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Sedia del Diavolo is an archaeological site located in the low valley of the Aniene river (Rome, Latium) that, despite being known since the end of the 19th century, has been thoroughly investigated since the 1930’s. The site yielded a lithic assemblage referrable to the Middle Palaeolithic as well as numerous fossil remains, including two human specimens: a fragment of a femoral diaphysis (SdD1) and a complete second metatarsal (SdD2). Initially the site was dated to the end of the Middle Pleistocene and, coherently with the intended chronology, the first anthropological analysis attributed the remains to Homo neanderthalensis. Recently, a reappraisal of the geochronology of the sites of the low valley of the Aniene river redated Sedia del Diavolo to MIS 7, between 295-290 ka, making the site one of the oldest occurrences of the Levallois technology ever found in Europe. This contribution presents new advanced morphological analyses of SdD2, which shows signs of a probable stress fracture on the distal portion of the diaphysis. We obtained high resolution images of SdD2 by means of laboratory-based X-ray computed micrortomography at the FAITH station of the Elettra synchrotron in Trieste (Italy). We used cross-sectional geometry to investigate the robustness of the diaphysis and geometric morphometric approach to analyse the shape of the epiphyses. Results were compared to a series of modern human and fossil hominin second metatarsals. SdD2 is characterized by thicker cortical bone than H. sapiens and H. neanderthalensis. This suggests that the individual likely experienced high levels of mechanical loading and mobility. Moreover, the distribution of the bone around the longitudinal axis as well as the morphology of the proximal epiphysis make it more similar to H. sapiens than to H. neanderthalensis. Although results may be influenced by the presence of the stress fracture, the analyses suggest that the metatarsal belonged to an individual whose morphology was less derived than the more recent Neandertal comparative specimens.

OBJECTIVES: The statistical analysis of fossil remains is essential to understand the evolution of the genus Homo. Unfortunately, the human fossil record is straight away scarce and plagued with severe loss of information caused by taphonomic processes. The recently developed field of Virtual Anthropology helps to ameliorate this situation by using digital techniques to restore damaged and incomplete fossils. MATERIALS AND METHODS: We present the package Arothron, an R software suite meant to process and analyze digital models of skeletal elements. Arothron includes tools to digitally extract virtual cavities such as cranial endocasts, to statistically align disarticulated or broken bony elements, and to visualize local variations between surface meshes and landmark configurations. RESULTS: We describe the main functionalities of Arothron and illustrate their usage through reproducible case studies. We describe a tool for segmentation of skeletal cavities by showing its application on a malleus bone, a Neanderthal tooth, and a modern human cranium, reproducing their shape and calculating their volume. We illustrate how to digitally align a disarticulated model of a modern human cranium, and how to combine piecemeal shape information on individual specimens into one. In addition, we present useful visualization tools by comparing the morphological differences between the right hemisphere of the Neanderthal and the modern human brain. CONCLUSIONS: The Arothron R package is designed to study digital models of fossil specimens. By using Arothron, scientists can handle digital models with ease, investigate the inner morphology of 3D skeletal models, gain a full representation of the original shapes of damaged specimens, and compare shapes across specimens.

Paper1 - morphomap - AJPA - Peer-reviewed article and supplementary data

Paper3 - Humerus asymmetry - SYMMETRY- Peer-reviewed article and supplementary data

Aging of the head and especially the face has been studied intensively, yet questions remain about the timing and rates of aging throughout adulthood and about the extent to which aging differs between men and women. Here we address these issues by developing statistical models of craniofacial aging to describe and compare aging through the life course in both sexes. We selected cranial surface meshes from 254 females and 252 males, aged from 20 to 90 years from the Headspace project, Liverpool, UK. Sixteen anatomical landmarks and 59 semilandmarks on curves and surfaces were used to parameterize these. Modes and degrees of aging throughout adulthood were assessed and compared among sexes using Procrustes-based geometric morphometric methods. Regression analyses of form through the whole age range indicate that age accounts for a small proportion of total variance in both sexes, but form is significantly related to age and males and females age in significantly different ways. Further analyses indicate that aging differs in character, timing, and rates in both sexes between early and later phases of adulthood. Sexual differences in aging are evident in the early and later phases of adulthood. The study adds to knowledge of the aging of adult craniofacial form and sexual dimorphism. It is based on a local population and so the findings are directly applicable to that population. Further studies are needed to assess generalizability and provide better data on population differences to facilitate clinical assessment and treatment planning.

