Taphonomic Deformation Research Articles

Geometric morphometric analysis of an ontogenetic cranial series of the Permian dicynodont Diictodon feliceps.

The Karoo Basin of South Africa is renowned for its abundance and diversity of therapsid fossils. Among the most ubiquitous and persistent of the Permian fauna is the small herbivorous dicynodont Diictodon feliceps. Intraspecific variation in Diictodon is historically confounding, and while ontogeny is frequently cited as a potential source of variation, observable developmental changes have never been calibrated. The present study revisits this issue, comparing three-dimensional landmark configurations of 82 Diictodon crania to investigate the association between shape, size and dimorphism. Beyond the statistically significant relationship between shape and allometry, our results determine the shape differences between juvenile and adult skulls of Diictodon, aligned with common craniofacial features documented in other tetrapod taxa. Functionally, these changes are attributed to development of the jaw musculature for feeding on larger, tougher plant matter during later ontogeny. Cranial morphological variation owing to sexual dimorphism is negligible, but distinct differences are noted in the allometric trajectories of each morphotype. A component of non-allometric variation cannot be accounted for, and we propose that this represents natural variation, rather than an artefact of taphonomic deformation.

Virtual reconstruction of the Canis arnensis type (Canidae, Mammalia) from the Upper Valdarno Basin (Italy, Early Pleistocene)

Taphonomic deformation, whether it be brittle or plastic, is possibly the most influential process hindering the correct understanding of fossil species morphology. This is especially true if the deformation affects type specimens or applies to or obscures taxonomically diagnostic or functionally significant traits. Target Deformation, a recently developed virtual manipulation protocol, was implemented to address this issue by applying landmark-guided restoration of the original, deformed fossils, using undeformed specimens (or parts thereof) of the same species as a reference. The enigmatic Early Pleistocene canid Canis arnensis provides a typical example of a fossil species in dire need of virtual restoration. Its lectotype specimen is heavily deformed and none of the few known skulls are well preserved, obscuring the recognition of its systematic and phylogenetic position. Our results indicate that the algorithm effectively countered the lectotype skull’s laterolateral compression and its concomitant rostrocaudal elongation. Morphometrically, comparison of the retrodeformed cranium (IGF 867_W) with other specimens of the same species, and to other fossil and extant canid material, confirms IGF 867_W consistently clusters within C. arnensis variability. Overall, the evidence presented here confirms that Target Deformation provides a powerful tool to better characterize complex taxa like C. arnensis, whose knowledge is severely affected by the state of preservation of its fossil material.

Bone abnormalities in the middle Anisian marine sauropsids from Winterswijk.

While the occurrence of skeletal pathologies in Middle Triassic marine reptiles has been poorly documented until now, massive accumulations of bone remains from the Germanic Basin provide the opportunities for documentation. Herein, we describe skeletal abnormalities in the Middle Triassic bone material from the Vossenveld Formation of Winterswijk, the Netherlands. The aim of the study is to distinguish in the studied bones pathologies resulting from malady or trauma and taphonomic alterations. Furthermore, an attempt was made to assess on how the pathologies also represent paleoecological data. Our survey led to the identification of one broken and healed bone, one case of abnormal coossification, and one case of posttraumatic fibro-osseous dysplasia. While the latter two pathologies give little insight into the ecology and function of the affected animals, the fractured dentary is attributed to Nothosaurus marchicus, a common sauropterygian macropredator. It proves that the individual survived long enough to heal, despite the injury hampering its hunting potential. One abnormally shaped humerus is interpreted as postmortem taphonomic deformation, emphasizing the necessity of utilization of detailed diagnostics to distinguish actual paleopathologies from nonbiological distortion.

The report of a rare deformed eagle ray (Myliobatiformes: Myliobatidae) tooth plate from the Neogene of Calvert Cliffs, Maryland, U.S.A.

