1,354,312 research outputs found
Old and new methods in geometric morphometrics applied to the study of human evolution: case studies
No full textThe main aim of this thesis is the application of Geometric Morphometric methods on different case-studies for the study of human evolution. When combined with techniques of acquisition of 3D models, Geometric Morphometrics allows us: - to investigate different experimental designs;
- to analyse the interaction of several aspects on morphological adaptations detected within taxon-specific studies (e.g., allometry, phylogenetic signal, functional factors);
- to study fragmentary fossils and incomplete specimens, through estimation of missing data and 3D virtual restoration (e.g., surface and curve slid semilandmark);
- to plan, code and test new algorithms and/or methodological approaches.
The first part deals with the use of smoothing filters applied to 3D model for Geometric Morphometric studies. These algorithms are used to remove the background noise deriving from digital acquisition (e.g., photogrammetry, laser scan and computerized tomography scan). The effects of the different smoothing filters have been assessed. In particular have been defined guidelines for a correct use of these algorithms, besides the developing of an automatized tool, in R environment, to find the best combination between algorithm type, settings and number of iterations.
The second part consists of a protocol developed, with the collaboration of the University of Freiburg, for the digital retrodeformation of fossil specimens showing evidence of shearing, bending and compressing alterations due to taphonomic processes. Traditional methods of retrodeformation only use a sparse set of bilateral landmarks; the number of points appears to affects the success of retrodeformation. On the contrary, this method uses, in addition to the landmark configurations, the curve and surface semilandmarks, which allow us to capture
morphological information more accurately. This protocol was applied here to the neanderthalian cranium of Saccopastore 1.
The third part reports the results of the first analysis on the specimen nicknamed "Pàus” (St.n.166623), recently discovered near Spinadesco in the Po Valley (Northern Italy). A set of 100 semilandmarks was built on the specimen and slid, using a set of 6 landmark, on a comparative sample including specimens dated to the Middle-to-Late Pleistocene. The results show how the morphology of “Pàus” is consistent with the variability observed in the Neanderthal lineage.
The fourth part concerns a Geometric Morphometric investigation performed on two human cranial fossil remains from Melka Kunture, dated to about 850 ka. The two cranial fragments consist in a partial left parietal (MK73/GOM II- 6769; formally Melka Kunture 1, or MK1) and a right portion of the frontal bone (MK76/GOM II - 576, or MK2). Specifically, evenly-spaced semilandmark sets were used acquired along the sagittal suture and the inferior temporal line on MK1 and MK2 respectively. The results of the analyses, in agreement with the chronology of the fossils, represent at present, evidence of one of the best candidates to be the most ancient example of H. heidelbergensis.
The fifth part treats with the external morphology of the cranial base in extant and living Hominoids in relation to ontogenetic, allometric, locomotor and phylogenetic factors. The sample selected consists of 3D landmark configurations acquired on specimens (male and female) including infant, sub-adult and adult individuals. The centroid size of the landmark set configuration was used as indicator of size while the pattern of dental eruption (at death) was used to define six age groups. The relation between morphology and locomotion was explored through the estimation of the position of the foramen magnum along the Frankfurt plane.