Background: The range of normal variation of growth and development of the craniofacial region is of direct clinical interest but incompletely understood. Here we develop a statistical model of craniofacial growth and development to compare craniofacial ontogeny between age groups and sexes and pilot an approach to modeling that is relatively straightforward to apply in the context of clinical research and assessment. Methods: The sample comprises head surface meshes captured using a 3dMD five-camera system from 65 males and 47 females (range 3–20 years) from the Headspace project, Liverpool, UK. The surface meshes were parameterized using 16 anatomical landmarks and 59 semilandmarks on curves and surfaces. Modes and degrees of growth and development were assessed and compared among ages and sexes using Procrustes based geometric morphometric methods. Results: Regression analyses indicate that 3–10 year olds undergo greater changes than 11–20 year olds and that craniofacial growth and development differs between these age groups. The analyses indicate that males extend growth allometrically into larger size ranges, contributing substantially to adult dimorphism. Comparisons of ontogenetic trajectories between sexes find no significant differences, yet when hypermorphosis is accounted for in the older age group there is a significant residual sexual dimorphism. Conclusions: The study adds to knowledge of how adult craniofacial form and sexual dimorphism develop. It was carried out using readily available software which facilitates replication of this work in diverse populations to underpin clinical assessment of deformity and the outcomes of corrective interventions.

Wrist shape varies greatly across primates and previous studies indicate that the numerous morphological differences among them are related to a complex mixture of phylogeny and function. However, little is known about whether the variation in these various anatomical differences is linked and to what extent the wrist bones vary independently. Here, we used 3D geometric morphometrics on a sample of extant hominids (Homo sapiens, Pan troglodytes, Gorilla gorilla, and Gorilla beringei), to find the model that best describes the covariation patterns among four of the eight carpals (i.e., capitate, lunate, scaphoid, and trapezium). For this purpose, 15 modular hypotheses were tested using the Covariation Coefficient. Results indicate that there is a covariation structure common to all hominids, which corresponds to stronger covariation within each carpal as compared to the covariation between carpals. However, the results also indicate that that there is a degree of codependence in the variation of some carpals, which is unique in humans, chimpanzees, and gorillas, respectively. In humans there is evidence of associated shape changes between the lunate and capitate, and between the scaphoid and trapezium. This covariation between lunate and capitate is also apparent in gorillas, while chimpanzees display the greatest disassociation among carpals, showing low covariation values in all pairwise comparisons. Our analyses indicate that carpals have an important level of variational independence which might suggest a high degree of independent evolvability in the wrists of hominids, and that although weak, the structure of associated changes of these four carpals varies across genera. To our knowledge this is the first report on the patterns of modularity between these four wrist bones in the Homininae and future studies might attempt to investigate whether the anatomical shape associations among carpals are functionally related to locomotion and manipulation.

The geometric morphometric (GM) analysis of complex anatomical structures is an ever more powerful tool to study biological variability, adaptation and evolution. Here, we propose a new method (combinland), developed in R, meant to combine the morphological information contained in different landmark coordinate sets into a single dataset, under a GM context. combinland builds a common ordination space taking into account the entire shape information encoded in the starting configurations. We applied combinland to a Primate case study including 133 skulls belonging to 14 species. On each specimen, we simulated photo acquisitions converting the 3D landmark sets into six 2D configurations along standard anatomical views. The application of combinland shows statistically negligible differences in the ordination space compared to that of the original 3D objects, in contrast to a previous method meant to address the same issue. Hence, we argue combinland allows to correctly retrieve 3D-quality statistical information from 2D landmark configurations. This makes combinland a viable alternative when the extraction of 3D models is not possible, recommended, or too expensive, and to make full use of disparate sources (and views) of morphological information regarding the same specimens. The code and examples for the application of combinland are available in the Arothron R package. © 2018 Associazione Teriologica Italiana.

A natural brain endocast from the Late Pleistocene site of Ingarano (Apulia, Southern Italy) has been investigated in detail using CT scanning, image processing techniques and Geometric Morphometrics. Our analyses provide relevant information about the taxonomy and taphonomy of the specimen. The external morphology of the endocast was compared to those of the brains of living felids. This combination of techniques is commonly used in palaeoneurology for neuroanatomical and behavioural inferences and enables us to classify the fossil as the first reported natural brain endocast of a Late Pleistocene lynx. In addition, the investigation structure of the internal strctures of the natural endocast aloud us to reconstruct its taphonomic history. Download the complete issue.

Kolponomos newportensis is an enigmatic Miocene mammal allied to stem Pinnipedimorpha. It has been suggested that Kolponomos fed on hard-shelled benthic marine invertebrates by using its mandible as a wedge to dislodge its prey from the sea bottom by means of strong pull and torque forces. This unique feeding style was thought to originate from a singular case of mosaic convergence in mandible biomechanics between Kolponomos and the sabretoothed cat Smilodon, which complied with similarly strong torque forces when grappling with prey. As such forces must have reflected on the cranium as well, we hypothesize that the convergence between Kolponomos and the sabretoothed cats could have affected its shape. To test this hypothesis, we looked for patterns of morphological convergence in cranial shape between Kolponomos and sabretoothed cats. We found that Kolponomos is not distinctly closer to Smilodon than a number of other pinnipeds. Yet, local areas of shape convergence with Smilodon are observed in the canine area and the posterior part of the cranium, that is where the bite applies and the temporalis muscle is located, respectively. These results indicate that the mosaic convergence present between the mandibles of Kolponomos and Smilodon is partially reflected in the cranium as well.

