spectroscopy, the negative effect of HF treatment is not substantial, as the bands characteristic of proteins, that is, amide A, amide B, amide I, amide II, and amide III, are still present after the 48-h treatment. If the target is a secondary structure, the effect of HF treatment should be considered. When HF treatment is necessary, limiting the treatment duration to less than 4h may be a choice.

The diagenetic fate of collagen as revealed by analytical pyrolysis of fossil fish scales from deep time

The mechanism of protein degradation has remained a topic of debate (specifically concerning their preservation in deep time), which has recently been invigorated due to multiple published reports of preservation ranging from Miocene to the Triassic that potentially challenge the convention that protein preservation beyond the Cenozoic is extremely uncommon or is expected to be absent altogether, and thus have attracted skepticism. In this paper, we analyze fossil fish scales from the Cretaceous, Jurassic, and Triassic using comprehensive pyrolysis gas chromatography coupled with time-of-flight mass spectrometry and compare the pyrolytic products so obtained with a well-preserved fish scale from Late Pliocene, in an attempt to better understand the effects of diagenesis on protein degradation at the molecular level through deep time. We find that the Pliocene fish scale displays a large number of N-bearing pyrolytic products, including abundant substituted cyclic 2,5-diketopiperazines (2,5-DKPs) which are diagnostic products of peptide and amino acid pyrolysis. We identify N-bearing compounds in the Mesozoic fish scales-however, among the 2,5-DKPs that were identified in the Pliocene scale, only diketodipyrrole (or cyclo (Pyr-Pyr)) is present in the Mesozoic scales. We discuss the implications of N-bearing pyrolytic products with emphasis on 2,5-DKPs in geological samples and conclude that the discrepancy in abundance and variety of N-bearing products between Pliocene and Mesozoic scales indicates that the protein component in the latter has been extensively diagenetically altered, while a suite of DKPs such as in the former would imply stronger evidence to indicate preservation of protein. We conclude that analytical pyrolysis is an effective tool for detecting preservation of intact proteins, as well as for providing insights into their degradation mechanisms, and can potentially be utilized to assign proteinaceous origin to a fossil sample of unknown affinity.

Biomolecular histology as a novel proxy for ancient DNA and protein sequence preservation

Researchers' ability to accurately screen fossil and subfossil specimens for preservation of DNA and protein sequences remains limited. Thermal exposure and geologic age are usable proxies for sequence preservation on a broad scale but are of nominal use for specimens of similar depositional environments. Cell and tissue biomolecular histology is thus proposed as a novel proxy for determining sequence preservation potential of ancient specimens with improved accuracy. Biomolecular histology as a proxy is hypothesized to elucidate why fossils/subfossils of some depositional environments preserve sequences while others do not and to facilitate selection of ancient specimens for use in molecular studies.

Biostratinomic alterations of an Edmontosaurus "mummy" reveal a pathway for soft tissue preservation without invoking "exceptional conditions"

Removal or protection from biostratinomic agents of decomposition, such as predators and scavengers, is widely seen as a requirement for high-quality preservation of soft tissues in the fossil record. In this context, extremely rapid burial is an oft-cited mechanism for shielding remains from degradation, but not all fossils fit nicely into this paradigm. Dinosaurian mummies in particular seemingly require two mutually exclusive taphonomic processes to preserve under that framework: desiccation and rapid burial. Here we present a recently prepared Edmontosaurus mummy that reveals an alternate fossilization pathway for resistant soft tissues (e.g., skin and nails). While the skin on this specimen is well-preserved in three dimensions and contains biomarkers, it is deflated and marked by the first documented examples of injuries consistent with carnivore activity on dinosaurian soft tissue during the perimortem interval. Incomplete scavenging of the carcass provided a route for the gases, fluids, and microbes associated with decomposition to escape, allowing more durable soft tissues to persist through the weeks to months required for desiccation prior to entombment and fossilization. This pathway is consistent with actualistic observations and explains why dinosaurian skin, while rare, is more commonly preserved than expected if extreme circumstances were required for its preservation. More broadly, our assumptions guide specimen collection and research, and the presence of soft tissues and biomolecules in fossils that demonstrably were not rapidly buried, such as this mummy, suggests that such types of evidence may be substantially more common than previously assumed.

Taphonomic and Diagenetic Pathways to Protein Preservation, Part II: The Case of Brachylophosaurus canadensis Specimen MOR 2598

Simple Summary

Reports of the recovery of proteins and other molecules from fossils have become so common over the last two decades that some paleontologists now focus almost entirely on studying how biologic molecules can persist in fossils. In this study, we explored the fossilization history of a specimen of the hadrosaurid dinosaur Brachylophosaurus which was previously shown to preserve original cells, tissues, and structural proteins. Trace element analyses of the tibia of this specimen revealed that after its bones were buried in a brackish estuarine channel, they fossilized under wet conditions which shifted in redox state multiple times. The successful recovery of proteins from this specimen, despite this complex history of chemical alterations, shows that the processes which bind and stabilize biologic molecules shortly after death provide them remarkable physical and chemical resiliency. By uniting our results with those of similar studies on other dinosaur fossils known to also preserve original proteins, we also conclude that exposure to oxidizing conditions in the initial ~48 h postmortem likely promotes molecular stabilization reactions, and the retention of early-diagenetic trace element signatures may be a useful proxy for molecular recovery potential.

