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

A lynx natural brain endocast from ingarano (Southern Italy; late pleistocene): Taphonomic, morphometric and phylogenetic approaches

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 to obtain information about the taxonomy and taphonomy of the specimen. Based on its characteristically felid shape, we compared several measurements of the endocast with those of the brains of living Felidae, with a special emphasis on Panthera pardus, Lynx lynx and Felis silvestris earlier reported from the same locality. The applied combination of techniques revealed that this specimen is morphometrically closest to the brains of lynxes, and so can be reported as the first natural endocranial cast of Late Pleistocene Lynx sp. In addition, CT scanning of the Ingarano endocast allowed us to reconstruct the early stages of its taphonomy (i.e., the process of infilling of the braincase with the sediment)

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

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.Evolutionary rates embody the velocity of evolution. Parcellating different velocities across the phenotype is difficult. RRmorph resolves this conundrum by charting evolutionary patterns on 3D shapes, according to their magnitude and direction

Exploration of the covariation signal between cortical bone and dentine volumes across the upper limb bones and anterior teeth in modern humans and relevance to evolutionary anthropology

Cortical bone and dentine are two mineralized tissues sharing a common embryological origin, developmental, and genetic background, distinct from those of enamel. Understanding their relationship is crucial to decipher the factors acting on their postnatal development, and shedding light on the evolutionary patterns of tissue proportions. Here, we investigate the coordinated variation between cortical bone and dentine volumes measured from arm and forearm bones (humeri, ulnae, radii) and upper anterior teeth (central incisors, lateral incisors, canines) of modern humans. Given the shared characteristics of cortical bone and dentine, we expect similarities in their postnatal development, which may lead to covariation between their volumes. The degree of bone-dentine covariation may be influenced by the physiological response of upper limb bones to mechanical loading. No such covariation is expected with enamel volumes, due to the greater developmental independence of bone and enamel. Our sample includes 55 adults of African and European ancestries from South African osteological collections. Principal component analysis of cortical thickness variation along the shafts of paired humeri, ulnae, and radii is used to assess asymmetry. Bone regions with bilateral asymmetry in cortical bone thickness are considered sensitive to functional loads, while regions with minimal bilateral variation likely reflect genetic influences during bone postnatal development. Statistical analyses reveal strong positive correlations between cortical bone and dentine volumes across all bones and teeth, and weaker correlations between cortical bone and enamel. We outline a complex pattern of bone-dentine covariation that varies by skeletal location and tooth type. Contrary to our expectations, the presumed functional sensitivity of bone regions does not influence the covariation signal. Additionally, the strength of the covariation appears to align with the developmental sequence of the anterior teeth, with the upper canines showing the strongest correlation with cortical bone volumes, followed by lateral and central incisors. These results provide insights into the functional and biological factors influencing the coordinated variation of cortical bone and dentine volumes during postnatal development. Further research on the cortical bone-dentine covariation across different skeletal parts, including lower limb elements, would enhance our understanding of the effects of both endogenous and exogenous factors on the development of the mineralized tissues

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

The Middle Pleistocene human metatarsal from Sedia del Diavolo (Rome, Italy)

The peopling of Europe during the Middle Pleistocene is a debated topic among paleoanthropologists. Some authors suggest the coexistence of multiple human lineages in this period, while others propose a single evolving lineage from Homo heidelbergensis to Homo neanderthalensis. The recent reassessment of the stratigraphy at the Sedia del Diavolo (SdD) site (Latium, Italy), now dated to the beginning of marine isotope stage (MIS) 8, calls for a revision of the human fossils from the site. In this paper, we present the morphometric, biomechanical and palaeopathological study of the second right metatarsal SdD2, to both re-evaluate its taxonomical affinities and possibly determine the levels of physical activity experienced by the individual during lifetime. Results demonstrate the persistence of archaic features in SdD2 suggesting new insights into the technology and hunting strategies adopted by Homo between MIS 9 and MIS 8