Dinosaur origin of egg color: oviraptors laid blue-green eggs

Molecular Taphonomy of Heme: Chemical Degradation of Hemin under Presumed Fossilization Conditions

The metalloporphyrin heme acts as the oxygen-complexing prosthetic group of hemoglobin in blood. Heme has been noted to survive for many millions of years in fossils. Here, we investigate its stability and degradation under various conditions expected to occur during fossilization. Oxidative, reductive, aerobic, and anaerobic conditions were studied at neutral and alkaline pH values. Elevated temperatures were applied to accelerate degradation. High-performance liquid chromatography coupled to tandem mass spectrometry (HPLC-MS/MS) identified four main degradation products. The vinyl residues are oxidized to formyl and further to carboxylate groups. In the presence of air or H₂O₂, cleavage of the tetrapyrrole ring occurs, and hematinic acid is formed. The highest stability of heme was observed under anaerobic reductive conditions (half-life 9.5 days), while the lowest stability was found in the presence of H₂O₂ (half-life 1 min). We confirmed that the iron cation plays a crucial role in degradation, since protoporphyrin IX, lacking iron, remained significantly more stable. Under anaerobic, reductive conditions, the above-mentioned degradation products were not observed, suggesting a different degradation pathway. To our knowledge, this is the first molecular taphonomy study on heme, which will be useful for understanding its fate during fossilization.

Independent Evidence for the Preservation of Endogenous Bone Biochemistry in a Specimen of Tyrannosaurus rex

Biomolecules preserved in deep time have potential to shed light on major evolutionary questions, driving the search for new and more rigorous methods to detect them. Despite the increasing body of evidence from a wide variety of new, high resolution/high sensitivity analytical techniques, this research is commonly met with skepticism, as the long standing dogma persists that such preservation in very deep time (>1 Ma) is unlikely. The Late Cretaceous dinosaur Tyrannosaurus rex (MOR 1125) has been shown, through multiple biochemical studies, to preserve original bone chemistry. Here, we provide additional, independent support that deep time bimolecular preservation is possible. We use synchrotron X-ray fluorescence imaging (XRF) and X-ray absorption spectroscopy (XAS) to investigate a section from the femur of this dinosaur, and demonstrate preservation of elements (S, Ca, and Zn) associated with bone remodeling and redeposition. We then compare these data to the bone of an extant dinosaur (bird), as well as a second non-avian dinosaur, Tenontosaurus tilletti (OMNH 34784) that did not preserve any sign of original biochemistry. Our data indicate that MOR 1125 bone cortices have similar bone elemental distributions to that of an extant bird, which supports preservation of original endogenous chemistry in this specimen.

A new molecular mechanism supports that blue-greenish egg color evolved independently across chicken breeds

Chicken blue-greenish coloration (BGC) was known as a classic Mendel trait caused by a retrovirus (EAV-HP) insertion in the SLCO1B3 gene. Lueyang black-boned chicken (LBC) BGC is light and varies continuously, implying that LBC BGC may be controlled by a new molecular mechanism. The aim of this study was to provide an insight into the molecular basis of LBC BGC. The EAV-HP was detected in the BGC (n = 105) and non-BGC LBC (n = 474) using a PCR-based method. The association of SLCO1B3 expression in shell glands and sequence variants in a 1.6-kb region upstream from the transcription start site of SLCO1B3 with eggshell color and biliverdin (pigment for BGC) concentration was studied. Promoter activities of haplotypes in the 1.6-kb region were analyzed by luciferase reporter assay. This study did not found the EAV-HP in BGC and Non-BGC LBC, but detected a strong positive correlation between levels of SLCO1B3 expression in shell glands and biliverdin concentrations. A total of 31 SNP were found in the 1.6-kb region. Twenty-two of 31 SNP formed 42 types of haplotypes in the re-sequenced samples (n = 94). Haplotype 4 was present in higher frequency in the BGC (52%) than Non-BGC (3%). Haplotype 13 was significantly associated with Non-BGC (Non-BGC vs. BGC = 26% vs. 6%). In line with the above associations, Haplotype 4 showed higher (P < 0.05) levels of SLCO1B3 expression in shell glands, biliverdin concentration, and promoter activity than Haplotype 13. This study confirms that LBC BGC is not caused by the EAV-HP, but remains to be associated with the change of SLCO1B3 expression. Haplotype 4 accounts to some extents for the molecular basis of LBC BGC. The new molecular mechanism supports LBC BGC independently evolved.

