Arothron: An R package for geometric morphometric methods and virtual anthropology applications

RRmorph-a new R package to map phenotypic evolutionary rates and patterns on 3D meshes

The study of evolutionary rates and patterns is the key to understand how natural selection shaped the current and past diversity of phenotypes. Phylogenetic comparative methods offer an array of solutions to undertake this challenging task, and help understanding phenotypic variation in full in most circumstances. However, complex, three-dimensional structures such as the skull and the brain serve disparate goals, and different portions of these phenotypes often fulfil different functions, making it hard to understand which parts truly were recruited by natural selection. In the recent past, we developed tools apt to chart evolutionary rate and patterns directly on three-dimensional shapes, according to their magnitude and direction. Here, we present further developments of these tools, which now allow to restitute the mapping of rates and patterns with full biological realism. The tools are condensed in a new R software package.

Direct Occipital Remodeling in Sagittal Synostosis Improves 2-Year Posterior Morphology after Modified Pi Procedure

BACKGROUND

Modifications of the pi craniectomy technique are meant to address the occipital bullet deformity of sagittal synostosis, but it is not clear whether they result in persistent improvement. The authors' purpose was to use morphometric analysis to determine whether a low occipital osteotomy with verticalization results in improved occipital shape after a modified pi procedure 2 years after surgery.

METHOD

The authors performed a retrospective cohort study comparing modified pi technique with and without a low occipital osteotomy with verticalization immediately and 2 years after surgery relative to age-matched normal controls. The authors used anthropometric measures and population-level anatomical templates using the multivariate template construction script from advanced normalization tools for comparison between groups. A subgroup analysis was performed for severe occipital bullet deformity at presentation.

RESULTS

The authors observed stable improvement in the angle of the inferior occiput with the occipital remodeling modification that persisted 2 years after surgery. This improvement was seen in the entire cohort and was greater in the severe subgroup analysis. Complications and blood transfusion volumes were not different between the 2 techniques. The low occipital osteotomy group demonstrated improved posterior vertical height and cephalic index immediately after surgery, but these did not persist 2 years later.

CONCLUSIONS

Occipital remodeling improves the bullet deformity but does not affect posterior vertical height 2 years after surgery. The authors recommend direct inferior occipital remodeling when using the pi technique for young patients with acute occipital incline angles and occipital constriction.

CLINICAL QUESTION/LEVEL OF EVIDENCE

Therapeutic, III.

Sella turcica and facial bones: Morphological integration in the human fetal cranium

OBJECTIVES

The cranial base plays a significant role in facial growth, and closer analyses of the morphological relationship between these two regions are needed to understand the morphogenesis of the face. Here, we aimed to study morphological integration between the sella turcica (ST) and facial bones during the fetal period using geometric morphometrics.

MATERIALS AND METHODS

Magnetic resonance images of 47 human fetuses in the Kyoto Collection, with crown-rump lengths of 29.8-225 mm, were included in this study. Anatomical homologous landmarks and semilandmarks were registered on the facial bones and the midsagittal contour of the ST, respectively. The shape variations in the craniofacial skeleton and the ST were statistically investigated by reducing dimensionality using principal component analysis (PCA). Subsequently, the morphological integration between the facial bones and ST was investigated using two-block partial least squares (2B-PLS) analysis.

RESULTS

PCA showed that small specimens represented the concave facial profile, including the mandibular protrusion and maxillary retrusion. The 2B-PLS showed a strong integration (RV coefficient = 0.523, r = .79, p < .01) between the facial bones and ST. The curvature of the anterior wall of the ST was highly associated with immature facial morphology characterized by a concave profile.

CONCLUSION

The strong integration between the two regions suggested that the anterior ST may be associated with facial morphology. This result quantitatively confirms previous studies reporting ST deformities in facial anomalies and induces further research using postnatal subjects.

