Reconstructing the past:methods and techniques for the digital restoration of fossils

During fossilization, the remains of extinct organisms are subjected to taphonomic and diagenetic processes. As a result, fossils show a variety of preservational artefacts, which can range from small breaks and cracks, disarticulation and fragmentation, to the loss and deformation of skeletal structures and other hard parts. Such artefacts can present a considerable problem, as the preserved morphology of fossils often forms the basis for palaeontological research. Phylogenetic and taxonomic studies, inferences on appearance, ecology and behaviour and functional analyses of fossil organisms strongly rely on morphological information. As a consequence, the restoration of fossil morphology is often a necessary prerequisite for further analyses. Facilitated by recent computational advances, virtual reconstruction and restoration techniques offer versatile tools to restore the original morphology of fossils. Different methodological steps and approaches, as well as software are outlined and reviewed here, and advantages and disadvantages are discussed. Although the complexity of the restorative processes can introduce a degree of interpretation, digitally restored fossils can provide useful morphological information and can be used to obtain functional estimates. Additionally, the digital nature of the restored models can open up possibilities for education and outreach and further research

Evaluation of a New Method of Fossil Retrodeformation by Algorithmic Symmetrization: Crania of Papionins (Primates, Cercopithecidae) as a Test Case

Diagenetic distortion can be a major obstacle to collecting quantitative shape data on paleontological specimens, especially for three-dimensional geometric morphometric analysis. Here we utilize the recently -published algorithmic symmetrization method of fossil reconstruction and compare it to the more traditional reflection & averaging approach. In order to have an objective test of this method, five casts of a female cranium of Papio hamadryas kindae were manually deformed while the plaster hardened. These were subsequently “retrodeformed” using both algorithmic symmetrization and reflection & averaging and then compared to the original, undeformed specimen. We found that in all cases, algorithmic retrodeformation improved the shape of the deformed cranium and in four out of five cases, the algorithmically symmetrized crania were more similar in shape to the original crania than the reflected & averaged reconstructions. In three out of five cases, the difference between the algorithmically symmetrized crania and the original cranium could be contained within the magnitude of variation among individuals in a single subspecies of Papio. Instances of asymmetric distortion, such as breakage on one side, or bending in the axis of symmetry, were well handled, whereas symmetrical distortion remained uncorrected. This technique was further tested on a naturally deformed and fossilized cranium of Paradolichopithecus arvernensis. Results, based on a principal components analysis and Procrustes distances, showed that the algorithmically symmetrized Paradolichopithecus cranium was more similar to other, less-deformed crania from the same species than was the original. These results illustrate the efficacy of this method of retrodeformation by algorithmic symmetrization for the correction of asymmetrical distortion in fossils. Symmetrical distortion remains a problem for all currently developed methods of retrodeformation

Symmetry in Human Evolution, from Biology to Behaviours

Our knowledge of human evolution has made particular progress recently, due to the discovery of new fossils, the use of new methods and multidisciplinary approaches. Moreover, studies on the departure from symmetry, including variations in fluctuating or directional asymmetries, have contributed to the expansion of this knowledge. This Special Issue brings together articles that deal with symmetry and human evolution. The notion of symmetry is addressed, including whether to reconstruct deformed fossil specimens, study biological variations within hominins or compare them with extant primates, address the shape of the brain or seek possible relationships between biological and behavioural data

