Arothron: an R package for virtual anthropology to build endocast and to perform digital reconstruction

Arothron is an R package [1] containing brand new tools for geometric morphometric analysis. The package comes with examples pertaining to the field of virtual anthropology, yet it is addressed to the entire audience of geometric morphometricians. The functions embedded in the package allow aligning disarticulated parts belonging to a single specimen (i.e. broken skull fragments), to build internal cavities such as endocasts, and to reproduce and analyse the shapes of three-dimensional objects. Arothron functions import and export landmark coordinates and 3D paths into ’landmarkAscii’ and ’am’ format files. The Digital Tool for Alignment (DTA) is a landmark-based methodology which allows aligning two or more portions of a 3D mesh (i.e. a disarticulated model, DM) by using a reference sample or model (RM) for comparison. To run DTA, a set of anatomical landmarks is defined on two separated portions of the DM. Each point of the landmark sets is moved to the nearest vertex of the triangles. This way, each landmark is identified by a number corresponding to a row of the vertex matrix of the mesh and its position is tracked on the 3D models moved in the Cartesian coordinate system.The second step is the alignment via Generalized Procrustes Analysis (GPA) of each part of the DM on each RM of the comparative sample, where the same landmark configuration as with the DM has been previously defined. The items of the reference sample are previously scaled to the mean of the single scale factors calculated for each half of the DM, separately, and symmetrized via reflection and relabelling, thereby producing a perfectly symmetrical, bilateral, and scaled landmark configurations (to avoid alignment error as introduced by asymmetry). The last step consists in the quantification of the morphological (Euclidean) distances between each part of the DM and the corresponding landmark configurations on each item in the RM set. Computer-Aided Laser Scanner Emulator (CA-LSE) and Automatic Segmentation Tool for 3D objects (AST-3D) are two new tools designed for the reconstruction of virtual cavities and external shapes [2]. CA-LSE provides the reconstruction of the external portions of a 3D mesh by simulating the action of a laser scanner. AST-3D performs the digital reconstruction of anatomical cavities as endocasts. Both tools use the definition of points of views that can be placed externally to the object (CA-LSE) or inside the object (AST-3D). By applying these tools is possible in few minutes to build virtual cavities as endocast, maxillary sinuses and trabecular bone. In the Arothron R package, we supplied three examples of reconstructing: the dental pulp cavity within a deciduous Neanderthal tooth, the network of blood vessels within a human malleus bone, and an endocast of a human skull.The tools could be used in virtual anthropology application.The digital alignment tool is efficient in find ideal alignments of broken pieces. It could be applied as the first step in virtual reconstruction on human fossil specimens that often consist of a disarticulated fragments such as BOU-VP12/130 (Australopithecus garhi), AL-442 (Australopithecus afarensis), OH5 (Paranthropus boisei), ATD6-15 and ATD6-69 (Homo antecessor), Amud 1 (Homo neanderthalensis), Le Moustier 1 (Homo neanderthalensis). The easily and quickly use of the Arothron R package to build virtual cavities may provide a new means largely applicable in virtual Anthropology. References:[1] Profico A., Veneziano A., Melchionna M., Piras P. & Raia P., 2018. Arothron: Geometric Morphometrics Analyses. R package version 1.0.1, developer version available at https://github/Arothron DOI:10.5281/zenodo.1218712.[2] Profico A., Schlager S., Valoriani V., Buzi C., Melchionna M., Veneziano A., Raia P., MoggifiCecchi J. & Manzi G., 2018. Reproducing the internal and external anatomy of fossil bones: Two new automatic digital tools. American Journal of Physical Anthropology

Morphometric maps of bilateral asymmetry in the human humerus: An implementation in the R package morphomap

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

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

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

In situ observations on the dentition and oral cavity of the Neanderthal skeleton from Altamura (Italy)