Virtual reconstruction and geometric morphometric analysis of the Kocabaş hominin fossil from Turkey: Implications for taxonomy and evolutionary significance

The Kocabaş specimen comes from a travertine quarry near the homonymous village in the Denizli basin (Turkey). The specimen comprises three main fragments: portions of the right and left parietal and left and right parts of the frontal bone. The fossil was assumed to belong to the Homo erectus s.l. hypodigm by some authors, whereas others see similarities with Middle Pleistocene fossils (Broken Hill 1/Kabwe, Bodo, or Ceprano). Here, we present the first attempt to make a complete reconstruction of the missing medial portion of the frontal bone and a comprehensive geometric morphometric analysis of this bone. We restored the calotte by aligning and mirroring the three preserved fragments. Afterward, we restored the missing portion by applying the thin-plate spline interpolation algorithm of target fossils onto the reconstructed Kocabaş specimen. For the geometric morphometric analyses, we collected 80 landmarks on the frontal bone (11 osteometric points, 14 bilateral curve semilandmarks, and 41 surface semilandmarks). The comparative sample includes 21 fossils from different chronological periods and geographical areas and 30 adult modern humans from different populations. Shape analyses highlighted the presence in Kocabaş of features usually related to Middle Pleistocene Homo, such as a developed supraorbital torus associated with a relatively short frontal squama and reduced post-toral sulcus. Cluster analysis and linear discriminant analysis classification procedure suggest Kocabaş being part of the same taxonomic unit of Eurasian and African Middle Pleistocene Homo. In light of our results, we consider that attributing the Kocabaş hominin to H. erectus s.l. may be unwarranted. Results of our analyses are compatible with different evolutionary scenarios, but a more precise chronological framework is needed for a thorough discussion of the evolutionary significance of this specimen. Future work should clarify its geological age, given uncertainties regarding its stratigraphic provenance.

Comparison of Morphometric Outcomes following Open Posterior Expansion versus Endoscopic Strip Craniectomy for Sagittal Synostosis

BACKGROUND

Open middle and posterior cranial vault expansion (OPVE) or endoscopic (ES) strip craniectomy are two surgical techniques for normalization of head shape in isolated sagittal synostosis. This study aims to compare 2-year cranial morphometrics after these two approaches.

METHODS

The authors performed morphometric analysis on preoperative [time (T) 0], immediately postoperative (T1), and 2-year (T2) postoperative computed tomographic scans of patients who underwent OPVE or ES before 4 months of age. Perioperative data and morphometrics were compared between the two groups and age-matched controls.

RESULTS

Nineteen patients were included in the ES cohort, 19 age-matched patients were included in the OPVE cohort, and 57 were included as controls. Median surgery time and blood transfusion volume were less for the ES approach (118 minutes and 0 cc, respectively) compared with OPVE (204 minutes and 250 cc, respectively). Anthropometric measurements after OPVE were closer in normal controls at T1 compared with ES, but the skull shapes were comparable at T2. In the midsagittal plane, anterior vault was higher after OPVE at T2 compared with both ES and controls, but the posterior length was shorter and closer to controls than in the ES cohort. Cranial volumes were like controls for both cohorts at T2. There was no difference in complication rate.

CONCLUSIONS

Both OPVE and ES techniques result in normalization of cranial shape in patients with isolated sagittal synostosis after 2 years with minimal morphometric differences. Family decision-making between the two approaches should be based on age at presentation, avoidance of blood transfusion, scar pattern, and availability of helmet molding and not on expected outcome.

CLINICAL QUESTION/LEVEL OF EVIDENCE

Therapeutic, III.

Dynamic evolutionary interplay between ontogenetic skull patterning and whole-head integration

The arrangement and morphology of the vertebrate skull reflect functional and ecological demands, making it a highly adaptable structure. However, the fundamental developmental and macroevolutionary mechanisms leading to different vertebrate skull phenotypes remain unclear. Here we exploit the morphological diversity of squamate reptiles to assess the developmental and evolutionary patterns of skull variation and covariation in the whole head. Our geometric morphometric analysis of a complex squamate ontogenetic dataset (209 specimens, 169 embryos, 44 species), covering stages from craniofacial primordia to fully ossified bones, reveals that morphological differences between snake and lizard skulls arose gradually through changes in spatial relationships (heterotopy) followed by alterations in developmental timing or rate (heterochrony). Along with dynamic spatiotemporal changes in the integration pattern of skull bone shape and topology with surrounding brain tissues and sensory organs, we identify a relatively higher phenotypic integration of the developing snake head compared with lizards. The eye, nasal cavity and Jacobson's organ are pivotal in skull morphogenesis, highlighting the importance of sensory rearrangements in snake evolution. Furthermore, our findings demonstrate the importance of early embryonic, ontogenetic and tissue interactions in shaping craniofacial evolution and ecological diversification in squamates, with implications for the nature of cranio-cerebral relations across vertebrates.