There is controversy around the mechanisms that guided the change in brain shape during the evolution of modern humans. It has long been held that different cortical areas evolved independently from each other to develop their unique functional specializations. However, some recent studies suggest that high integration between different cortical areas could facilitate the emergence of equally extreme, highly specialized brain functions. Here, we analyse the evolution of brain shape in primates using three-dimensional geometric morphometrics of endocasts. We aim to determine, firstly, whether modern humans present unique developmental patterns of covariation between brain cortical areas; and secondly, whether hominins experienced unusually high rates of evolution in brain covariation as compared to other primates. On the basis of analyses including modern humans and other extant great apes at different developmental stages, we first demonstrate that, unlike our closest living relatives, Homo sapiens retain high levels of covariation between cortical areas into adulthood. Among the other great apes, high levels of covariation are only found in immature individuals. Secondly, at the macro-evolutionary level, our analysis of 400 endocasts, representing 148 extant primate species and 6 fossil hominins, shows that strong covariation between different areas of the brain in H. sapiens and Homo neanderthalensis evolved under distinctly higher evolutionary rates than in any other primate, suggesting that natural selection favoured a greatly integrated brain in both species. These results hold when extinct species are excluded and allometric effects are accounted for. Our findings demonstrate that high covariation in the brain may have played a critical role in the evolution of unique cognitive capacities and complex behaviours in both modern humans and Neanderthals.

Morphological convergence is an intensely studied macroevolutionary phenomenon. It refers to the morphological resemblance between phylogenetically distant taxa. Currently available methods to explore evolutionary convergence either: rely on the analysis of the phenotypic resemblance between sister clades as compared to their ancestor, fit different evolutionary regimes to different parts of the tree to see whether the same regime explains phenotypic evolution in phylogenetically distant clades, or assess deviations from the congruence between phylogenetic and phenotypic distances. We introduce a new test for morphological convergence working directly with non-ultrametric (i.e. paleontological) as well as ultrametric phylogenies and multivariate data. The method (developed as the function search.conv within the R package RRphylo) tests whether unrelated clades are morphologically more similar to each other than expected by their phylogenetic distance. It additionally permits using known phenotypes as the most recent common ancestors of clades, taking full advantage of fossil information. We assessed the power of search.conv and the incidence of false positives by means of simulations, and then applied it to three well-known and long-discussed cases of (purported) morphological convergence: the evolution of grazing adaptation in the mandible of ungulates with high-crowned molars, the evolution of mandibular shape in sabertooth cats, and the evolution of discrete ecomorphs among anoles of Caribbean islands. The search.conv method was found to be powerful, correctly identifying simulated cases of convergent morphological evolution in 95% of the cases. Type I error rate is as low as 4–6%. We found search.conv is some three orders of magnitude faster than a competing method for testing convergence.

In biological anthropology, parameters relating to cross-sectional geometry are calculated in paired long bones to evaluate the degree of lateralization of anatomy and, by inference, function. Here, we describe a novel approach, newly added to the morphomap R package, to assess the lateralization of the distribution of cortical bone along the entire diaphysis. The sample comprises paired long bones belonging to 51 individuals (10 females and 41 males) from The New Mexico Decedent Image Database with known biological profile, occupational and loading histories. Both males and females show a pattern of right lateralization. In addition, males are more lateralized than females, whereas there is not a significant association between lateralization with occupation and loading history. Body weight, height and long-bone length are the major factors driving the emergence of asymmetry in the humerus, while interestingly, the degree of lateralization decreases in the oldest individuals.

In two publications from 1967 and 1971, M. Masali described human skeletal remains presumed to have been found in the Balzi Rossi caves (Ventimiglia, Italy), based on a signed note dated to 1908. Since then, the remains - dubbed "Conio's Finds" and preserved at the University of Torino - had not been further studied. We performed a multidisciplinary investigation aimed at clarifying the geographical and chronological attribution of these specimens. Collagen extraction for AMS dating was unsuccessful, but we obtained two direct dates on the best- preserved crania via 231Pa/235U direct gamma-ray spectrometry (10,500±2,000 years BP and 12,500±2,500 years BP). We analyzed the metrics and morphology of the crania and femora by comparing them with samples belonging to the Upper Paleolithic, Mesolithic, and Neolithic periods, and evidenced that the "Conio's Finds" are morphologically more compatible with a Late Pleistocene rather than Holocene attribution. We analyzed the literature regarding the history of excavations at Balzi Rossi, and we propose that - if any credence should be given to the note accompanying the material - the remains may have been found in front of Grotta dei Fanciulli or Grotta del Caviglione, in the redeposited soil dug up during the installation of lime kilns carried out between the late 18th and the early 19th centuries. These hypotheses may be tested in the future by comparing the speleothem deposited on one of the crania and the remaining deposit at the site.

