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 underrepresented recently (~the last decade) and often criticized. Since dimorphism is widespread in sexually reproducing organisms today, underrepresentation 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, likely 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 secondarily 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 analyze 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.Funding provided by: National Science FoundationCrossref Funder Registry ID: http://dx.doi.org/10.13039/100000001Award Number: PLR 1341645 and FRES 192588

Soft-Bodied Fossils Are Not Simply Rotten Carcasses – Toward a Holistic Understanding of Exceptional Fossil Preservation:Exceptional Fossil Preservation Is Complex and Involves the Interplay of Numerous Biological and Geological Processes

Exceptionally preserved fossils are the product of complex interplays of biological and geological processes including burial, autolysis and microbial decay, authigenic mineralization, diagenesis, metamorphism, and finally weathering and exhumation. Determining which tissues are preserved and how biases affect their preservation pathways is important for interpreting fossils in phylogenetic, ecological, and evolutionary frameworks. Although laboratory decay experiments reveal important aspects of fossilization, applying the results directly to the interpretation of exceptionally preserved fossils may overlook the impact of other key processes that remove or preserve morphological information. Investigations of fossils preserving non-biomineralized tissues suggest that certain structures that are decay resistant (e.g., the notochord) are rarely preserved (even where carbonaceous components survive), and decay-prone structures (e.g., nervous systems) can fossilize, albeit rarely. As we review here, decay resistance is an imperfect indicator of fossilization potential, and a suite of biological and geological processes account for the features preserved in exceptional fossils.</p

Data from: Additional information on the primitive contour and wing feathering of paravian dinosaurs

Identifying feather morphology in extinct dinosaurs is challenging due to dense overlapping of filaments within fossilized plumage and the fact that some extinct feather morphologies are unlike those of extant birds or those predicted from an ‘evo-devo’ model of feather evolution. Here, we compare a range of dinosaur taxa with preserved integumentary appendages using high-resolution photographs to better understand fossil feather morphology and gain insight into their function and evolution. A specimen of the basal paravian Anchiornis possesses contour feathers disarticulated from the plumage, revealing a novel feather type: a ‘shaggy’, open-vaned, bifurcated feather with long barbs attached to a short rachis, which is much simpler than the contour feathers of most extant birds. In contrast, it is likely that the contour feathers of Sinosauropteryx were simpler than those seen in Anchiornis; a ‘tuft’ morphology of multiple barbs connected at their bases (e.g. via a shared follicle), but lacking a rachis, is tentatively inferred. However, conclusive morphological descriptions await the discovery of isolated Sinosauropteryx contour feathers. Paravian wing feathers also show potentially plesiomorphic traits. Comparison with Confuciusornis suggests that Anchiornis wing feathers were at least partially open-vaned. Combined with the interpretation of Anchiornis contour feathers, this suggests that differentiated barbicels are relatively derived compared to pennaceous feathers and the appearance of wings. ‘Shaggy’ contour feathers probably influenced thermoregulatory and water repellence abilities, and, in combination with open-vaned wing feathers, would have decreased aerodynamic efficiency. Simplified, open-vaned wing feathers were also observed on the oviraptorosaur Caudipteryx, consistent with, but not necessarily diagnostic of, its suggested flightlessness. Taken together, these observations have broad implications for how we depict a wide variety of dinosaurs and how we view the function and evolution of feathers

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Table of observations on Sinosauropteryx contour feathers and how they are expected support various plausible morphologies. Does the observation support a particular morphology? Y, yes. “?”, maybe or uncertain. N, no. Scoring system is arbitrary with Y=1, “?”=0.5, and N=0. Highest score is the tentatively preferred morphology

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Diagram showing how simple, non-branching filaments could result in the observed overlapping patterns seen in Sinosauropteryx. A, simple, non-branching filaments arranged in multiple, parallel tracts in vivo with some tracks more latero-ventral on the tail than others. B, filaments in A copied but where the area representing the flesh of the tail in vivo is not preserved. Only filaments dorsal to the tail are visible, as is mostly the case in such fossil specimens. Selective preservation of filaments dorsal to the vertebra gives the illusion of branching structures

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 metagenomeassembled 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

Py/GC/MS .CDF files

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