Biomechanical and taxonomic diversity in the Early Pleistocene in East Africa: Structural analysis of a recently discovered femur shaft from Olduvai Gorge (bed I)

Recent Plio-Pleistocene hominin findings have revealed the complexity of human evolutionary history and the difficulties involved in its interpretation. Moreover, the study of hominin long bone remains is particularly problematic, since it commonly depends on the analysis of fragmentary skeletal elements that in many cases are merely represented by small diaphyseal portions and appear in an isolated fashion in the fossil record. Nevertheless, the study of the postcranial skeleton is particularly important to ascertain locomotor patterns. Here we report on the discovery of a robust hominin femoral fragment (OH 84) at the site of Amin Mturi Korongo dated to 1.84 Ma (Olduvai Bed I). External anatomy and internal bone structure of OH 84 were analyzed and compared with previously published data for modern humans and chimpanzees, as well as for Australopithecus, Paranthropus and Homo specimens ranging from the Late Pliocene to Late Pleistocene. Biomechanical analyses based on transverse cross-sections and the comparison of OH 84 with another robust Olduvai specimen (OH 80) suggest that OH 84 might be tentatively allocated to Paranthropus boisei. More importantly, the identification of a unique combination of traits in OH 84 could indicate both terrestrial bipedalism and an arboreal component in the locomotor repertoire of this individual. If interpreted correctly, OH 84 could thus add to the already mounting evidence of substantial locomotor diversity among Early Pleistocene hominins. Likewise, our results also highlight the difficulties in accurately interpreting the link between form and function in the human fossil record based on fragmentary remains, and ultimately in distinguishing between coeval hominin groups due to the heterogeneous pattern of inter- and intraspecific morphological variability detected among fossil femora.

Reconstructing the origin and early evolution of the snake brain

Snakes represent one-eighth of terrestrial vertebrate diversity, encompassing various lifestyles, ecologies, and morphologies. However, the ecological origins and early evolution of snakes are controversial topics in biology. To address the paucity of well-preserved fossils and the caveats of osteological traits for reconstructing snake evolution, we applied a different ecomorphological hypothesis based on high-definition brain reconstructions of extant Squamata. Our predictive models revealed a burrowing lifestyle with opportunistic behavior at the origin of crown snakes, reflecting a complex ancestral mosaic brain pattern. These findings emphasize the importance of quantitatively tracking the phenotypic diversification of soft tissues-including the accurate definition of intact brain morphological traits such as the cerebellum-in understanding snake evolution and vertebrate paleobiology. Furthermore, our study highlights the power of combining extant and extinct species, soft tissue reconstructions, and osteological traits in tracing the deep evolution of not only snakes but also other groups where fossil data are scarce.

Normal human craniofacial growth and development from 0 to 4 years

Knowledge of human craniofacial growth (increase in size) and development (change in shape) is important in the clinical treatment of a range of conditions that affects it. This study uses an extensive collection of clinical CT scans to investigate craniofacial growth and development over the first 48 months of life, detail how the cranium changes in form (size and shape) in each sex and how these changes are associated with the growth and development of various soft tissues such as the brain, eyes and tongue and the expansion of the nasal cavity. This is achieved through multivariate analyses of cranial form based on 3D landmarks and semi-landmarks and by analyses of linear dimensions, and cranial volumes. The results highlight accelerations and decelerations in cranial form changes throughout early childhood. They show that from 0 to 12 months, the cranium undergoes greater changes in form than from 12 to 48 months. However, in terms of the development of overall cranial shape, there is no significant sexual dimorphism in the age range considered in this study. In consequence a single model of human craniofacial growth and development is presented for future studies to examine the physio-mechanical interactions of the craniofacial growth.

Virtual excavation and analysis of the early Neanderthal cranium from Altamura (Italy)

Complete Neanderthal skeletons are almost unique findings. A very well-preserved specimen of this kind was discovered in 1993 in the deepest recesses of a karstic system near the town of Altamura in Southern Italy. We present here a detailed description of the cranium, after we virtually extracted it from the surrounding stalagmites and stalactites. The morphology of the Altamura cranium fits within the Neanderthal variability, though it retains features occurring in more archaic European samples. Some of these features were never observed in Homo neanderthalensis, i.e. in fossil specimens dated between 300 and 40 ka. Considering the U-Th age we previously obtained (>130 ka), the morphology of Altamura suggests that the archaic traits it retains may have been originated by geographic isolation of the early Neanderthal populations from Southern Italy.