Abstract

Recent recoveries of peptide sequences from two Cretaceous dinosaur bones require paleontologists to rethink traditional notions about how fossilization occurs. As part of this shifting paradigm, several research groups have recently begun attempting to characterize biomolecular decay and stabilization pathways in diverse paleoenvironmental and diagenetic settings. To advance these efforts, we assessed the taphonomic and geochemical history of Brachylophosaurus canadensis specimen MOR 2598, the left femur of which was previously found to retain endogenous cells, tissues, and structural proteins. Combined stratigraphic and trace element data show that after brief fluvial transport, this articulated hind limb was buried in a sandy, likely-brackish, estuarine channel. During early diagenesis, percolating groundwaters stagnated within the bones, forming reducing internal microenvironments. Recent exposure and weathering also caused the surficial leaching of trace elements from the specimen. Despite these shifting redox regimes, proteins within the bones were able to survive through diagenesis, attesting to their remarkable resiliency over geologic time. Synthesizing our findings with other recent studies reveals that oxidizing conditions in the initial ~48 h postmortem likely promote molecular stabilization reactions and that the retention of early-diagenetic trace element signatures may be a useful proxy for molecular recovery potential.

Soft-Tissue, Rare Earth Element, and Molecular Analyses of Dreadnoughtus schrani, an Exceptionally Complete Titanosaur from Argentina

Evidence that organic material preserves in deep time (>1 Ma) has been reported using a wide variety of analytical techniques. However, the comprehensive geochemical data that could aid in building robust hypotheses for how soft-tissues persist over millions of years are lacking from most paleomolecular reports. Here, we analyze the molecular preservation and taphonomic history of the Dreadnougtus schrani holotype (MPM-PV 1156) at both macroscopic and microscopic levels. We review the stratigraphy, depositional setting, and physical taphonomy of the D. schrani skeletal assemblage, and extensively characterize the preservation and taphonomic history of the humerus at a micro-scale via: (1) histological analysis (structural integrity) and X-ray diffraction (exogenous mineral content); (2) laser ablation-inductively coupled plasma mass spectrometry (analyses of rare earth element content throughout cortex); (3) demineralization and optical microscopy (soft-tissue microstructures); (4) in situ and in-solution immunological assays (presence of endogenous protein). Our data show the D. schrani holotype preserves soft-tissue microstructures and remnants of endogenous bone protein. Further, it was exposed to LREE-enriched groundwaters and weakly-oxidizing conditions after burial, but experienced negligible further chemical alteration after early-diagenetic fossilization. These findings support previous hypotheses that fossils that display low trace element uptake are favorable targets for paleomolecular analyses.

Identification of Chitin in Pliocene Fungi Using Py-GC × GC-TOFMS: Potential Implications for the Study of the Evolution of the Fungal Clade in Deep Time

Molecular dating estimates the origin of the fungal clade to the Pre-Cambrian. Yet, the oldest unambiguous fungal fossils date to the Ordovician and show remarkable diversity and organizational development. Recent studies have suggested that the dates for the emergence of fungi in the fossil record may be pushed back to the Proterozoic. However, the nonspecificity of the methods used in those studies necessitates the employment of a wider variety of analytical techniques that can independently verify the presence of chitin, a crucial prerequisite in the assignment of fungal affinity, particularly of putative fossils from the Pre-Cambrian. In this paper, we propose Py-GC × GC-TOFMS as an example of one such technique. We analyze fungal fossils from the Pliocene. We find that a suite of N-bearing compounds are present in the pyrolysis products of these fossils, from which we suggest that 3-acetamidopyrones and their methylated homologues can serve as specific pyrolytic markers for chitin. We discuss both how this technique can potentially be used to differentiate between biopolymers, including those similar to chitin such as peptidoglycan, and the potential implications of identifying such markers in fossils from deep time. We conclude that Py-GC × GC-TOFMS is a promising technique that can potentially be used alongside, or independent of, staining methods to detect the presence of chitin in fossils.

Morphology and distribution of scales, dermal ossifications, and other non-feather integumentary structures in non-avialan theropod dinosaurs