An isolated and deformed lower tooth plate of an eagle ray (Aetomylaeus sp., Myliobatidae, Myliobatiformes) is reported herein from the Miocene deposits along Calvert Cliffs, Maryland, U.S.A. Deformed myliobatid tooth plates like this, either fossil or modern, are exceedingly rare. All medial teeth are deformed/skewed such that the right side of each tooth forms an angle of about 10 degrees to the transverse axis of the dental plate. The skewed abnormal form of the teeth in USNM PAL 726325 is not thought to be the result of modern or taphonomic deformation. Rather, the deformity exhibited by USNM PAL 726325 gives every indication that successive similarly deformed teeth came about as a result of a persistent anatomical deformity of the dental lamina. From the consistency in the deformed shape of each tooth, it would appear as though the dental lamina retained this anomalous shape at least throughout the time represented by the age of the tooth plate. If this interpretation is correct, the deformity was not fatal and did not significantly impair the functionality of the tooth pavement over a protracted part (or all) of the individual's life span.

Topology-Based Three-Dimensional Reconstruction of Delicate Skeletal Fossil Remains and the Quantification of Their Taphonomic Deformation

Taphonomic and diagenetic processes inevitably distort the original skeletal morphology of fossil vertebrate remains. Key aspects of palaeobiological datasets may be directly impacted by such morphological deformation, such as taxonomic diagnoses and phylogenetic hypotheses, interpretations of the shape and orientation of anatomical structures, and assessments of interspecific and intraspecific variation. In order to overcome these ubiquitous challenges we present a novel reconstruction workflow combining retopology and retrodeformation, allowing the original morphology of both symmetrically and asymmetrically damaged areas of fossils to be reconstructed. As case studies, we present idealised three-dimensional reconstructions of the sternum of the crownward stem-bird Ichthyornis dispar, and cervical vertebrae of the diplodocid sauropod Galeamopus pabsti. Multiple Ichthyornis sterna were combined into a single, idealised composite representation through superimposition and alignment of retopologised models, and this composite was subsequently retrodeformed. The Galeamopus vertebrae were individually retrodeformed and symmetrised. Our workflow enabled us to quantify deformation of individual specimens with respect to our reconstructions, and to characterise global and local taphonomic deformation. Our workflow can be integrated with geometric morphometric approaches to enable quantitative morphological comparisons among multiple specimens, as well as quantitative interpolation of “mediotypes” of serially homologous elements such as missing vertebrae, haemal arches, or ribs.

Computerized restoration of a fossil cranium based on selective elimination of estimated taphonomic deformation

AbstractObjectivesDue to taphonomic processes, fossils have often undergone plastic deformation. To correctly assess the morphological affinities of such specimens, the original antemortem shape of the deformed specimens must be reconstructed. Here we describe a method to mathematically isolate and selectively eliminate the taphonomic deformation of a fossil cranium for restoration of its original antemortem appearance, and apply this method to reconstruction of a cranium of Mesopithecus from the late Miocene of Greece.Materials and methodsThree‐dimensional (3D) models of the fossil cranium and the crania of phylogenetically close extant species were generated, and 3D shape variations of the crania were analyzed based on anatomical and sliding semi‐landmarks. Using principal component analysis, we attempt to extract the taphonomic deformation component of the shape variation that is presumably orthogonal to the hyperplane describing interspecific variations of the intact crania of the extant species. Landmarks were repositioned so that the extracted taphonomic component is selectively eliminated. A thin‐plate spline was used to describe the 3D transformation from original and repositioned landmarks, and the entire surface of the fossil was restored.ResultsThe proposed method successfully extracted and eliminated the component of the taphonomic deformation and enabled restoration of the original antemortem appearance of the deformed fossil cranium.DiscussionUnlike conventional methodologies, the proposed method does not rely on the assumption of symmetry for correction of taphonomic deformation. Although some methodological limitations apply, the proposed method may contribute to improved accuracy, objectivity, and transparency in virtual reconstruction of deformed cranial fossils.

3D geometric morphometrics of the hind limb in the titanosaur sauropods from Lo Hueco (Cuenca, Spain)