The diverse terminology of reptile eggshell microstructure and its effect on phylogenetic comparative analyses

Reptile eggshell ensures water and gas exchange during incubation and plays a key role in reproductive success. The diversity of reptilian incubation and life history strategies has led to many clade-specific structural adaptations of their eggshell, which have been studied in extant taxa (i.e. birds, crocodilians, turtles, and lepidosaurs). Most studies on non-avian eggshells were performed over 30 years ago and categorized reptile eggshells into two main types: "hard" and "soft" - sometimes with a third intermediate category, "semi-rigid." In recent years, however, debate over the evolution of eggshell structure of major reptile clades has revealed how definitions of hard and soft eggshells influence inferred deep-time evolutionary patterns. Here, we review the diversity of extant and fossil eggshell with a focus on major reptile clades, and the criteria that have been used to define hard, soft, and semi-rigid eggshells. We show that all scoring approaches that retain these categories discretize continuous quantitative traits (e.g. eggshell thickness) and do not consider independent variation of other functionally important microstructural traits (e.g. degree of calcification, shell unit inner structure). We demonstrate the effect of three published approaches to discretizing eggshell type into hard, semi-rigid, and soft on ancestral state reconstructions using 200+ species representing all major extant and extinct reptile clades. These approaches result in different ancestral states for all major clades including Archosauria and Dinosauria, despite a difference in scoring for only 1-4% of the sample. Proposed scenarios of reptile eggshell evolution are highly conditioned by sampling, tree calibration, and lack of congruence between definitions of eggshell type. We conclude that the traditional "soft/hard/semi-rigid" classification of reptilian eggshells should be abandoned and provide guidelines for future descriptions focusing on specific functionally relevant characteristics (e.g. inner structures of shell units, pores, and membrane elements), analyses of these traits in a phylogenetic context, and sampling of previously undescribed taxa, including fossil eggs.

Chemistry and Analysis of Organic Compounds in Dinosaurs

This review provides an overview of organic compounds detected in non-avian dinosaur fossils to date. This was enabled by the development of sensitive analytical techniques. Non-destructive methods and procedures restricted to the sample surface, e.g., light and electron microscopy, infrared (IR) and Raman spectroscopy, as well as more invasive approaches including liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS), time-of-flight secondary ion mass spectrometry, and immunological methods were employed. Organic compounds detected in samples of dinosaur fossils include pigments (heme, biliverdin, protoporphyrin IX, melanin), and proteins, such as collagens and keratins. The origin and nature of the observed protein signals is, however, in some cases, controversially discussed. Molecular taphonomy approaches can support the development of suitable analytical methods to confirm reported findings and to identify further organic compounds in dinosaur and other fossils in the future. The chemical properties of the various organic compounds detected in dinosaurs, and the techniques utilized for the identification and analysis of each of the compounds will be discussed.