Finally, a phylogenetic tree was build using molecular and paleontological data, with the phylogenetic signal investigated through centroid size and shape
Arothron: an R package for virtual anthropology to build endocast and to perform digital reconstruction
No full textArothron 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
Three-dimensional visualisation of skeletal cavities
No full textBones contain spaces within them. The extraction and the analysis of those cavities are crucial in the study of bone tissue function and can inform about pathologies or past traumatic events. The use of medical imaging techniques allows a non-invasive visualisation of skeletal cavities opening a new frontier in medical inspection and diagnosis. Here, we report the application of a new mesh-based approach for the isolation of skeletal cavities of different size and geometrical structure. We apply a mesh-based approach to extract (i) the main virtual cavities inside the human skull, (ii) a complete human endocast, (iii) the inner vas-culature of the malleus bone and (iv) the medullary of a human femur. The detailed description of the mesh-based isolation method and its pioneristic application to four different case-studies show the potential of this approach in medical visualisation
From Smart Apes to Human Brain Boxes. A Uniquely Derived Brain Shape in Late Hominins Clade
No full textModern humans have larger and more globular brains when compared to other primates. Such anatomical features are further reflected in the possession of a moderately asymmetrical brain with the two hemispheres apparently rotated counterclockwise and slid anteroposteriorly on one another, in what is traditionally described as the Yakovlevian torque. Developmental disturbance in human brain asymmetry, or lack thereof, has been linked to several cognitive disorders including schizophrenia and depression. More importantly, the presence of the Yakovlevian torque is often advocated as the exterior manifestation of our unparalleled cognitive abilities. Consequently, studies of brain size and asymmetry in our own lineage indirectly address the question of what, and when, made us humans, trying to trace the emergence of brain asymmetry and expansion of cortical areas back in our Homo antecedents. Here, we tackle this same issue by studying the evolution of human brain size, shape, and asymmetry on a phylogenetic tree including 19 apes and Homo species, inclusive of our fellow ancestors. We found that a significant positive shift in the rate of brain shape evolution pertains to the clade including modern humans, Neanderthals, and Homo heidelbergensis. Although the Yakovlevian torque is well evident in these species and levels of brain asymmetry are correlated to changes in brain shape, further early Homo species possess the torque. Even though a strong allometric component is present in hominoid brain shape variability, this component seems unrelated to asymmetry and to the rate shift we recorded. These results suggest that changes in brain size and asymmetry were not the sole factors behind the fast evolution of brain shape in the most recent Homo species. The emergence of handedness and early manifestations of cultural modernity in the archeological record nicely coincide with the same three species sharing the largest and most rapidly evolving brains among all hominoids. © Copyright © 2020 Melchionna, Profico, Castiglione, Sansalone, Serio, Mondanaro, Di Febbraro, Rook, Pandolfi, Di Vincenzo, Manzi and Raia
) from central Texas with comparison to other early American and modern crania
No full textObjectives: Craniofacial morphology (CFM) is often used to address questions about the biological affinities of the earliest Americans, or Paleoindians, but resolution is complicated in part by a lack of well-preserved crania. The Wilson-Leonard 2 (WL-2) Paleoindian skull from Texas has never been fully analyzed because it is crushed and cannot be physically reconstructed. This study employs a digital restoration for comprehensive assessment and analysis of WL-2.Materials and methods: High-resolution CT data and geometric morphometrics are used to restore the WL-2 skull and analyze its morphology using 65 craniometric measurements acquired on the restoration. These data allow for a full morphological description and multivariate (Mahalanobis Distance and Principal Component) comparisons to other Paleoindians and recent populations.Results: WL-2 has a long, narrow braincase, and a short, modestly prognathic face. Compared with other Paleoindians, she is individually similar to several skulls from Brazil, but aligns most closely with pooled samples from the US and Mexico. WL-2 is most similar to recent populations from Europe, Asia, and the Americas, and markedly different to those from Africa and Australia.Discussion: The overall morphology of WL-2 and her association with Asians and Europeans align well with trends identified in other CFM analyses. Her affinity to recent Amerindians contrasts with the findings of many previous CFM studies, but is seemingly consistent with molecular analyses suggesting a close relationship between some Paleoindians and modern American Indians. This study demonstrates the potential for using digital anthropological methods to study other Paleoindian crania whose data value is limited by physical destruction and/or deformation
Endomaker, a new algorithm for fully automatic extraction of cranial endocasts and the calculation of their volumes
No full textObjectives: Reproducing cranial endocasts is a major goal of researchers interested in vertebrate brain evolution. We present a new R software, named endomaker, which allows the automatic extraction of endocasts from skull meshes along with the calculation of its volume. Materials and methods: We applied endomaker on non-primate and primate skulls including the Australopithecus africanus specimen Sts-5. Results: We proved endomaker is faster, more feature-rich and possibly more accurate than competing software. Discussion: Endomaker is the only available program endowed with the possibility to process an entire mesh directory straight away, promising to expand the scope and phylogenetic breadth of comparative studies of brain evolution