The Campanian–Maastrichtian Konzentrat-Lagerstätte at Lo Hueco (Spain) has yielded a large sample of appendicular elements referable to sauropod titanosaurs that exhibit considerable morphological variability. The taxonomic assessment of these elements is difficult, they display various degrees of preservation (including fragmentary preservation and taphonomic deformation, each of which were addressed in the methods applied in this study), and also many of the appendicular elements are found as isolated remains. Accurate taxonomic determinations are generally difficult to achieve from the morphological information available on appendicular remains of sauropods, and particularly in groups such as titanosaurirformes. In these cases, the geometric morphometrics (GMM) tool kit is a suitable methodology to explore morphological variability for taxonomic assessment. In this study, several femora, tibiae and fibulae from Lo Hueco were analyzed. To this purpose, the remains were digitized, and the resultant mesh representations were used for definition of 3D landmarks and curves that were analyzed through GMM methods. The quantification of shape variables allowed the use of clustering and K-means techniques as well as a proposed statistical workflow. Several hypotheses of a priori anatomically-defined morphotypes and the results from our machine learning algorithms revealed the presence of two main morphotypes as the most plausible explanation for the morphological variability in the sample of titanosaurian hind limb elements from Lo Hueco.

Retrodeformation of the Steinheim Cranium: Insights into the Evolution of Neanderthals

A number of different approaches are currently available to digitally restore the symmetry of a specimen deformed by taphonomic processes. These tools include mirroring and retrodeformation to approximate the original shape of an object by symmetrisation. Retrodeformation has the potential to return a rather faithful representation of the original shape, but its power is limited by the availability of bilateral landmarks. A recent protocol proposed by Schlager and colleagues (2018) overcomes this issue by using bilateral landmarks and curves as well as semilandmarks. Here we applied this protocol to the Middle Pleistocene human cranium from Steinheim (Germany), the holotype of an abandoned species named Homo steinheimensis. The peculiar morphology of this fossil, associated with the taphonomic deformation of the entire cranium and the lack of a large portion of the right side of the face, has given rise to different hypotheses over its phylogenetic position. The reconstruction presented here sheds new light on the taphonomic origin of some features observed on this crucial specimen and results in a morphology consistent with its attribution to the Neanderthal lineage.

Effects of taphonomic deformation on geometric morphometric analysis of fossils: a study using the dicynodont Diictodon feliceps (Therapsida, Anomodontia).

Taphonomic deformation, the distortion of fossils as a result of geological processes, poses problems for the use of geometric morphometrics in addressing paleobiological questions. Signal from biological variation, such as ontogenetic trends and sexual dimorphism, may be lost if variation from deformation is too high. Here, we investigate the effects of taphonomic deformation on geometric morphometric analyses of the abundant, well known Permian therapsid Diictodon feliceps. Distorted Diictodon crania can be categorized into seven typical styles of deformation: lateral compression, dorsoventral compression, anteroposterior compression, “saddle-shape” deformation (localized collapse at cranial mid-length), anterodorsal shear, anteroventral shear, and right/left shear. In simulated morphometric datasets incorporating known “biological” signals and subjected to uniform shear, deformation was typically the main source of variance but accurate “biological” information could be recovered in most cases. However, in empirical datasets, not only was deformation the dominant source of variance, but little structure associated with allometry and sexual dimorphism was apparent, suggesting that the more varied deformation styles suffered by actual fossils overprint biological variation. In a principal component analysis of all anomodont therapsids, deformed Diictodon specimens exhibit significant dispersion around the “true” position of this taxon in morphospace based on undistorted specimens. The overall variance associated with deformation for Anomodontia as a whole is minor, and the major axes of variation in the study sample show a strong phylogenetic signal instead. Although extremely problematic for studying variation in fossil taxa at lower taxonomic levels, the cumulative effects of deformation in this study are shown to be random, and inclusion of deformed specimens in higher-level analyses of morphological disparity are warranted. Mean morphologies of distorted specimens are found to approximate the morphology of undistorted specimens, so we recommend use of species-level means in higher-level analyses when possible.

Ngwevu intloko: a new early sauropodomorph dinosaur from the Lower Jurassic Elliot Formation of South Africa and comments on cranial ontogeny in Massospondylus carinatus.

Our knowledge of Early Jurassic palaeobiodiversity in the upper Elliot Formation of South Africa has increased markedly in recent years with the discovery of new fossils, re-assessments of previously collected material and a better understanding of Stormberg Group stratigraphy. Here, Ngwevu intloko, a new genus of upper Elliot basal sauropodomorph is named on the basis of a complete skull and partial skeleton (BP/1/4779) previously assigned to Massospondylus carinatus. It can be distinguished from all other basal sauropodomorphs by a combination of 16 cranial and six postcranial characters. The new species is compared to a small ontogenetic series of M. carinatus as well as to a range of closely related taxa. Taphonomic deformation, sexual dimorphism and ontogeny are rejected as possible explanations for the morphological differences present between BP/1/4779 and other taxa. Osteohistological examination reveals that BP/1/4779 had nearly reached adult size at the time of its death at a minimum age of 10 years.

