Diving dinosaurs? Caveats on the use of bone compactness and pFDA for inferring lifestyle

The lifestyle of spinosaurid dinosaurs has been a topic of lively debate ever since the unveiling of important new skeletal parts for Spinosaurus aegyptiacus in 2014 and 2020. Disparate lifestyles for this taxon have been proposed in the literature; some have argued that it was semiaquatic to varying degrees, hunting fish from the margins of water bodies, or perhaps while wading or swimming on the surface; others suggest that it was a fully aquatic underwater pursuit predator. The various proposals are based on equally disparate lines of evidence. A recent study by Fabbri and coworkers sought to resolve this matter by applying the statistical method of phylogenetic flexible discriminant analysis to femur and rib bone diameters and a bone microanatomy metric called global bone compactness. From their statistical analyses of datasets based on a wide range of extant and extinct taxa, they concluded that two spinosaurid dinosaurs (S. aegyptiacus, Baryonyx walkeri) were fully submerged "subaqueous foragers," whereas a third spinosaurid (Suchomimus tenerensis) remained a terrestrial predator. We performed a thorough reexamination of the datasets, analyses, and methodological assumptions on which those conclusions were based, which reveals substantial problems in each of these areas. In the datasets of exemplar taxa, we found unsupported categorization of taxon lifestyle, inconsistent inclusion and exclusion of taxa, and inappropriate choice of taxa and independent variables. We also explored the effects of uncontrolled sources of variation in estimates of bone compactness that arise from biological factors and measurement error. We found that the ability to draw quantitative conclusions is limited when taxa are represented by single data points with potentially large intrinsic variability. The results of our analysis of the statistical method show that it has low accuracy when applied to these datasets and that the data distributions do not meet fundamental assumptions of the method. These findings not only invalidate the conclusions of the particular analysis of Fabbri et al. but also have important implications for future quantitative uses of bone compactness and discriminant analysis in paleontology.

An effect size statistical framework for investigating sexual dimorphism in non-avian dinosaurs and other extinct taxa

Despite reports of sexual dimorphism in extinct taxa, such claims in non-avian dinosaurs have been rare over the last decade and have often been criticized. Since dimorphism is widespread in sexually reproducing organisms today, under-reporting in the literature might suggest either methodological shortcomings or that this diverse group exhibited highly unusual reproductive biology. Univariate significance testing, especially for bimodality, is ineffective and prone to false negatives. Species recognition and mutual sexual selection hypotheses, therefore, may not be required to explain supposed absence of sexual dimorphism across the grade (a type II error). Instead, multiple lines of evidence support sexual selection and variation of structures consistent with secondary sexual characteristics, strongly suggesting sexual dimorphism in non-avian dinosaurs. We propose a framework for studying sexual dimorphism in fossils, focusing on likely secondary sexual traits and testing against all alternate hypotheses for variation in them using multiple lines of evidence. We use effect size statistics appropriate for low sample sizes, rather than significance testing, to analyse potential divergence of growth curves in traits and constrain estimates for dimorphism magnitude. In many cases, estimates of sexual variation can be reasonably accurate, and further developments in methods to improve sex assignments and account for intrasexual variation (e.g. mixture modelling) will improve accuracy. It is better to compare estimates for the magnitude of and support for dimorphism between datasets than to dichotomously reject or fail to reject monomorphism in a single species, enabling the study of sexual selection across phylogenies and time. We defend our approach with simulated and empirical data, including dinosaur data, showing that even simple approaches can yield fairly accurate estimates of sexual variation in many cases, allowing for comparison of species with high and low support for sexual variation.

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

BACKGROUND

Exceptional preservation of endogenous organics such as collagens and blood vessels has been frequently reported in Mesozoic dinosaur fossils. The persistence of these soft tissues in Mesozoic fossil bones has been challenged because of the susceptibility of proteins to degradation and because bone porosity allows microorganisms to colonize the inner microenvironments through geological time. Although protein lability has been studied extensively, the genomic diversity of microbiomes in dinosaur fossil bones and their potential roles in bone taphonomy remain underexplored. Genome-resolved metagenomics was performed, therefore, on the microbiomes recovered from a Late Cretaceous Centrosaurus bone and its encompassing mudstone in order to provide insight into the genomic potential for microbial alteration of fossil bone.