Modern birds are typified by the presence of feathers, complex evolutionary innovations that were already widespread in the group of theropod dinosaurs (Maniraptoriformes) that include crown Aves. Squamous or scaly reptilian-like skin is, however, considered the plesiomorphic condition for theropods and dinosaurs more broadly. Here, we review the morphology and distribution of non-feathered integumentary structures in non-avialan theropods, covering squamous skin and naked skin as well as dermal ossifications. The integumentary record of non-averostran theropods is limited to tracks, which ubiquitously show a covering of tiny reticulate scales on the plantar surface of the pes. This is consistent also with younger averostran body fossils, which confirm an arthral arrangement of the digital pads. Among averostrans, squamous skin is confirmed in Ceratosauria (Carnotaurus), Allosauroidea (Allosaurus, Concavenator, Lourinhanosaurus), Compsognathidae (Juravenator), and Tyrannosauroidea (Santanaraptor, Albertosaurus, Daspletosaurus, Gorgosaurus, Tarbosaurus, Tyrannosaurus), whereas dermal ossifications consisting of sagittate and mosaic osteoderms are restricted to Ceratosaurus. Naked, non-scale bearing skin is found in the contentious tetanuran Sciurumimus, ornithomimosaurians (Ornithomimus) and possibly tyrannosauroids (Santanaraptor), and also on the patagia of scansoriopterygids (Ambopteryx, Yi). Scales are surprisingly conservative among non-avialan theropods compared to some dinosaurian groups (e.g. hadrosaurids); however, the limited preservation of tegument on most specimens hinders further interrogation. Scale patterns vary among and/or within body regions in Carnotaurus, Concavenator and Juravenator, and include polarised, snake-like ventral scales on the tail of the latter two genera. Unusual but more uniformly distributed patterning also occurs in Tyrannosaurus, whereas feature scales are present only in Albertosaurus and Carnotaurus. Few theropods currently show compelling evidence for the co-occurrence of scales and feathers (e.g. Juravenator, Sinornithosaurus), although reticulate scales were probably retained on the mani and pedes of many theropods with a heavy plumage. Feathers and filamentous structures appear to have replaced widespread scaly integuments in maniraptorans. Theropod skin, and that of dinosaurs more broadly, remains a virtually untapped area of study and the appropriation of commonly used techniques in other palaeontological fields to the study of skin holds great promise for future insights into the biology, taphonomy and relationships of these extinct animals.

Proteoglycans and Diseases of Soft Tissues

Proteoglycans consist of protein cores to which at least one glycosaminoglycan chain is attached. They play important roles in the physiology and biomechanical function of tendons, ligaments, cardiovascular system, and other systems through their involvement in regulation of assembly and maintenance of extracellular matrix, and through their participation in cell proliferation together with growth factors. They can be divided into two main groups, small and large proteoglycans. The small proteoglycans are also known as small leucine-rich proteoglycans (SLRPs) which are encoded by 18 genes and are further subclassified into Classes I-V. Several members of Class I and II, such as decorin and biglycan from Class I, and Class II fibromodulin and lumican, are known to regulate collagen fibrillogenesis. Decorin limits the diameter of collagen fibrils during fibrillogenesis. The function of biglycan in fibrillogenesis is similar to that of decorin. Though biomechanical function of tendon is compromised in decorin-deficient mice, decorin can substitute for lack of biglycan in biglycan-deficient mice. New data also indicate an important role for biglycan in disorders of the cardiovascular system, including aortic valve stenosis and aortic dissection. Two members of the Class II of SLRPs, fibromodulin and lumican bind to the same site within the collagen molecule and can substitute for each other in fibromodulin- or lumican-deficient mice.Aggrecan and versican are the major representatives of the large proteoglycans. Though they are mainly found in the cartilage where they provide resilience and toughness, they are present also in tensile portions of tendons and, in slightly different biochemical form in fibrocartilage. Degradation by aggrecanase is responsible for the appearance of different forms of aggrecan and versican in different parts of the tendon where these cleaved forms play different roles. In addition, they are important components of the ventricularis of cardiac valves. Mutations in the gene for versican or in the gene for elastin (which binds to versican ) lead to severe disruptions of normal developmental of the heart at least in mice.

Exceptionally preserved 'skin' in an Early Cretaceous fish from Colombia

Studies of soft tissue, cells and original biomolecular constituents preserved in fossil vertebrates have increased greatly in recent years. Here we report preservation of 'skin' with chemical and molecular characterization from a three-dimensionally preserved caudal portion of an aspidorhynchid Cretaceous fish from the equatorial Barremian of Colombia, increasing the number of localities for which exceptional preservation is known. We applied several analytical techniques including SEM-EDS, FTIR and ToF-SIMS to characterize the micromorphology and molecular and elemental composition of this fossil. Here, we show that the fossilized 'skin' exhibits similarities with those from extant fish, including the wrinkles after suffering compression stress and flexibility, as well as architectural and tissue aspects of the two main layers (epidermis and dermis). This similarity extends also to the molecular level, with the demonstrated preservation of potential residues of original proteins not consistent with a bacterial source. Our results show a potential preservation mechanism where scales may have acted as an external barrier and together with an internal phosphate layer resulting from the degradation of the dermis itself creating an encapsulated environment for the integument.

Anatomy of a dinosaur-Clarification of vertebrae in vertebrate anatomy

The flat-end surfaces of dinosaur vertebral centra led to the presumption that intervertebral discs occupied the space between their vertebrae. A set of fused hadrosaur vertebrae allowed that hypothesis to be tested. The Tyrannosaurus rex responsible for this pathology did not escape unscathed. It left behind a tooth crown that had fractured. Fragments of that tooth were scattered through the intervertebral space, evidencing that there was no solid structure to impede its movement. That eliminates the possibility of an intervertebral disc and instead proves the presence of an articular space, similar to that in modern reptiles, but at variance to what is noted in birds. While avian cervical vertebral centra appear to be separated by diarthrodial joints, the preponderance of their thoracic vertebral centra is not separated by synovial joints.