Digital reconstruction of the Ceprano calvarium (Italy), and implications for its interpretation

The Ceprano calvarium was discovered in fragments on March 1994 near the town of Ceprano in southern Latium (Italy), embedded in Middle Pleistocene layers. After reconstruction, its morphological features suggests that the specimen belongs to an archaic variant of H. heidelbergensis, representing a proxy for the last common ancestor of the diverging clades that respectively led to H. neanderthalensis and H. sapiens. Unfortunately, the calvarium was taphonomically damaged. The postero-lateral vault, in particular, appears deformed and this postmortem damage may have influenced previous interpretations. Specifically, there is a depression on the fragmented left parietal, while the right cranial wall is warped and angulated. This deformation affected the shape of the occipital squama, producing an inclination of the transverse occipital torus. In this paper, after X-ray microtomography (μCT) of both the calvarium and several additional fragments, we analyze consistency and pattern of the taphonomic deformation that affected the specimen, before the computer-assisted retrodeformation has been performed; this has also provided the opportunity to reappraise early attempts at restoration. As a result, we offer a revised interpretation for the Ceprano calvarium’s original shape, now free from the previous uncertainties, along with insight for its complex depositional and taphonomic history.

Missing data estimation in tyrannosaurid dinosaurs: Can diameter take the place of circumference?

Missing data, due to taphonomic deformation, inaccessibility of specimens, or human error in collecting, cataloguing and measuring features, is a formidable problem in current palaeontological studies. Missing values within a data set can undermine confidence in analyses, skew results in promoting analyses of small portions of a population, not necessarily representative of the entire data set, and drastically decrease sample sizes. Missing data estimation methods, however, may reduce the effects of these missing values and potentially boost sample sizes for palaeontological studies. Here, six missing data estimation models for the prediction of femoral circumferences in tyrannosaurids were statistically tested and their predictive success measured against true circumferences, and other models. The statistical analyses suggest that estimation models based on anteroposterior diameter values of tyrannosaurid femora were poor predictors of circumference, whereas those based on mediolateral diameters were much more successful. Three out of the six models, were presented as viable alternatives to missing measured circumferences and may be used to boost tyrannosaurid samples with significant levels of missing data.

Terreneuvian Orthothecid (Hyolitha) Digestive Tracts from Northern Montagne Noire, France; Taphonomic, Ontogenetic and Phylogenetic Implications

More than 285 specimens of Conotheca subcurvata with three-dimensionally preserved digestive tracts were recovered from the Terreneuvian (early Cambrian) Heraultia Limestone of the northern Montagne Noire, southern France. They represent one of the oldest occurrences of such preserved guts. The newly discovered operculum of some complete specimens provides additional data allowing emendation of the species diagnosis. Infestation of the U-shaped digestive tracts by smooth uniseriate, branching to anastomosing filaments along with isolated botryoidal coccoids attests to their early, microbially mediated phosphatisation. Apart from taphonomic deformation, C. subcurvata exhibits three different configurations of the digestive tract: (1) anal tube and gut parallel, straight to slightly undulating; (2) anal tube straight and loosely folded gut; and (3) anal tube straight and gut straight with local zigzag folds. The arrangement of the digestive tracts and its correlation with the mean apertural diameter of the specimens are interpreted as ontogenetically dependent. The simple U-shaped gut, usually considered as characteristic of the Hyolithida, developed in earlier stages of C. subcurvata, whereas the more complex orthothecid type-3 only appears in largest specimens. This growth pattern suggests a distinct phylogenetic relationship between these two hyolith orders through heterochronic processes.