Raman spectroscopy is a powerful tool in molecular paleobiology: An analytical response to Alleon et al. (https://doi.org/10.1002/bies.202000295)

A recent article argued that signals from conventional Raman spectroscopy of organic materials are overwhelmed by edge filter and fluorescence artefacts. The article targeted a subset of Raman spectroscopic investigations of fossil and modern organisms and has implications for the utility of conventional Raman spectroscopy in comparative tissue analytics. The inferences were based on circular reasoning centered around the unconventional analysis of spectra from just two samples, one modern, and one fossil. We validated the disputed signals with in situ Fourier-Transform Infrared (FT-IR) Spectroscopy and through replication with different lasers, filters, and operators in independent laboratories. Our Raman system employs a holographic notch filter which is not affected by edge filter or other artefacts. Multiple lines of evidence confirm that conventional Raman spectra of fossils contain biologically and geologically meaningful information. Statistical analyses of large Raman and FT-IR spectral data sets reveal patterns in fossil composition and yield valuable insights into the history of life.

The evolution of egg colour and patterning in Australian songbirds

To understand why avian eggs are so variable in colour and patterning, we investigated the characteristics of extant bird species that provide insight into the evolutionary transitions that occurred during the early radiation of the songbirds. We quantified egg colour and patterning from museum collections of 269 species of Australian passerine and collated it to nest type data (cup- or dome-nesting species). Using phylogenetically reconstructed trait data, we showed that the ancestral passerine egg was likely to be white, and to have been laid inside a domed nest. Egg colouration and nest type were both phylogenetically clustered, and there was evidence of correlated evolution between the two traits. As nests transitioned from domes to cups, there was an increase in the range of egg colours observed, presumably as a response to additional stressors. Finally, we found that egg colour changes occurred more than twice as frequently in cup-nesting species than in dome-nesting species. This suggests that colour may be an adaptive trait that compensates for the loss of the protective nest roof in cup-nesting species.

Morphological research on amniote eggs and embryos: An introduction and historical retrospective

Evolution of the terrestrial egg of amniotes (reptiles, birds, and mammals) is often considered to be one of the most significant events in vertebrate history. Presence of an eggshell, fetal membranes, and a sizeable yolk allowed this egg to develop on land and hatch out well-developed, terrestrial offspring. For centuries, morphologically-based studies have provided valuable information about the eggs of amniotes and the embryos that develop from them. This review explores the history of such investigations, as a contribution to this special issue of Journal of Morphology, titled Developmental Morphology and Evolution of Amniote Eggs and Embryos. Anatomically-based investigations are surveyed from the ancient Greeks through the Scientific Revolution, followed by the 19th and early 20th centuries, with a focus on major findings of historical figures who have contributed significantly to our knowledge. Recent research on various aspects of amniote eggs is summarized, including gastrulation, egg shape and eggshell morphology, eggs of Mesozoic dinosaurs, sauropsid yolk sacs, squamate placentation, embryogenesis, and the phylotypic phase of embryonic development. As documented in this review, studies on amniote eggs and embryos have relied heavily on morphological approaches in order to answer functional and evolutionary questions.

Fluorescent proteins for in vivo imaging, where's the biliverdin?

Noninvasive fluorescent imaging requires far-red and near-infrared fluorescent proteins for deeper imaging. Near-infrared light penetrates biological tissue with blood vessels due to low absorbance, scattering, and reflection of light and has a greater signal-to-noise due to less autofluorescence. Far-red and near-infrared fluorescent proteins absorb light >600 nm to expand the color palette for imaging multiple biosensors and noninvasive in vivo imaging. The ideal fluorescent proteins are bright, photobleach minimally, express well in the desired cells, do not oligomerize, and generate or incorporate exogenous fluorophores efficiently. Coral-derived red fluorescent proteins require oxygen for fluorophore formation and release two hydrogen peroxide molecules. New fluorescent proteins based on phytochrome and phycobiliproteins use biliverdin IXα as fluorophores, do not require oxygen for maturation to image anaerobic organisms and tumor core, and do not generate hydrogen peroxide. The small Ultra-Red Fluorescent Protein (smURFP) was evolved from a cyanobacterial phycobiliprotein to covalently attach biliverdin as an exogenous fluorophore. The small Ultra-Red Fluorescent Protein is biophysically as bright as the enhanced green fluorescent protein, is exceptionally photostable, used for biosensor development, and visible in living mice. Novel applications of smURFP include in vitro protein diagnostics with attomolar (10-18 M) sensitivity, encapsulation in viral particles, and fluorescent protein nanoparticles. However, the availability of biliverdin limits the fluorescence of biliverdin-attaching fluorescent proteins; hence, extra biliverdin is needed to enhance brightness. New methods for improved biliverdin bioavailability are necessary to develop improved bright far-red and near-infrared fluorescent proteins for noninvasive imaging in vivo.

