Cellular preservation of musculoskeletal specializations in the Cretaceous bird Confuciusornis

New enantiornithine diversity in the Hell Creek Formation and the functional morphology of the avisaurid tarsometatarsus

Enantiornithines were the most diverse group of birds during the Cretaceous, comprising over half of all known species from this period. The fossil record and subsequently our knowledge of this clade is heavily skewed by the wealth of material from Lower Cretaceous deposits in China. In contrast, specimens from Upper Cretaceous deposits are rare and typically fragmentary, yet critical for understanding the extinction of this clade across the K-Pg boundary. The most complete North American Late Cretaceous enantiornithine is Mirarce eatoni, a member of the diverse clade Avisauridae. Except for Mirarce, avisaurids are known only from isolated hindlimb elements from North and South America. Here we describe three new enantiornithines from the Maastrichtian Hell Creek Formation, two of which represent new avisaurid taxa. These materials represent a substantial increase in the known diversity of Enantiornithes in the latest Cretaceous. Re-examination of material referred to Avisauridae through phylogenetic analysis provides strong support for a more exclusive Avisauridae consisting of six taxa. Exploration of the functional morphology of the avisaurid tarsometatarsus indicates potential strong constriction and raptorial attributes. The lower aspect ratio of the tarsometatarsus facilitates a more biomechanically efficient lever system which in extant birds of prey equates to lifting proportionally heavier prey items. In addition, the proportional size and distal position of the m. tibialis cranialis tubercle of the tarsometatarsus is similar to the morphology seen in extant birds of prey. Together with the deeply-grooved metatarsal trochlea facilitating robust and likely powerful pedal digits, morphologies of the hindlimb suggest avisaurids as Late Cretaceous birds of prey.

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.

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.

Deep Time Paleoproteomics: Looking Forward

The goal of paleoproteomics is to characterize proteins from specimens that have been subjected to the degrading and obscuring effects of time, thus obtaining biological information about tissues or organisms both unobservable in the present and unobtainable through morphological study. Although the description of sequences from Tyrannosaurus rex and Brachylophosaurus canadensis suggested that proteins may persist over tens of millions of years, the majority of paleoproteomic analyses have focused on historical, archeological, or relatively young paleontological samples that rarely exceed 1 million years in age. However, recent advances in methodology and analyses of diverse tissues types (e.g., fossil eggshell, dental enamel) have begun closing the large window of time that remains unexplored in the fossil history of the Cenozoic. In this perspective, we discuss the history and current state of deep time paleoproteomics (DTPp), here defined as paleoproteomic study of samples ∼1 million years (1 Ma) or more in age. We then discuss the future of DTPp research, including what we see as critical ways the field can expand, advancements in technology that can be utilized, and the types of questions DTPp can address if such a future is realized.

Nuclear preservation in the cartilage of the Jehol dinosaur Caudipteryx

Previous findings on dinosaur cartilage material from the Late Cretaceous of Montana suggested that cartilage is a vertebrate tissue with unique characteristics that favor nuclear preservation. Here, we analyze additional dinosaur cartilage in Caudipteryx (STM4-3) from the Early Cretaceous Jehol biota of Northeast China. The cartilage fragment is highly diagenetically altered when observed in ground-sections but shows exquisite preservation after demineralization. It reveals transparent, alumino-silicified chondrocytes and brown, ironized chondrocytes. The histochemical stain Hematoxylin and Eosin (that stains the nucleus and cytoplasm in extant cells) was applied to both the demineralized cartilage of Caudipteryx and that of a chicken. The two specimens reacted identically, and one dinosaur chondrocyte revealed a nucleus with fossilized threads of chromatin. This is the second example of fossilized chromatin threads in a vertebrate material. These data show that some of the original nuclear biochemistry is preserved in this dinosaur cartilage material and further support the hypothesis that cartilage is very prone to nuclear fossilization and a perfect candidate to further understand DNA preservation in deep time.

Confirmation of ovarian follicles in an enantiornithine (Aves) from the Jehol biota using soft tissue analyses

The remains of ovarian follicles reported in nine specimens of basal birds represents one of the most remarkable examples of soft-tissue preservation in the Early Cretaceous Jehol Biota. This discovery was immediately contested and the structures alternatively interpreted as ingested seeds. Fragments of the purported follicles preserved in an enantiornithine (STM10-12) were extracted and subjected to multiple high-resolution analyses. The structures in STM10-12 possess the histological and histochemical characteristics of smooth muscles fibers intertwined together with collagen fibers, resembling the contractile structure in the perifollicular membrane (PFM) of living birds. Fossilized blood vessels, very abundant in extant PFMs, are also preserved. Energy Dispersive Spectroscopy shows the preserved tissues primarily underwent alumino-silicification, with minor mineralization via iron oxides. No evidence of plant tissue was found. These results confirm the original interpretation as follicles within the left ovary, supporting the interpretation that the right ovary was functionally lost early in avian evolution.

Bailleul et al. employ histology, histochemistry and Energy Dispersive Spectroscopy to confirm the presence of disputed ovarian follicles in a specimen of fossil Cretaceous bird. These findings have implications for the evolution of the avian breeding system seen in birds today.

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.