Summary At least six different Homo species populated the World during the latest Pliocene to the Pleistocene. The extinction of all but one of them is currently shrouded in mystery, and no consistent explanation has yet been advanced, despite the enormous importance of the matter. Here, we use a recently implemented past climate emulator and an extensive fossil database spanning 2,754 archaeological records to model climatic niche evolution in Homo. We find statistically robust evidence that the three Homo species representing terminating, independent lineages, H. erectus, H. heidelbergensis, and H. neanderthalensis, lost a significant portion of their climatic niche space just before extinction, with no corresponding reduction in physical range. This reduction coincides with increased vulnerability to climate change. In the case of Neanderthals, the increased extinction risk was probably exacerbated by competition with H. sapiens. This study suggests that climate change was the primary factor in the extinction of Homo species.

Objectives This study describes and demonstrates the functionalities and application of a new R package, morphomap, designed to extract shape information as semilandmarks in multiple sections, build cortical thickness maps, and calculate biomechanical parameters on long bones. Methods morphomap creates, from a single input (an oriented 3D mesh representing the long bone surface), multiple evenly spaced virtual sections. morphomap then directly and rapidly computes morphometric and biomechanical parameters on each of these sections. The R package comprises three modules: (a) to place semilandmarks on the inner and outer outlines of each section, (b) to extract cortical thicknesses for 2D and 3D morphometric mapping, and (c) to compute cross-sectional geometry. Results In this article, we apply morphomap to femora from Homo sapiens and Pan troglodytes to demonstrate its utility and show its typical outputs. morphomap greatly facilitates rapid analysis and functional interpretation of long bone form and should prove a valuable addition to the osteoarcheological analysis software toolkit. Conclusions Long bone loading history is commonly retrodicted by calculating biomechanical parameters such as area moments of inertia, analyzing external shape and measuring cortical thickness. morphomap is a software written in the open source R environment, it integrates the main methodological approaches (geometric morphometrics, cortical morphometric maps, and cross-sectional geometry) used to parametrize long bones.

OBJECTIVES: We present two new automatic tools, developed under the R environment, to reproduce the internal and external structures of bony elements. The first method, Computer-Aided Laser Scanner Emulator (CA-LSE), provides the reconstruction of the external portions of a 3D mesh by simulating the action of a laser scanner. The second method, Automatic Segmentation Tool for 3D objects (AST-3D), performs the digital reconstruction of anatomical cavities. MATERIALS AND METHODS: We present the application of CA-LSE and AST-3D methods to different anatomical remains, highly variable in terms of shape, size and structure: a modern human skull, a malleus bone, and a Neanderthal deciduous tooth. Both methods are developed in the R environment and embedded in the packages "Arothron" and "Morpho," where both the codes and the data are fully available. RESULTS: The application of CA-LSE and AST-3D allows the isolation and manipulation of the internal and external components of the 3D virtual representation of complex bony elements. In particular, we present the output of the four case studies: a complete modern human endocast and the right maxillary sinus, the dental pulp of the Neanderthal tooth and the inner network of blood vessels of the malleus. DISCUSSION: Both methods demonstrated to be much faster, cheaper, and more accurate than other conventional approaches. The tools we presented are available as add-ons in existing software within the R platform. Because of ease of application, and unrestrained availability of the methods proposed, these tools can be widely used by paleoanthropologists, paleontologists and anatomists.

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.

The enigmatic Early Miocene fossorial mammal Mesoscalops montanensis shows one of the most modified humeri among terrestrial mammals. It has been suggested, on qualitative considerations, that this species has no extant homologues for humerus kinematics and that, functionally, the closest extant group is represented by Chrysochloridae. We combine here three dimensional geometric morphometrics, finite element analysis and phylogenetic comparative methods to explore the shape and mechanical stress states of Mesoscalops montanensis as well as of extant and extinct Talpidae and Chrysochloridae under realistic digging simulations. Evolutionary convergence analyses reveal that the shape of Mesoscalops montanensis represents a unique morphology in the context of fossorial mammals and that its functional performance, albeit superficially similar to that of extant Chrysochloridae, still represents a nonconvergent optimum for adaptation to digging. J. Morphol. 276:1157-1171, 2015. (c) 2015 Wiley Periodicals, Inc.