Recent advances in amniote palaeocolour reconstruction and a framework for future research

Preserved melanin pigments have been discovered in fossilised integumentary appendages of several amniote lineages (fishes, frogs, snakes, marine reptiles, non-avialan dinosaurs, birds, and mammals) excavated from lagerstätten across the globe. Melanisation is a leading factor in organic integument preservation in these fossils. Melanin in extant vertebrates is typically stored in rod- to sphere-shaped, lysosome-derived, membrane-bound vesicles called melanosomes. Black, dark brown, and grey colours are produced by eumelanin, and reddish-brown colours are produced by phaeomelanin. Specific morphotypes and nanostructural arrangements of melanosomes and their relation to the keratin matrix in integumentary appendages create the so-called 'structural colours'. Reconstruction of colour patterns in ancient animals has opened an exciting new avenue for studying their life, behaviour and ecology. Modern relationships between the shape, arrangement, and size of avian melanosomes, melanin chemistry, and feather colour have been applied to reconstruct the hues and colour patterns of isolated feathers and plumages of the dinosaurs Anchiornis, Sinosauropteryx, and Microraptor in seminal papers that initiated the field of palaeocolour reconstruction. Since then, further research has identified countershading camouflage patterns, and informed subsequent predictions on the ecology and behaviour of these extinct animals. However, palaeocolour reconstruction remains a nascent field, and current approaches have considerable potential for further refinement, standardisation, and expansion. This includes detailed study of non-melanic pigments that might be preserved in fossilised integuments. A common issue among existing palaeocolour studies is the lack of contextualisation of different lines of evidence and the wide variety of techniques currently employed. To that end, this review focused on fossil amniotes: (i) produces an overarching framework that appropriately reconstructs palaeocolour by accounting for the chemical signatures of various pigments, morphology and local arrangement of pigment-bearing vesicles, pigment concentration, macroscopic colour patterns, and taphonomy; (ii) provides background context for the evolution of colour-producing mechanisms; and (iii) encourages future efforts in palaeocolour reconstructions particularly of less-studied groups such as non-dinosaur archosaurs and non-archosaur amniotes.

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.

Incubation behaviours of oviraptorosaur dinosaurs in relation to body size

Most birds sit on their eggs during incubation, a behaviour that likely evolved among non-avian dinosaurs. Several 'brooding' specimens of smaller species of oviraptorosaurs and troodontids reveal these non-avian theropods sat on their eggs, although little is known of incubation behaviour in larger theropod species. Here we examine egg clutches over a large body size range of oviraptorosaurs in order to understand the potential effect of body size on incubation behaviour. Eggshell porosity indicates that the eggs of all oviraptorosaurs were exposed in the nest, similar to brooding birds. Although all oviraptorosaur clutches consist of radially arranged eggs in a ring configuration, clutch morphology varies in that the central opening is small or absent in the smallest species, becomes significantly larger in larger species, and occupies most of the nest area in giant species. Our results suggest that the smallest oviraptorosaurs probably sat directly on the eggs, whereas with increasing body size more weight was likely carried by the central opening, reducing or eliminating the load on the eggs and still potentially allowing for some contact during incubation in giant species. This adaptation, not seen in birds, appears to remove the body size constraints of incubation behaviour in giant oviraptorosaurs.