Analyzing Taphonomic Deformation of Ankylosaur Skulls Using Retrodeformation and Finite Element Analysis

Taphonomic deformation can make the interpretation of vertebrate fossil morphology difficult. The effects of taphonomic deformation are investigated in two ankylosaurid dinosaur taxa, Euoplocephalus tutus (to investigate effects on our understanding of intraspecific variation) and Minotaurasaurus ramachandrani (to investigate the validity of this genus). The ratio of orbit maximum rostrocaudal length to perpendicular height is used as a strain ellipse, which can be used to determine if ankylosaur skull fossils have been dorsoventrally compacted during fossilization and diagenesis. The software program Geomagic is used to retrodeform three-dimensional (3D) digital models of the ankylosaur skulls. The effects of sediment compaction are modeled using finite element analysis, and the resulting strain distributions are compared with the retrodeformed models as a test of the retrodeformation method. Taphonomic deformation can account for a large amount of intraspecific variation in Euoplocephalus, but finite element analysis and retrodeformation of Minotaurasaurus shows that many of its diagnostic features are unlikely to result from deformation.

Virtual reconstruction: a primer in computer-assisted paleontology and biomedicine

Preface. Acknowledgments. Introduction. 1. Virtual Reconstruction. 1.1 A Virtual Reality Contest. 1.2 Virtual Reconstruction. 1.3 Computer-Assisted Paleontology. 1.3.1 Data Acquisition. 1.3.2 Data Segmentation and Three-Dimensional Reconstruction. 1.3.3 Virtual Fossil Reconstruction. 1.3.4 From Virtual Reality to Real Virtuality. 1.3.5 Databases and Morphometry. 1.3.6 Virtual Reconstruction in Space and Time. 1.4 Computer-Assisted Surgery. 1.5 Further Reading. 2. Data Representation. 2.1 World Food on a Chessboard. 2.2 Facts About Data to Get Data About Facts. 2.2.1 Analog and Digital Data. 2.2.2 Bits, Bytes, and Words. 2.2.3 Characters, Numbers, Pixels, and Voxels. 2.2.4 Representing Gray Tones and Colors. 2.2.5 Data Compression. 2.2.6 Some Common Image File Formats. 2.2.7 Implicit Versus Explicit Representation of Object Data. 2.2.8 Modeling Three-Dimensional Objects. 2.3 A Taxonomy of Biomedical Data. 2.3.1 Perspectives on Data. 2.3.2 Volume Data. 2.3.3 Surface Data. 2.3.4 Landmark Data. 2.3.5 Extent-Based Data. 2.3.6 Relational Data. 2.4 Further Reading. 3. Data Acquisition. 3.1 Data and the Physical World. 3.2 Vision and Photography as Data Acquisition: Performance Considerations. 3.3 Computed Tomography. 3.3.1 Frau RAntgena s Wedding Ring. 3.3.2 Radiographic Projections. 3.3.3 Reconstructing CT Images. 3.3.4 CT Scanning: Technical Considerations. 3.3.5 Limitations of CT Data Acquisition. 3.3.6 Slice-to-Slice, Helical, and Multislice CT. 3.3.7 Industrial and Micro Computed Tomography. 3.3.8 Three-Dimensional Data Acquisition with a Medical Scanner. 3.4 Magnetic Resonance Imaging. 3.5 Surface Scanners. 3.6 3D Digitizers. 3.7 Further Reading. 4. Image Data Processing. 4.1 Recovering Objects from Images. 4.2 Converting a CT Image into a Screen Image. 4.3 Filtering Images. 4.3.1 Coffee and Kernels. 4.3.2 Convolution and Fourier Analysis. 4.3.3 Statistical Filters. 4.3.4 Edge Detection Filters. 4.4 Extracting Isosurfaces. 4.4.1 Determining Boundaries in CT Images. 4.4.2 From Edges to Isocontours and Isosurfaces. 4.5 Interactive Segmentation. 4.6 Further Reading. 5. Visualization and Interaction. 5.1 Visualizing Data in Two and More Dimensions. 5.2 Interaction with Virtual Worlds. 5.3 The Graphics Rendering Pipeline. 5.4 Setting Up a Virtual Environment. 5.4.1 Object Materials, Lighting, and Shading. 5.4.2 Setting Up the Camera. 5.4.3 Object Manipulation and Interaction. 5.5 Volume Rendering. 5.6 Further Reading. 6. Virtual Fossil Reconstruction. 6.1 A Baroque Puzzle. 6.2 Principles of Reconstruction. 