Taphonomic experiments resolve controls on the preservation of melanosomes and keratinous tissues in feathers

Fossils are a key source of data on the evolution of feather structure and function through deep time, but their ability to resolve macroevolutionary questions is compromised by an incomplete understanding of their taphonomy. Critically, the relative preservation potential of two key feather components, melanosomes and keratinous tissue, is not fully resolved. Recent studies suggesting that melanosomes are preferentially preserved conflict with observations that melanosomes preserve in fossil feathers as external moulds in an organic matrix. To date, there is no model to explain the latter mode of melanosome preservation. We addressed these issues by degrading feathers in systematic taphonomic experiments incorporating decay, maturation and oxidation in isolation and combination. Our results reveal that the production of mouldic melanosomes requires interactions with an oxidant and is most likely to occur prior to substantial maturation. This constrains the taphonomic conditions under which melanosomes are likely to be fossilized. Critically, our experiments also confirm that keratinous feather structures have a higher preservation potential than melanosomes under a range of diagenetic conditions, supporting hitherto controversial hypotheses that fossil feathers can retain degraded keratinous structures.

Proteomes of the past: the pursuit of proteins in paleontology

Introduction: Despite an extensive published literature, skepticism over the claim of original biochemicals including proteins preserved in the fossil record persists and the issue remains controversial. Workers using many different techniques including mass spectrometry, X-ray, electron microscopy and optical spectroscopic techniques, have attempted to verify proteinaceous or other biochemicals that appear endogenous to fossils found throughout the geologic column.Areas covered: This paper presents a review of the relevant literature published over the last 50 years. A comparative survey of the reported techniques used is also given.Expert opinion: Morphological and molecular investigations show that original biochemistry is geologically extensive, geographically global, and taxonomically wide-ranging. The survival of endogenous organics in fossils remains the subject of widespread and increasing research investigation.

Integumentary structure and composition in an exceptionally well-preserved hadrosaur (Dinosauria: Ornithischia)

Preserved labile tissues (e.g., skin, muscle) in the fossil record of terrestrial vertebrates are increasingly becoming recognized as an important source of biological and taphonomic information. Here, we combine a variety of synchrotron radiation techniques with scanning electron and optical microscopy to elucidate the structure of 72 million-year-old squamous (scaly) skin from a hadrosaurid dinosaur from the Late Cretaceous of Alberta, Canada. Scanning electron and optical microscopy independently reveal that the three-dimensionally preserved scales are associated with a band of carbon-rich layers up to a total thickness of ∼75 microns, which is topographically and morphologically congruent with the stratum corneum in modern reptiles. Compositionally, this band deviates from that of the surrounding sedimentary matrix; Fourier-transform infrared spectroscopy and soft X-ray spectromicroscopy analyses indicate that carbon appears predominantly as carbonyl in the skin. The regions corresponding to the integumentary layers are distinctively enriched in iron compared to the sedimentary matrix and appear with kaolinite-rich laminae. These hosting carbonyl-rich layers are apparently composed of subcircular bodies resembling preserved cell structures. Each of these structures is encapsulated by calcite/vaterite, with iron predominantly concentrated at its center. The presence of iron, calcite/vaterite and kaolinite may, independently or collectively, have played important roles in the preservation of the layered structures.

Applications of chemical imaging techniques in paleontology

Chemical imaging techniques, based on a combination of microscopy and spectroscopy, are designed to analyse the composition and spatial distribution of heterogeneous chemical complexes within a sample. Over the last few decades, it has become an increasingly popular tool for characterizing trace elements, isotopic information and organic biomarkers (molecular biosignatures) found in fossils. Here, we introduce the analytical principle of each technique and the interpretation of the chemical signals, followed by a review of the main applications of these techniques in paleontology. We also demonstrate that each technique is associated with pros and cons, and the current limitations and obstacles associated with the use of each specific technique should be taken into account before being applied to fossil samples. Finally, we propose that, due to the rapid advances in the available technology and overall trends towards more multi-disciplinary studies in paleontology, chemical imaging techniques can be expected to have broader applications in paleontology in the near future.

Paleoproteomics of Mesozoic Dinosaurs and Other Mesozoic Fossils

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.

Pheomelanin pigment remnants mapped in fossils of an extinct mammal

Recent progress has been made in paleontology with respect to resolving pigmentation in fossil material. Morphological identification of fossilized melanosomes has been one approach, while a second methodology using chemical imaging and spectroscopy has also provided critical information particularly concerning eumelanin (black pigment) residue. In this work we develop the chemical imaging methodology to show that organosulfur-Zn complexes are indicators of pheomelanin (red pigment) in extant and fossil soft tissue and that the mapping of these residual biochemical compounds can be used to restore melanin pigment distribution in a 3 million year old extinct mammal species (Apodemus atavus). Synchotron Rapid Scanning X-ray Fluorescence imaging showed that the distributions of Zn and organic S are correlated within this fossil fur just as in pheomelanin-rich modern integument. Furthermore, Zn coordination chemistry within this fossil fur is closely comparable to that determined from pheomelanin-rich fur and hair standards. The non-destructive methods presented here provide a protocol for detecting residual pheomelanin in precious specimens.