An Early Cretaceous enantiornithine (Aves) preserving an unlaid egg and probable medullary bone

Understanding non-crown dinosaur reproduction is hindered by a paucity of directly associated adults with reproductive traces. Here we describe a new enantiornithine, Avimaia schweitzerae gen. et sp. nov., from the Lower Cretaceous Xiagou Formation with an unlaid egg two-dimensionally preserved within the abdominothoracic cavity. Ground-sections reveal abnormal eggshell proportions, and multiple eggshell layers best interpreted as a multi-layered egg resulting from prolonged oviductal retention. Fragments of the shell membrane and cuticle are both preserved. SEM reveals that the cuticle consists of nanostructures resembling those found in neornithine eggs adapted for infection-prone environments, which are hypothesized to represent the ancestral avian condition. The femur preserves small amounts of probable medullary bone, a tissue found today only in reproductively active female birds. To our knowledge, no other occurrence of Mesozoic medullary bone is associated with indications of reproductive activity, such as a preserved egg, making our identification unique, and strongly supported.

The fossil record of the reproductive traits of early birds is limited. Here, Bailleul and colleagues describe the Cretaceous enantiornithine bird Avimaia schweitzerae, which preserves an unlaid egg in the abdominal cavity and putative medullary bone.

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.

Fossil eggshell cuticle elucidates dinosaur nesting ecology

The cuticle layer consisting mainly of lipids and hydroxyapatite (HAp) atop the mineralized avian eggshell is a protective structure that prevents the egg from dehydration and microbial invasions. Previous ornithological studies have revealed that the cuticle layer is also involved in modulating the reflectance of eggshells in addition to pigments (protoporphyrin and biliverdin). Thus, the cuticle layer represents a crucial trait that delivers ecological signals. While present in most modern birds, direct evidence for cuticle preservation in stem birds and non-avian dinosaurs is yet missing. Here we present the first direct and chemical evidence for the preservation of the cuticle layer on dinosaur eggshells. We analyze several theropod eggshells from various localities, including oviraptorid Macroolithus yaotunensis eggshells from the Late Cretaceous deposits of Henan, Jiangxi, and Guangdong in China and alvarezsaurid Triprismatoolithus eggshell from the Two Medicine Formation of Montana, United States, with the scanning electron microscope (SEM), electron probe micro-analysis (EPMA), and Raman spectroscopy (RS). The elemental analysis with EPMA shows high concentration of phosphorus at the boundary between the eggshell and sediment, representing the hydroxyapatitic cuticle layer (HAp). Depletion of phosphorus in sediment excludes the allochthonous origin of the phosphorus in these eggshells. The chemometric analysis of Raman spectra collected from fossil and extant eggs provides further supportive evidence for the cuticle preservation in oviraptorid and probable alvarezsaurid eggshells. In accordance with our previous discovery of pigments preserved in Cretaceous oviraptorid dinosaur eggshells, we validate the cuticle preservation on dinosaur eggshells through deep time and offer a yet unexplored resource for chemical studies targeting the evolution of dinosaur nesting ecology. Our study also suggests that the cuticle structure can be traced far back to maniraptoran dinosaurs and enhance their reproductive success in a warm and mesic habitat such as Montana and southern China during the Late Cretaceous.

Cracking the egg: the use of modern and fossil eggs for ecological, environmental and biological interpretation

A myriad of extant and extinct vertebrates produce eggs. Eggs and eggshells provide a useful substrate for reconstructing environment, ecology and biology over a range of time scales from deep time to the present. In this review, methods for analysing and understanding records of diet, climate, environment and biology preserved in eggshells are presented. Topics covered include eggshell structure, assessing diagenesis, stable isotope geochemistry and morphological investigations of eggshell characteristics. This review emphasizes the use of eggshells in the modern and fossil record, as they allow for interpretation of characteristics of a wide variety of amniotes across geological history, uniquely informing environmental and ecological investigations.