6.3 Physical and Virtual Reconstruction. 6.4 Preparing and Restoring Fossils on the Computer Screen. 6.5 Reconstructing Fossil Morphologies. 6.5.1 Recovering Implicit Anatomic Information. 6.5.2 Combining Computer Graphics and Anatomy: The Globe Paradigm. 6.5.3 Inferring Missing Information. 6.5.4 Interpolation and Extrapolation. 6.6 Correcting Fossil Deformation. 6.6.1 Taphonomic Scenarios. 6.6.2 Correcting Plastic Deformation. 6.7 Validating Virtual Reconstructions. 6.8 Paleodiagnostics and Paleoforensics. 6.9 Inferring Soft Tissue Structures. 6.9.1 Motivation. 6.9.2 Fossil Soft Tissue Reconstruction: Classic and Virtual Approaches. 6.9.3 What Shall Be Reconstructed? 6.9.4 Soft Tissue Reconstruction and Measurement. 6.10 Virtual Surgery: A Paleoanthropologista s Eye View. 6.10.1 Motivation. 6.10.2 Virtual Planning and Simulation of Surgical Interventions. 6.10.3 Custom Implant Design. 6.10.4 Soft Tissue Reconstruction. 6.11 Further Reading. 7. From Virtual Reality to Real Virtuality. 7.1 Reifying Virtual Objects. 7.2 Principles of Rapid Prototyping. 7.3 Combining Virtual Reality and Real Virtuality. 7.4 Further Reading. 8. Morphometric Analysis. 8.1 Morphometry as Reconstruction. 8.2 Morphometry and Geometry. 8.2.1 The Role of Geometry. 8.2.2 The Role of Size and Shape. 8.2.3 Multivariate Morphometry. 8.2.4 Principal Components Analysis and Dimension Reduction. 8.2.5 Classic Multivariate Morphometry: Geometry Lost. 8.2.6 Geometric Morphometrics: Geometry Recovered. 8.3 Shape Space Analysis. 8.3.1 From Da Arcy Thompson to Kendall. 8.3.2 The Workflow of Shape Space Analysis. 8.3.3 Determining a Reference Shape. 8.3.4 Analyzing Data in Shape Space. 8.3.5 Visualizing Patterns of Shape Difference and Shape Change. 8.3.5 Visualizing Patterns of Shape Difference and Shape Change. 8.4 Euclidean Distance Matrix Analysis. 8.4.1 In Search of the Golden Mean. 8.4.2 Exploring Form Variability with EDMA. 8.5 Outline Analysis. 8.6 A Comparison of Geometric Morphometric Methods. 8.6.1 Criteria for Comparison. 8.6.2 From Pattern to Process. 8.7 Exploring Morphometric Patterns. 8.8 Further Reading. Appendix A. Image Data Acquisition Systems: Performance Considerations. Appendix B. Parameters Influencing the Quality of CT Image Data. Appendix C. CT Scanning of Fossil Specimens and Recent Skeletal Specimens: How to Proceed? Appendix D. Object Manipulation in Virtual Space. Appendix E. A Parsimonious Approach to Correction of Taphonomic Deformation. Appendix F. Morphometry. References. Index.

Three-dimensional Computerized Modeling of the Skull of Proconsul heseloni

The skull of Proconsul heseloni (KNM-RU-7290A) is three-dimensionally reconstructed in a virtual environment for morphological analyses of the evolution of Miocene hominoid skulls by the means of Computer Assisted Anthropology. The volume of the fossil is extracted from the CT-scan images and the surface is approximated by very tiny triangles. Such a computerized technique enables visualization, manipulation and measurements of its 3 D shape in a computer. Moreover, a replica of the virtually constructed model can be created by stereo-lithography.Taking advantage of the computerized system, non-homogeneous taphonomic deformation of the fossil is corrected based on skull’s basic geometry, that is, bilateral symmetry with respect to its midsagittal plane. Morphological landmarks of the skull are transferred so as to fulfill the geometrical conditions, and the entire shape of the skull is transformed according to the movements of the landmarks using a thin-plate spline function. Although the reconstruction is still incomplete due to inherent lack of information that can be extracted from the fossil for reversal of deformation, tentative results indicate efficacy of the proposed computerized system for advanced morphometrical and biomechanical studies of fossil skulls.