Chemical imaging and spectroscopy have previously been used to identify eumelanin residue in fossils and infer dark coloration. Here, Manning and colleagues develop an approach to identify pheomelanin (red pigment) residues and ascertain their distribution in fossils.

The sandwich structure of keratinous layers controls the form and growth orientation of chicken rhinotheca

The upper beak bone of birds is known to be overlain by the rhinotheca, which is composed of the horny sheath of keratinous layers. However, the details of the structure and growth pattern of the rhinotheca are yet to be understood. In this study, the microstructure of the rhinotheca from chicken specimens of different growth stages (ranging from 1 to ~ 80 days old) was analyzed using a combination of thin section and scanning electron microscopy observations, and small-angle X-ray scattering analysis. We found that the rhinotheca comprises three different layers - outer, intermediate, and inner layers - throughout its growth. The outer layer arises from the proximal portion of the beak bone and covers the dorsal surface of the rhinotheca, whereas the intermediate and inner layers originate in the distal portion of the beak bone and underlie the outer layer. This tri-layered structure of the rhinotheca was also observed in wild bird specimens (grey wagtail, king quail, and brown dipper). On the median plane, micro-layers making up the outer and inner layers are bedded nearly parallel to the rostral bone at the base. However, more distally positioned micro-layers of the outer layer are more anteverted distally. The micro-layers of the intermediate layer are bedded nearly perpendicular to those of the outer and inner layers on the median plane. The growth of micro-layers in the intermediate layer adds thickness to the rhinotheca, which causes the difference in profile between the beak bone and the rhinotheca in the distal portion of the beak. Moreover, the entire intermediate layer grows distally as new proximal micro-layers form. The outer layer is dragged distally by the intermediate layer as a result of its distal growth, for the three layers are closely packed to each other at their boundaries. Furthermore, the occurrence of the intermediate and inner layers in the distal portion of the rostral bone may be because the distal end of the beak is frequently used and worn, and the rhinotheca therefore needs to be replaced more frequently at the distal end. The rhinotheca structure described here will be an important and useful factor in the reconstruction of the beaks of birds in extinct taxa.

Fossilization transforms vertebrate hard tissue proteins into N-heterocyclic polymers

Vertebrate hard tissues consist of mineral crystallites within a proteinaceous scaffold that normally degrades post-mortem. Here we show, however, that decalcification of Mesozoic hard tissues preserved in oxidative settings releases brownish stained extracellular matrix, cells, blood vessels, and nerve projections. Raman Microspectroscopy shows that these fossil soft tissues are a product of diagenetic transformation to Advanced Glycoxidation and Lipoxidation End Products, a class of N-heterocyclic polymers generated via oxidative crosslinking of proteinaceous scaffolds. Hard tissues in reducing environments, in contrast, lack soft tissue preservation. Comparison of fossil soft tissues with modern and experimentally matured samples reveals how proteinaceous tissues undergo diagenesis and explains biases in their preservation in the rock record. This provides a target, focused on oxidative depositional environments, for finding cellular-to-subcellular soft tissue morphology in fossils and validates its use in phylogenetic and other evolutionary studies.

Fossilized skin reveals coevolution with feathers and metabolism in feathered dinosaurs and early birds

Feathers are remarkable evolutionary innovations that are associated with complex adaptations of the skin in modern birds. Fossilised feathers in non-avian dinosaurs and basal birds provide insights into feather evolution, but how associated integumentary adaptations evolved is unclear. Here we report the discovery of fossil skin, preserved with remarkable nanoscale fidelity, in three non-avian maniraptoran dinosaurs and a basal bird from the Cretaceous Jehol biota (China). The skin comprises patches of desquamating epidermal corneocytes that preserve a cytoskeletal array of helically coiled α-keratin tonofibrils. This structure confirms that basal birds and non-avian dinosaurs shed small epidermal flakes as in modern mammals and birds, but structural differences imply that these Cretaceous taxa had lower body heat production than modern birds. Feathered epidermis acquired many, but not all, anatomically modern attributes close to the base of the Maniraptora by the Middle Jurassic.

In addition to the evolutionary innovation of feathers, bird skin has complex adaptations. Here, McNamara and colleagues examine exceptionally preserved skin from feathered dinosaurs and ancient birds from the Cretaceous and show the early acquisition of many skin attributes seen in modern species.