The Neanderthal specimen from Lamalunga Cave, near Altamura (Apulia, Italy), was discovered during a speleological survey in 1993. The specimen is one of the most complete fossil hominins in Europe and its state of preservation is exceptional, although it is stuck in calcareous concretions and the bones are mostly covered by calcite depositions. Nevertheless, it is possible to carry out some observations on craniodental features that have not previously been described. In this work, we present an account of the oral cavity, made possible by the use of a videoscope, which allowed us to reach some hidden parts of the mandible and palate. This is the first detailed overview of the teeth and maxillary bones of the Neanderthal skeleton from Altamura. The dentition is almost complete. However, two teeth (upper right P3 and upper left M1) were lost ante mortem and four teeth (lower right I1 and P3 and lower left I1 and I2) were lost most probably post mortem. Dental wear is marked. The erupted M3s and the inversion of the compensating curve of Wilson in the M1s and M2s but not in the M3s suggest that the individual is fully adult, but not old. Although most of the teeth have their roots exposed for several millimeters, the periodontal bone appears to be in good condition overall, except in correspondence of the two ante-mortem tooth losses. X-rays of the anterior teeth show a periapical lesion, probably linked to the advanced dental wear. We also observed a weak expression of taurodontism in the posterior dentition and the presence of a retromolar space, features consistent with an attribution to the Neanderthal hypodigm; this attribution is also supported by aspects of the cranial morphology, the morphometric analysis of the scapula and preliminary mtDNA data. There is also a well-developed palatine torus, to the best of our knowledge a feature not previously described in Neanderthals

Fluctuating Asymmetry and Stress in Macaca fuscata: Does Captivity Affect Morphology?

Fluctuating Asymmetry (FA) in morphology is used as a proxy for developmental instability in response to stress factors. FA has important implications for understanding the impact of differential environments and stressors on the skeletal phenotype. Here, we explore FA in the mandibular morphology of wild and captive Macaca fuscata to detect differences induced by the captive environment. We use two different approaches in Geometric Morphometrics to characterise the degree and patterns of FA and Directional Asymmetry (DA) based on 3D mandibular landmarks. Our results show that the wild and captive groups exhibit morphological dissimilarities in the symmetric component of shape while no significant degree of asymmetry (fluctuating or directional) was detected. Based on our results and on previous literature on the subject, we suggest that (I) captivity is likely to affect the mandibular morphology of M. fuscata; (II) FA may not be a suitable indicator to detect stress in the conditions analysed; and that (III) the mandible may not be the ideal region to study asymmetry because of its functional nature

Decoupling Functional and Morphological Convergence, the Study Case of Fossorial Mammalia

Morphological similarity between biological structures in phylogenetically distant species is usually regarded as evidence of convergent evolution. Yet, phenotypic similarity is not always a sign of natural selection acting on a particular trait, therefore adaptation to similar conditions may fail to generate convergent lineages. Herein we tested whether convergent evolution occurred in the humerus of fossorial mammals, one of the most derived biological structures among mammals. Clades adapting to digging kinematics possess unusual, by mammalian standards, humeral shapes. The application of a new, computationally fast morphological test revealed a single significant instance of convergence pertaining to the Japanese fossorial moles (Mogera) and the North-American fossorial moles (Scalopini). Yet, the pattern only manifests when trade-off performance data (derived from finite element analysis) are added to shape data. This result indicates that fossorial mammals have found multiple solutions to the same adaptive challenge, independently moving around multiple adaptive peaks. This study suggests the importance of accounting for functional trade-off measures when studying morpho-functional convergence. We revealed that fossorial mammals, a classic example of convergent evolution, evolved multiple strategies to exploit the subterranean ecotope, characterized by different functional trade-offs rather than converging toward a single adaptive optimum

A method for mapping morphological convergence on three-dimensional digital models: the case of the mammalian sabre-tooth