Dinosaur paleohistology: review, trends and new avenues of investigation

In the mid-19th century, the discovery that bone microstructure in fossils could be preserved with fidelity provided a new avenue for understanding the evolution, function, and physiology of long extinct organisms. This resulted in the establishment of paleohistology as a subdiscipline of vertebrate paleontology, which has contributed greatly to our current understanding of dinosaurs as living organisms. Dinosaurs are part of a larger group of reptiles, the Archosauria, of which there are only two surviving lineages, crocodilians and birds. The goal of this review is to document progress in the field of archosaur paleohistology, focusing in particular on the Dinosauria. We briefly review the "growth age" of dinosaur histology, which has encompassed new and varied directions since its emergence in the 1950s, resulting in a shift in the scientific perception of non-avian dinosaurs from "sluggish" reptiles to fast-growing animals with relatively high metabolic rates. However, fundamental changes in growth occurred within the sister clade Aves, and we discuss this major evolutionary transition as elucidated by histology. We then review recent innovations in the field, demonstrating how paleohistology has changed and expanded to address a diversity of non-growth related questions. For example, dinosaur skull histology has elucidated the formation of curious cranial tissues (e.g., "metaplastic" tissues), and helped to clarify the evolution and function of oral adaptations, such as the dental batteries of duck-billed dinosaurs. Lastly, we discuss the development of novel techniques with which to investigate not only the skeletal tissues of dinosaurs, but also less-studied soft-tissues, through molecular paleontology and paleohistochemistry-recently developed branches of paleohistology-and the future potential of these methods to further explore fossilized tissues. We suggest that the combination of histological and molecular methods holds great potential for examining the preserved tissues of dinosaurs, basal birds, and their extant relatives. This review demonstrates the importance of traditional bone paleohistology, but also highlights the need for innovation and new analytical directions to improve and broaden the utility of paleohistology, in the pursuit of more diverse, highly specific, and sensitive methods with which to further investigate important paleontological questions.

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.

The most complete enantiornithine from North America and a phylogenetic analysis of the Avisauridae

The most complete known North American enantiornithine was collected in 1992 but never formally described. The so-called "Kaiparowits avisaurid" remains one of the most exceptional Late Cretaceous enantiornithine fossils. We recognize this specimen as a new taxon, Mirarce eatoni (gen. et sp. nov.), and provide a complete anatomical description. We maintain that the specimen is referable to the Avisauridae, a clade previously only known in North America from isolated tarsometatarsi. Information from this specimen helps to clarify evolutionary trends within the Enantiornithes. Its large body size supports previously observed trends toward larger body mass in the Late Cretaceous. However, trends toward increased fusion of compound elements across the clade as a whole are weak compared to the Ornithuromorpha. The new specimen reveals for the first time the presence of remige papillae in the enantiornithines, indicating this feature was evolved in parallel to dromaeosaurids and derived ornithuromorphs. Although morphology of the pygostyle and (to a lesser degree) the coracoid and manus appear to remain fairly static during the 65 million years plus of enantiornithine evolution, by the end of the Mesozoic at least some enantiornithine birds had evolved several features convergent with the Neornithes including a deeply keeled sternum, a narrow furcula with a short hypocleidium, and ulnar quill knobs-all features that indicate refinement of the flight apparatus and increased aerial abilities. We conduct the first cladistic analysis to include all purported avisuarid enantiornithines, recovering an Avisauridae consisting of a dichotomy between North and South American taxa. Based on morphological observations and supported by cladistic analysis, we demonstrate Avisaurus to be paraphyletic and erect a new genus for "A. gloriae," Gettyia gen. nov.

Archaeorhynchus preserving significant soft tissue including probable fossilized lungs

We describe a specimen of the basal ornithuromorph Archaeorhynchus spathula from the Lower Cretaceous Jiufotang Formation with extensive soft tissue preservation. Although it is the fifth specimen to be described, unlike the others it preserves significant traces of the plumage, revealing a pintail morphology previously unrecognized among Mesozoic birds, but common in extant neornithines. In addition, this specimen preserves the probable remnants of the paired lungs, an identification supported by topographical and macro- and microscopic anatomical observations. The preserved morphology reveals a lung very similar to that of living birds. It indicates that pulmonary specializations such as exceedingly subdivided parenchyma that allow birds to achieve the oxygen acquisition capacity necessary to support powered flight were present in ornithuromorph birds 120 Mya. Among extant air breathing vertebrates, birds have structurally the most complex and functionally the most efficient respiratory system, which facilitates their highly energetically demanding form of locomotion, even in extremely oxygen-poor environments. Archaeorhynchus is commonly resolved as the most basal known ornithuromorph bird, capturing a stage of avian evolution in which skeletal indicators of respiration remain primitive yet the lung microstructure appears modern. This adds to growing evidence that many physiological modifications of soft tissue systems (e.g., digestive system and respiratory system) that characterize living birds and are key to their current success may have preceded the evolution of obvious skeletal adaptations traditionally tracked through the fossil record.

A Comparison of Common Mass Spectrometry Approaches for Paleoproteomics

The last two decades have seen a broad diversity of methods used to identify and/or characterize proteins in the archeological and paleontological record. Of these, mass spectrometry has opened an unprecedented window into the proteomes of the past, providing protein sequence data from long extinct animals as well as historical and prehistorical artifacts. Thus, application of mass spectrometry to fossil remains has become an attractive source for ancient molecular sequences with which to conduct evolutionary studies, particularly in specimens older than the proposed limit of amplifiable DNA detection. However, "mass spectrometry" covers a range of mass-based proteomic approaches, each of which utilize different technology and physical principles to generate unique types of data, with their own strengths and challenges. Here, we discuss a variety of mass spectrometry techniques that have or may be used to detect and characterize archeological and paleontological proteins, with a particular focus on MALDI-MS, LC-MS/MS, TOF-SIMS, and MSi. The main differences in their functionality, the types of data they produce, and the potential effects of diagenesis on their results are considered.

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.