A fossil protein chimera; difficulties in discriminating dinosaur peptide sequences from modern cross-contamination

A decade ago, reports that organic-rich soft tissue survived from dinosaur fossils were apparently supported by proteomics-derived sequence information of exceptionally well-preserved bone. This initial claim to the sequencing of endogenous collagen peptides from an approximately 68 Myr Tyrannosaurus rex fossil was highly controversial, largely on the grounds of potential contamination from either bacterial biofilms or from laboratory practice. In a subsequent study, collagen peptide sequences from an approximately 78 Myr Brachylophosaurus canadensis fossil were reported that have remained largely unchallenged. However, the endogeneity of these sequences relies heavily on a single peptide sequence, apparently unique to both dinosaurs. Given the potential for cross-contamination from modern bone analysed by the same team, here we extract collagen from bone samples of three individuals of ostrich, Struthio camelus The resulting LC-MS/MS data were found to match all of the proposed sequences for both the original Tyrannosaurus and Brachylophosaurus studies. Regardless of the true nature of the dinosaur peptides, our finding highlights the difficulty of differentiating such sequences with confidence. Our results not only imply that cross-contamination cannot be ruled out, but that appropriate measures to test for endogeneity should be further evaluated.

Microscopic and immunohistochemical analyses of the claw of the nesting dinosaur, Citipati osmolskae

One of the most well-recognized Cretaceous fossils is Citipati osmolskae (MPC-D 100/979), an oviraptorid dinosaur discovered in brooding position on a nest of unhatched eggs. The original description refers to a thin lens of white material extending from a manus ungual, which was proposed to represent original keratinous claw sheath that, in life, would have covered it. Here, we test the hypothesis that this exceptional morphological preservation extends to the molecular level. The fossil sheath was compared with that of extant birds, revealing similar morphology and microstructural organization. In living birds, the claw sheath consists primarily of two structural proteins; alpha-keratin, expressed in all vertebrates, and beta-keratin, found only in reptiles and birds (sauropsids). We employed antibodies raised against avian feathers, which comprise almost entirely of beta-keratin, to demonstrate that fossil tissues respond with the same specificity, though less intensity, as those from living birds. Furthermore, we show that calcium chelation greatly increased antibody reactivity, suggesting a role for calcium in the preservation of this fossil material.

Cellular preservation of musculoskeletal specializations in the Cretaceous bird Confuciusornis

The hindlimb of theropod dinosaurs changed appreciably in the lineage leading to extant birds, becoming more ‘crouched' in association with changes to body shape and gait dynamics. This postural evolution included anatomical changes of the foot and ankle, altering the moment arms and control of the muscles that manipulated the tarsometatarsus and digits, but the timing of these changes is unknown. Here, we report cellular-level preservation of tendon- and cartilage-like tissues from the lower hindlimb of Early Cretaceous Confuciusornis. The digital flexor tendons passed through cartilages, cartilaginous cristae and ridges on the plantar side of the distal tibiotarsus and proximal tarsometatarsus, as in extant birds. In particular, fibrocartilaginous and cartilaginous structures on the plantar surface of the ankle joint of Confuciusornis may indicate a more crouched hindlimb posture. Recognition of these specialized soft tissues in Confuciusornis is enabled by our combination of imaging and chemical analyses applied to an exceptionally preserved fossil.

Birds have a more crouched posture compared to their theropod dinosaur ancestors. Here, Jiang and colleagues describe a lower hindlimb of the Early Cretaceous bird Confuciusornis with soft tissues apparently preserved even as molecules, indicating a somewhat more modern posture in ancient birds.

Fossilization of melanosomes via sulfurization

Fossil melanin granules (melanosomes) are an important resource for inferring the evolutionary history of colour and its functions in animals. The taphonomy of melanin and melanosomes, however, is incompletely understood. In particular, the chemical processes responsible for melanosome preservation have not been investigated. As a result, the origins of sulfur-bearing compounds in fossil melanosomes are difficult to resolve. This has implications for interpretations of original colour in fossils based on potential sulfur-rich phaeomelanosomes. Here we use pyrolysis gas chromatography mass spectrometry (Py-GCMS), fourier transform infrared spectroscopy (FTIR) and time of flight secondary ion mass spectrometry (ToF-SIMS) to assess the mode of preservation of fossil microstructures, confirmed as melanosomes based on the presence of melanin, preserved in frogs from the Late Miocene Libros biota (NE Spain). Our results reveal a high abundance of organosulfur compounds and non-sulfurized fatty acid methyl esters in both the fossil tissues and host sediment; chemical signatures in the fossil tissues are inconsistent with preservation of phaeomelanin. Our results reflect preservation via the diagenetic incorporation of sulfur, i.e. sulfurization (natural vulcanization), and other polymerization processes. Organosulfur compounds and/or elevated concentrations of sulfur have been reported from melanosomes preserved in various invertebrate and vertebrate fossils and depositional settings, suggesting that preservation through sulfurization is likely to be widespread. Future studies of sulfur-rich fossil melanosomes require that the geochemistry of the host sediment is tested for evidence of sulfurization in order to constrain interpretations of potential phaeomelanosomes and thus of original integumentary colour in fossils.