Geodesic shooting for anatomical curve registration on the plane

The aim of the work presented in this thesis is to develop a method of characterising the shape of curves in the plane that is independent of the parameterisation of the curve. It is important to remove the effect of a specific parameterisation of a curve because it is possible for two curves to have the same shape while having different parameterisations. The characterisation is accomplished by matching curves via deformations, and using the deformations to characterise the difference between them. We specifically aim for a method that is able to characterise the kind of complex curves found in cross sections of the human nasal cavity. In order to match one curve to another, we derive the equations of motion for a geodesic flow, and seeking the flow that deforms an embedded reference curve into the target curve we wish to characterise. The geodesic flow is itself characterised by a conjugate momentum on, and normal to, the reference curve, giving a one dimensional descriptive signal of the deformation. This descriptive signal contains all of the information required to generate the target curve from the reference curve. We therefore say that this descriptive signal characterises the target curve with respect to the reference curve. The descriptive signal is found using a shooting approach, requiring a functional to measure how closely overlaid are two curves. Formulating the problem as an optimisation problem, we first present a parameterisation-independent functional based on geometric currents, but show that we encounter problems in this matching functional due to local minima. We then present a second approach in which we formulate the problem as a landmark matching problem. Since we seek a characterisation that is independent of the choice of landmarks, and the landmark matching functional is parameterisation dependent, we minimise the functional over all reparameterisations of the reference curve. These two approaches solve equivalent problems. We present the results of the reparameterisation-based matching, and show that they overcome the problems observed in the currents-based method. In particular we demonstrate that the method is able to match complex nasal geometries, and show how the descriptive signal can be used to interpolate between two dimensional slices of three dimensional objects to reconstruct three dimensional surfaces representing the objects. Though here we implement the geodesic flow in two dimensions, we note that the flow could be extended to three dimensional space. Since the reparameterisation based matching functional is trivial to implement in three dimensions, this would allow for the characterisation of both curves and surfaces in three dimensional space

Evolution of Diplodocid Sauropod dinosaurs with emphasis on specimens from Howe Ranch, Wyoming (USA)

Diplodocidae are among the best known sauropod dinosaurs. Several species were described in the late 1800s or early 1900s. Since then, numerous additional specimens were recovered in the USA, Tanzania, Portugal, as well as possibly Spain, England, and Asia. To date, the clade includes about 12 to 15 different species, some of them with questionable taxonomic status (e.g. ‘Diplodocus’ hayi or Dyslocosaurus polyonychius). However, intrageneric relationships of the multi-species, iconic genera Apatosaurus and Diplodocus are still poorly known. The way to resolve this issue is a specimen-based phylogenetic analysis, which was done for Apatosaurus, but is here performed for the first time for the entire clade of Diplodocidae. New material from different localities and stratigraphic levels on the Howe Ranch (Shell,Wyoming, USA) sheds additional light on the evolution of Diplodocidae. Three new specimens are described herein, considerably increasing our knowledge of the anatomy of the group. The new specimens (SMA 0004, SMA 0011, and SMA 0087) represent two, to possibly three new diplodocid species. They preserve material from all parts of the skeleton, including two nearly complete skulls, as well as fairly complete manus and pedes, material which is generally rare in diplodocids. Thereby, they considerably increase anatomical overlap between the sometimes fragmentary holotype specimens of the earlier described diplodocid species, allowing for significant results in a specimenbased phylogenetic analysis. Furthermore, clavicles and interclavicles are identified, the latter for the first time in dinosaurs. Their presence seems restricted to early sauropods, flagellicaudatans, and early Macronaria, and might thus be a retained plesiomorphy, with the loss of these bones being synapomorphic for Titanosauriformes and possibly Rebbachisauridae. The new material allows to test previous hypotheses of diplodocid phylogeny. In order to do so, any type specimen previously proposed to belong to Diplodocidae was included in the study, as are relatively complete referred specimens, in order to increase the degree of overlapping material. For specimens subsequently suggested to be non-diplodocid sauropods, their hypothesized sister taxa were included as outgroups. The current phylogenetic analysis thus includes 76 operational taxonomic units, 45 of which belong to Diplodocidae. The specimens were scored for 477 morphological characters, representing one of the most extensive phylogenetic analyses done within sauropod dinosaurs. The resulting cladogram recovers the classical arrangement of diplodocid relationships. Basing on a newly developed numerical approach to reduce subjectivity in the decision of specific or generic separation, species that have historically been included into well-known genera like Apatosaurus or Diplodocus, were detected to be actually generically different. Thereby, the famous genus Brontosaurus is resuscitated, and evidence further suggests that also Elosaurus parvus (previously referred to Apatosaurus) or ‘Diplodocus’ hayi represent unique genera. The study increases our knowledge about individual variation, and helps to decide how to score multi-species genera. Such a specimen-based phylogenetic analysis thus proves a valuable tool to validate historic species in sauropods, and in paleontology as a whole.Fundação para a Ciência e a Tecnologia - (SFRH / BD / 66209 / 2009