Morphological convergence can be assessed using a variety of statistical methods. None of the methods proposed to date enable the visualization of convergence. All are based on the assumption that the phenotypes either converge, or do not. However, between species, morphologically similar regions of a larger structure may behave differently. Previous approaches do not identify these regions within the larger structures or quantify the degree to which they may contribute to overall convergence. Here, we introduce a new method to chart patterns of convergence on three-dimensional models using the R function conv.map. The convergence between pairs of models is mapped onto them to visualize and quantify the morphological convergence. We applied conv.map to a well-known case study, the sabre-tooth morphotype, which has evolved independently among distinct mammalian clades from placentals to metatherians. Although previous authors have concluded that sabre-tooths kill using a stabbing ‘bite’ to the neck, others have presented different interpretations for specific taxa, including the iconic Smilodon and Thylacosmilus. Our objective was to identify any shared morphological features among the sabre-tooths that may underpin similar killing behaviours. From a sample of 49 placental and metatherian carnivores, we found stronger convergence among sabre-tooths than for any other taxa. The morphological convergence is most apparent in the rostral and posterior parts of the cranium. The extent of this convergence suggests similarity in function among these phylogenetically distant species. In our view, this function is most likely to be the killing of relatively large prey using a stabbing bite. © 2021 The Authors. Palaeontology published by John Wiley & Sons Ltd on behalf of The Palaeontological Association

Multi-proxy analysis suggests Late Pleistocene affinities of human skeletal remains attributed to Balzi Rossi

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

Transplantation of clinical-grade human neural stem cells reduces neuroinflammation, prolongs survival and delays disease progression in the SOD1 rats.

Abstract Stem cells are emerging as a therapeutic option for incurable diseases, such as Amyotrophic Lateral Sclerosis (ALS). However, critical issues are related to their origin as well as to the need to deepen our knowledge of the therapeutic actions exerted by these cells. Here, we investigate the therapeutic potential of clinical-grade human neural stem cells (hNSCs) that have been successfully used in a recently concluded phase I clinical trial for ALS patients (NCT01640067). The hNSCs were transplanted bilaterally into the anterior horns of the lumbar spinal cord (four grafts each, segments L3–L4) of superoxide dismutase 1 G93A transgenic rats (SOD1 rats) at the symptomatic stage. Controls included untreated SOD1 rats (CTRL) and those treated with HBSS (HBSS). Motor symptoms and histological hallmarks of the disease were evaluated at three progressive time points: 15 and 40 days after transplant (DAT), and end stage. Animals were treated by transient immunosuppression (for 15 days, starting at time of transplantation). Under these conditions, hNSCs integrated extensively within the cord, differentiated into neural phenotypes and migrated rostro-caudally, up to 3.77 ± 0.63 cm from the injection site. The transplanted cells delayed decreases in body weight and deterioration of motor performance in the SOD1 rats. At 40DAT, the anterior horns at L3–L4 revealed a higher density of motoneurons and fewer activated astroglial and microglial cells. Accordingly, the overall survival of transplanted rats was significantly enhanced with no rejection of hNSCs observed. We demonstrated that the beneficial effects observed after stem cell transplantation arises from multiple events that counteract several aspects of the disease, a crucial feature for multifactorial diseases, such as ALS. The combination of therapeutic approaches that target different pathogenic mechanisms of the disorder, including pharmacology, molecular therapy and cell transplantation, will increase the chances of a clinically successful therapy for ALS

A method for mapping morphological convergence on three-dimensional digital models: the case of the mammalian sabre-tooth

Morphological convergence can be assessed using a variety of statistical methods. None of the methods proposed to date enable the visualization of convergence. All are based on the assumption that the phenotypes either converge, or do not. However, between species, morphologically similar regions of a larger structure may behave differently. Previous approaches do not identify these regions within the larger structures or quantify the degree to which they may contribute to overall convergence. Here, we introduce a new method to chart patterns of convergence on three-dimensional models using the R function conv.map. The convergence between pairs of models is mapped onto them to visualize and quantify the morphological convergence. We applied conv.map to a well-known case study, the sabre-tooth morphotype, which has evolved independently among distinct mammalian clades from placentals to metatherians. Although previous authors have concluded that sabre-tooths kill using a stabbing ‘bite’ to the neck, others have presented different interpretations for specific taxa, including the iconic Smilodon and Thylacosmilus. Our objective was to identify any shared morphological features among the sabre-tooths that may underpin similar killing behaviours. From a sample of 49 placental and metatherian carnivores, we found stronger convergence among sabre-tooths than for any other taxa. The morphological convergence is most apparent in the rostral and posterior parts of the cranium. The extent of this convergence suggests similarity in function among these phylogenetically distant species. In our view, this function is most likely to be the killing of relatively large prey using a stabbing bite