A new integrated tool to calculate and map bilateral asymmetry on three-dimensional digital models
No full textThe 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. © 2021 by the authors. Licensee MDPI, Basel, Switzerland
A geometric morphometric approach to the study of sexual dimorphism in the modern human frontal bone
No full textObjectives: We analyzed the main anatomical traits found in the human frontal bone by using a geometric morphometric approach. The objectives of this study are to explore how the frontal bone morphology varies between the sexes and to detect which part of the frontal bone are sexually dimorphic. Materials and methods: The sample is composed of 161 skulls of European and North American individuals of known sex. For each cranium, we collected 3D landmarks and semilandmarks on the frontal bone, to examine the entire morphology and separate modules (frontal squama, supraorbital ridges, glabellar region, temporal lines, and mid-sagittal profile). We used Procrustes ANOVAs and LDAs (linear discriminant analyses) to evaluate the relation between frontal bone morphology and sexual dimorphism and to calculate precision and accuracy in the classification of sex. Results: All the frontal bone traits are influenced by sexual dimorphism, though each in a different manner. Variation in shape and size differs between the sexes, and this study confirmed that the supraorbital ridges and glabella are the most important regions for sex determination, although there is no covariation between them. The variable size does not contribute significantly to the discrimination between sexes. Thanks to a geometric morphometric analysis, it was found that the size variable is not an important element for the determination of sex in the frontal bone. Conclusion: The usage of geometric morphometrics in analyzing the frontal bone has led to new knowledge on the morphological variations due to sexual dimorphism. The proposed protocol permits to quantify morphological covariation between modules, to calculate the shape variations related to sexual dimorphism including or omitting the variable size
morphomap: An R package for long bone landmarking, cortical thickness, and cross-sectional geometry mapping
No full textObjectives: 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
Cranial base variations in extant Hominoidea and fossil Hominins
No full textIn this communication, we present the results of a 3D geometric morphometric analysis of the cranial base variations in living and fossil Hominoidea. A number of studies on cranial base morphology have dealt with basicranial flexion, mainly in relationship with cranio/facial size and shape (Bastir et al., 2010; Bastir et al., 2011; Lieberman, 2011). By contrast, our aim is to test to what extent basicranial morphology is related to functional and/or ontogenetic patterns. Particularly, we are interested in the evaluation of factors that may have influenced the cranial base morphology in Plio-Pleistocene Hominins. We used a configuration of 18 landmarks distributed on the cranial base on a sample of 128 specimens (infants, juveniles, and adults) of Homo, Australopithecus, Paranthropus, Pan, Gorilla, and Pongo; the age at death of the specimens was determined by patterns of molar eruption. The landmark set has been transformed into shape coordinates by generalized Procrustes analysis and the variance-covariance matrix was explored through principal component analysis (PCA). Shape predictions were performed by regression of the PC scores on the centroid size in order to display the respective pattern of growth within the different OTUs. The results discriminates two main ontogenetic series independently from phylogenetic/taxonomic relationships. The distribution of these clusters in the morphospace may be viewed in relationship with ontogenetic trajectories as well as with posture and locomotion. Pongo, Gorilla, and Pan, share a common pattern of cranial base variation during growth, whereas modern humans show a different pattern of change with analogous ontogenetic polarity, shared with Mid-to-Late Pleistocene Homo. Australopiths and early-Homo specimens occupy a morpho-space that is distinct from both the other Homo, representatives and living great apes, while approach the ontogenetic series of the formers. It is worth mentioning that this is not in relationship with their degree of encephalization, but it is consistent with the Anova (p < 0.001) performed on PC scores on posture and locomotion variables. When dealing with shape predictions, the P-values of the regression analysis of size related trajectories are statistically significant for the extant Hominoidea, while adult Australopiths and early Homo, are closer to the trajectories of both modern humans and Mid-to-Late Pleistocene Homo, (including Neanderthal juveniles) than to those of great apes. The phenetic relationships based on UPGMA cluster analysis (adult samples only) further demonstrate the independence of the observed patterns of cranial base morphology from phylogenetic/taxonomic relationships.
References:Bastir, M., Rosas, A., Stringer, C., Cuétara, J.M., Kruszynski, R., Weber, G.W., Ross, C.F., Ravosa, M. J., 2010. Effects of brain and facial size on basicranial form in human and primate evolution. J. Hum. Evol., 58, 424-431. Bastir, M., Rosas, A., Gunz, P., Pena-Melian, A., Manzi, G., Harvati, K., Kruszynski, R., Stringer, C., Hublin, J-J., 2011. Evolution of the base of the brain in highly encephalized human species. Nat. Commun., 2, 588. (doi:10.1038/ncomms1593) Lieberman, D.E., 2011. The Evolution of the Human Head. Cambridge, MA: Harvard University Press
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