Reconstructing Carotenoid-Based and Structural Coloration in Fossil Skin

Evidence of original coloration in fossils provides insights into the visual communication strategies used by ancient animals and the functional evolution of coloration over time [1-7]. Hitherto, all reconstructions of the colors of reptile integument and the plumage of fossil birds and feathered dinosaurs have been of melanin-based coloration [1-6]. Extant animals also use other mechanisms for producing color [8], but these have not been identified in fossils. Here we report the first examples of carotenoid-based coloration in the fossil record, and of structural coloration in fossil integument. The fossil skin, from a 10 million-year-old colubrid snake from the Late Miocene Libros Lagerstätte (Teruel, Spain) [9, 10], preserves dermal pigment cells (chromatophores)-xanthophores, iridophores, and melanophores-in calcium phosphate. Comparison with chromatophore abundance and position in extant reptiles [11-15] indicates that the fossil snake was pale-colored in ventral regions; dorsal and lateral regions were green with brown-black and yellow-green transverse blotches. Such coloration most likely functioned in substrate matching and intraspecific signaling. Skin replicated in authigenic minerals is not uncommon in exceptionally preserved fossils [16, 17], and dermal pigment cells generate coloration in numerous reptile, amphibian, and fish taxa today [18]. Our discovery thus represents a new means by which to reconstruct the original coloration of exceptionally preserved fossil vertebrates.

Melanosomes and ancient coloration re-examined: A response to Vinther 2015 (DOI 10.1002/bies.201500018)

Round to elongate microbodies associated with fossil vertebrate soft tissues were interpreted as microbial traces until 2008, when they were re-described as remnant melanosomes - intracellular, pigment-containing eukaryotic organelles. Since then, multiple claims for melanosome preservation and inferences of organismal color, behavior, and physiology have been advanced, based upon the shape and size of these microstructures. Here, we re-examine evidence for ancient melanosomes in light of information reviewed in Vinther (2015), and literature regarding the preservation potential of microorganisms and their exopolymeric secretions. We: (i) address statements in Vinther's recent (2015) review that are incorrect or which misrepresent published data; (ii) discuss the need for caution in interpreting "voids" and microbodies associated with degraded fossil soft tissues; (iii) present evidence that microorganisms are in many cases an equally parsimonious source for these "voids" as are remnant melanosomes; and (iv) suggest methods/criteria for differentiating melanosomes from microbial traces in the fossil record.

Fibres and cellular structures preserved in 75-million-year-old dinosaur specimens

Exceptionally preserved organic remains are known throughout the vertebrate fossil record, and recently, evidence has emerged that such soft tissue might contain original components. We examined samples from eight Cretaceous dinosaur bones using nano-analytical techniques; the bones are not exceptionally preserved and show no external indication of soft tissue. In one sample, we observe structures consistent with endogenous collagen fibre remains displaying ∼ 67 nm banding, indicating the possible preservation of the original quaternary structure. Using ToF-SIMS, we identify amino-acid fragments typical of collagen fibrils. Furthermore, we observe structures consistent with putative erythrocyte remains that exhibit mass spectra similar to emu whole blood. Using advanced material characterization approaches, we find that these putative biological structures can be well preserved over geological timescales, and their preservation is more common than previously thought. The preservation of protein over geological timescales offers the opportunity to investigate relationships, physiology and behaviour of long extinct animals.

Mid-Pliocene warm-period deposits in the High Arctic yield insight into camel evolution

The mid-Pliocene was a global warm period, preceding the onset of Quaternary glaciations. Here we use cosmogenic nuclide dating to show that a fossiliferous terrestrial deposit that includes subfossil trees and the northern-most evidence of Pliocene ice wedge casts in Canada’s High Arctic (Ellesmere Island, Nunavut) was deposited during the mid-Pliocene warm period. The age estimates correspond to a general maximum in high latitude mean winter season insolation, consistent with the presence of a rich, boreal-type forest. Moreover, we report that these deposits have yielded the first evidence of a High Arctic camel, identified using collagen fingerprinting of a fragmentary fossil limb bone. Camels originated in North America and dispersed to Eurasia via the Bering Isthmus, an ephemeral land bridge linking Alaska and Russia. The results suggest that the evolutionary history of modern camels can be traced back to a lineage of giant camels that was well established in a forested Arctic.

Camels originated in North America during the Eocene period ~45 million years ago. This study reports evidence of a High Arctic camel from Ellesmere Island, which extends the range of North American camels northward by ~1,200 km to a lineage of giant camels that were well established in a forested Arctic.