Icex: Advances in the automatic extraction and volume calculation of cranial cavities

The use of non-destructive approaches for digital acquisition (e.g. computerised tomography-CT) allows detailed qualitative and quantitative study of internal structures of skeletal material. Here, we present a new R-based software tool, Icex, applicable to the study of the sizes and shapes of skeletal cavities and fossae in 3D digital images. Traditional methods of volume extraction involve the manual labelling (i.e. segmentation) of the areas of interest on each section of the image stack. This is time-consuming, error-prone and challenging to apply to complex cavities. Icex facilitates rapid quantification of such structures. We describe and detail its application to the isolation and calculation of volumes of various cranial cavities. The R tool is used here to automatically extract the orbital volumes, the paranasal sinuses, the nasal cavity and the upper oral volumes, based on the coordinates of 18 cranial anatomical points used to define their limits, from 3D cranial surface meshes obtained by segmenting CT scans. Icex includes an algorithm (Icv) for the calculation of volumes by defining a 3D convex hull of the extracted cavity. We demonstrate the use of Icex on an ontogenetic sample (0-19 years) of modern humans and on the fossil hominin crania Kabwe (Broken Hill) 1, Gibraltar (Forbes' Quarry) and Guattari 1. We also test the tool on three species of non-human primates. In the modern human subsample, Icex allowed us to perform a preliminary analysis on the absolute and relative expansion of cranial sinuses and pneumatisations during growth. The performance of Icex, applied to diverse crania, shows the potential for an extensive evaluation of the developmental and/or evolutionary significance of hollow cranial structures. Furthermore, being open source, Icex is a fully customisable tool, easily applicable to other taxa and skeletal regions.

A Comparison of Semilandmarking Approaches in the Visualisation of Shape Differences

In landmark-based analyses of size and shape variation and covariation among biological structures, regions lacking clearly identifiable homologous landmarks are commonly described by semilandmarks. Different algorithms may be used to apply semilandmarks, but little is known about the consequences of analytical results. Here, we assess how different approaches and semilandmarking densities affect the estimates and visualisations of mean and allometrically scaled surfaces. The performance of three landmark-driven semilandmarking approaches is assessed using two different surface mesh datasets with different degrees of variation and complexity: adult human head and ape cranial surfaces. Surfaces fitted to estimates of the mean and allometrically scaled landmark and semilandmark configurations arising from geometric morphometric analyses of these datasets are compared between semilandmarking approaches and different densities, as well as with those from warping to landmarks alone. We find that estimates of surface mesh shape (i.e., after re-semilandmarking and then re-warping) made with varying numbers of semilandmarks are generally consistent, while the warping of surfaces using landmarks alone yields surfaces that can be quite different to those based on semilandmarks, depending on landmark coverage and choice of template surface for warping. The extent to which these differences are important depends on the particular study context and aims.

Analysis of 3D-Models of Artificially Deformed Crania, Using Geometric Morphometry

The study of artificially deformed crania is complicated by difficulties in analyzing curvilinear shapes without reliable reference points for measurement. Methods of geometric morphometrics (GM) help to solve this problem. We generated 3D-models of deformed crania (26 male and 19 female) from burials of different chronological periods of the Okunev archaeological culture (Verkhniy Askiz I, Uybat III and V, Uybat-Charkov, Itkol I and II), Southern Siberia (2600–1700 BC). Using the Landmark IDAV software, each model was transformed into a set of six traditional craniometric landmarks and 450 semi-landmarks regularly distributed over the entire surface of the braincase. For further processing with the Procrustes and principal component analysis, functions of several R-packages (Morpho, Geomorph, and Arothron) were employed. Crania from early Okunev burials were found to have a small deformed area around lambda, spanning the posterior parts of parietal bones and the upper part of the occipital squama. In crania from later Okunev burials, the deformation extends on the parietal area, causing the reduction of cranial height owing to a lesser curvature of the parietal segment. The lateral walls of the braincase, the frontal squama, and the lower part of the occipital squama in such crania are more convex.

Paleomimetics: A Conceptual Framework for a Biomimetic Design Inspired by Fossils and Evolutionary Processes

In biomimetic design, functional systems, principles, and processes observed in nature are used for the development of innovative technical systems. The research on functional features is often carried out without giving importance to the generative mechanism behind them: evolution. To deeply understand and evaluate the meaning of functional morphologies, integrative structures, and processes, it is imperative to not only describe, analyse, and test their behaviour, but also to understand the evolutionary history, constraints, and interactions that led to these features. The discipline of palaeontology and its approach can considerably improve the efficiency of biomimetic transfer by analogy of function; additionally, this discipline, as well as biology, can contribute to the development of new shapes, textures, structures, and functional models for productive and generative processes useful in the improvement of designs. Based on the available literature, the present review aims to exhibit the potential contribution that palaeontology can offer to biomimetic processes, integrating specific methodologies and knowledge in a typical biomimetic design approach, as well as laying the foundation for a biomimetic design inspired by extinct species and evolutionary processes: Paleomimetics. A state of the art, definition, method, and tools are provided, and fossil entities are presented as potential role models for technical transfer solutions.