RESULTS

Co-assembly and binning of metagenomic reads resulted in a total of 46 high-quality metagenome-assembled genomes (MAGs) affiliated to six bacterial phyla (Actinobacteria, Proteobacteria, Nitrospira, Acidobacteria, Gemmatimonadetes and Chloroflexi) and 1 archaeal phylum (Thaumarchaeota). The majority of the MAGs represented uncultivated, novel microbial lineages from class to species levels based on phylogenetics, phylogenomics and average amino acid identity. Several MAGs from the classes Nitriliruptoria, Deltaproteobacteria and Betaproteobacteria were highly enriched in the bone relative to the adjacent mudstone. Annotation of the MAGs revealed that the distinct putative metabolic functions of different taxonomic groups were linked to carbon, nitrogen, sulfur and iron metabolism. Metaproteomics revealed gene expression from many of the MAGs, but no endogenous collagen peptides were identified in the bone that could have been derived from the dinosaur. Estimated in situ replication rates among the bacterial MAGs suggested that most of the microbial populations in the bone might have been actively growing but at a slow rate.

CONCLUSIONS

Our results indicate that excavated dinosaur bones are habitats for microorganisms including novel microbial lineages. The distinctive microhabitats and geochemistry of fossil bone interiors compared to that of the external sediment enrich a microbial biomass comprised of various novel taxa that harbor multiple gene sets related to interconnected biogeochemical processes. Therefore, the presence of these microbiomes in Mesozoic dinosaur fossils urges extra caution to be taken in the science of paleontology when hunting for endogenous biomolecules preserved from deep time.

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.

Cretaceous dinosaur bone contains recent organic material and provides an environment conducive to microbial communities

Fossils were thought to lack original organic molecules, but chemical analyses show that some can survive. Dinosaur bone has been proposed to preserve collagen, osteocytes, and blood vessels. However, proteins and labile lipids are diagenetically unstable, and bone is a porous open system, allowing microbial/molecular flux. These 'soft tissues' have been reinterpreted as biofilms. Organic preservation versus contamination of dinosaur bone was examined by freshly excavating, with aseptic protocols, fossils and sedimentary matrix, and chemically/biologically analyzing them. Fossil 'soft tissues' differed from collagen chemically and structurally; while degradation would be expected, the patterns observed did not support this. 16S rRNA amplicon sequencing revealed that dinosaur bone hosted an abundant microbial community different from lesser abundant communities of surrounding sediment. Subsurface dinosaur bone is a relatively fertile habitat, attracting microbes that likely utilize inorganic nutrients and complicate identification of original organic material. There exists potential post-burial taphonomic roles for subsurface microorganisms.

Experimental subaqueous burial of a bird carcass and compaction of plumage

'Exceptional fossils' of dinosaurs preserving feathers have radically changed the way we view their paleobiology and the evolution of birds. Understanding how such soft tissues preserve is imperative to accurately interpreting the morphology of fossil feathers. Experimental taphonomy has been integral to such investigations. One such experiment used a printing press to mimic compaction, done subaerially and without sediment burial, and concluded that the leaking of bodily fluid could lead to the clumping of feathers by causing barbs to stick together such that they superficially resemble simpler, less derived, filamentous structures. Here we use a novel, custom-built experimental setup to more accurately mimic subaqueous burial and compaction under low-energy, fine-grain depositional environments applicable to the taphonomic settings most plumage-preserving 'exceptional fossils' are found in. We find that when submerged and subsequently buried and compacted, feathers do not clump together and they maintain their original arrangement. Submersion in fluid in and of itself does not lead to clumping of barbs; this would only occur upon pulling feathers out from water into air. Furthermore, sediment encases the feathers, fixing them in place during compaction. Thus, feather clumping that leads to erroneously plesiomorphic morphological interpretations may not be a taphonomic factor of concern when examining fossil feathers. Our current methodology is amenable to further improvements that will continue to more accurately mimic subaqueous burial and compaction, allowing for various hypothesis testing.