The lambeosaurine dinosaur Magnapaulia laticaudus from the late cretaceous of Baja California, Northwestern Mexico

The taxonomy, osteology, phylogenetic position, and historical biogeography of the lambeosaurine hadrosaurid Magnapaulia laticaudus (new combination) are revised. The diagnosis of this species is amended on the basis on two autapomorphies (i.e., longest haemal arches of proximal caudal vertebrae being at least four times longer than the height of their respective centra; base of prezygapophyses in caudal vertebrae merging to form a bowl-shaped surface) and a unique combination of characters (i.e., downturned cranioventral process of the maxilla; tear-shaped external naris with length/width ratio between 1.85 and 2.85; neural spines of dorsal, sacral, and proximal caudal vertebrae being at least four times the height of their respective centra). A maximum parsimony analysis supports a sister taxon relationship between M. laticaudus and Velafrons coahuilensis. Both taxa constitute a clade of southern North American lambeosaurines, which forms a sister relationship with the diverse clade of helmet-crested lambeosaurines from northern North America that includes well-known genera like Corythosaurus, Lambeosaurus, and Hypacrosaurus. According to the results of a Dispersal-Vicariance analysis, southern North American lambeosaurines split from the northern forms via vicariance from a common ancestor that lived in both the northern and southern regions of the continent.

Chemical mapping of paleontological and archeological artifacts with synchrotron X-rays

The application of the recently developed synchrotron rapid scanning X-ray fluorescence (SRS-XRF) technique to the mapping of large objects is the focus of this review. We discuss the advantages of SRS-XRF over traditional systems and the use of other synchrotron radiation (SR) techniques to provide corroborating spectroscopic and diffraction analyses during the same analytical session. After reviewing routine techniques used to analyze precious specimens, we present several case studies that show how SR-based methods have been successfully applied in archeology and paleontology. For example, SRS-XRF imaging of a seventh-century Qur'ān palimpsest and an overpainted original opera score from Luigi Cherubini is described. We also review the recent discovery of soft-tissue residue in fossils of Archaeopteryx and an ancient reptile, as well as work that has successfully resolved the remnants of pigment in Confuciusornis sanctus, a 120-million-year-old fossil of the oldest documented bird with a fully derived avian beak.

Trace metals as biomarkers for eumelanin pigment in the fossil record

Well-preserved fossils of pivotal early bird and nonavian theropod species have provided unequivocal evidence for feathers and/or downlike integuments. Recent studies have reconstructed color on the basis of melanosome structure; however, the chemistry of these proposed melanosomes has remained unknown. We applied synchrotron x-ray techniques to several fossil and extant organisms, including Confuciusornis sanctus, in order to map and characterize possible chemical residues of melanin pigments. Results show that trace metals, such as copper, are present in fossils as organometallic compounds most likely derived from original eumelanin. The distribution of these compounds provides a long-lived biomarker of melanin presence and density within a range of fossilized organisms. Metal zoning patterns may be preserved long after melanosome structures have been destroyed.

Microspectroscopic evidence of cretaceous bone proteins

Low concentrations of the structural protein collagen have recently been reported in dinosaur fossils based primarily on mass spectrometric analyses of whole bone extracts. However, direct spectroscopic characterization of isolated fibrous bone tissues, a crucial test of hypotheses of biomolecular preservation over deep time, has not been performed. Here, we demonstrate that endogenous proteinaceous molecules are retained in a humerus from a Late Cretaceous mosasaur (an extinct giant marine lizard). In situ immunofluorescence of demineralized bone extracts shows reactivity to antibodies raised against type I collagen, and amino acid analyses of soluble proteins extracted from the bone exhibit a composition indicative of structural proteins or their breakdown products. These data are corroborated by synchrotron radiation-based infrared microspectroscopic studies demonstrating that amino acid containing matter is located in bone matrix fibrils that express imprints of the characteristic 67 nm D-periodicity typical of collagen. Moreover, the fibrils differ significantly in spectral signature from those of potential modern bacterial contaminants, such as biofilms and collagen-like proteins. Thus, the preservation of primary soft tissues and biomolecules is not limited to large-sized bones buried in fluvial sandstone environments, but also occurs in relatively small-sized skeletal elements deposited in marine sediments.

Infrared mapping resolves soft tissue preservation in 50 million year-old reptile skin

Non-destructive Fourier Transform InfraRed (FTIR) mapping of Eocene aged fossil reptile skin shows that biological control on the distribution of endogenous organic components within fossilized soft tissue can be resolved. Mapped organic functional units within this approximately 50 Myr old specimen from the Green River Formation (USA) include amide and sulphur compounds. These compounds are most probably derived from the original beta keratin present in the skin because fossil leaf- and other non-skin-derived organic matter from the same geological formation do not show intense amide or thiol absorption bands. Maps and spectra from the fossil are directly comparable to extant reptile skin. Furthermore, infrared results are corroborated by several additional quantitative methods including Synchrotron Rapid Scanning X-Ray Fluorescence (SRS-XRF) and Pyrolysis-Gas Chromatography/Mass Spectrometry (Py-GC/MS). All results combine to clearly show that the organic compound inventory of the fossil skin is different from the embedding sedimentary matrix and fossil plant material. A new taphonomic model involving ternary complexation between keratin-derived organic molecules, divalent trace metals and silicate surfaces is presented to explain the survival of the observed compounds. X-ray diffraction shows that suitable minerals for complex formation are present. Previously, this study would only have been possible with major destructive sampling. Non-destructive FTIR imaging methods are thus shown to be a valuable tool for understanding the taphonomy of high-fidelity preservation, and furthermore, may provide insight into the biochemistry of extinct organisms.