Mandible shape variation and feeding biomechanics in minks

European and American minks are very similar in ecology, behavior and morphology. Both species hunt terrestrial vertebrates and aquatic prey, but the American mink is a more generalist predator which, among other factors, allows it to outcompete the European mink in areas where it has been introduced. We used 3D geometric morphometrics and estimates of muscle mechanical advantage to assess the degree of variation in mandibular morphology, and to determine whether such variation reflects dietary differences between the two species. The three main axes of variation represented interspecific differences, a common allometric trajectory between species and sexes, and the interspecific effect of sexual size dimorphism, with males having overall stronger bites than females. Differences in mandible shape and biomechanical parameters suggest that American minks are better equipped for preying on terrestrial vertebrates, while the features seen in European mink could be related to tougher prey, fish capture, or both. Additionally, within each species, the larger specimens of each sex present indicators of a higher percentage of terrestrial prey in their diet. These results indicate a low potential dietary overlap between both species, suggesting that factors other than prey competition may have a role in the decline of the European mink.

Cranial shape variation in mink: Separating two highly similar species

European and American minks (Mustela lutreola and Neovison vison, respectively) are very similar in their ecology, behavior, and morphology. However, the American mink is a generalist predator and seems to adapt better to anthropized environments, allowing it to outcompete the European mink in areas where it has been introduced, threatening the survival of the native species. To assess whether morphological differences may be contributing to the success of the American mink relative to the European mink, we analyzed shape variation in the cranium of both species using 3D geometric morphometrics. A set of 38 landmarks and 107 semilandmarks was used to study shape variation between and within species, and to assess how differences in size factored into that variation. Sexual dimorphism in both size and shape was also studied. Significant differences between species were found in cranial shape, but not in size. Relative to American mink, European mink have a shorter facial region with a rounder forehead and wider orbits, a longer neurocranium with less developed crests and processes, and an antero-medially placed tympanic bullae with an anteriorly expanded cranial border. Within species, size-related sexual dimorphism is highly significant, but sexual dimorphism in shape is only significant in American mink, not in European mink. Additionally, two trends common to both species were discovered, one related to allometric changes and another to sexual size dimorphism. Shape changes related to increasing size can be subdivided into two, probably related, groups: increased muscle force and growth. The first group somewhat parallels the differences between both mink species, while the second group of traits includes an anterodorsal expansion of the face, and the neurocranium shifting from a globous shape in small individuals to a dorsoventrally flattened ellipse in the largest ones. Finally, the sexual dimorphism trend, while also accounting for differences in muscle force, seems to be related to the observed dietary differences between males and females. Overall, differences between species and sexes, and shape changes with increasing size, seem to mainly relate to differences in masticatory-muscle volume and therefore muscle force and bite force, which, in turn, relate to a wider range of potential prey (bigger prey, tougher shells). Thus, muscle force (and dietary range) would be larger in American mink than in European mink, in males than in females, and in larger individuals than in smaller ones.

A New Integrated Tool to Calculate and Map Bilateral Asymmetry on Three-Dimensional Digital Models

The observation and the quantification of asymmetry in biological structures are deeply investigated in geometric morphometrics. Patterns of asymmetry were explored in both living and fossil species. In living organisms, levels of directional and fluctuating asymmetry are informative about developmental processes and health status of the individuals. Paleontologists are primarily interested in asymmetric features introduced by the taphonomic process, as they may significantly alter the original shape of the biological remains, hampering the interpretation of morphological features which may have profound evolutionary significance. Here, we provide a new R tool that produces the numerical quantification of fluctuating and directional asymmetry and charts asymmetry directly on the specimens under study, allowing the visual inspection of the asymmetry pattern. We tested this show.asymmetry algorithm, written in the R language, on fossil and living cranial remains of the genus Homo. show.asymmetry proved successful in discriminating levels of asymmetry among sexes in Homo sapiens, to tell apart fossil from living Homo skulls, to map effectively taphonomic distortion directly on the fossil skulls, and to provide evidence that digital restoration obliterates natural asymmetry to unnaturally low levels.

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.