193 research outputs found
Old and new methods in geometric morphometrics applied to the study of human evolution: case studies
Get PDFThe 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: R Functions for Geometric Morphometrics Analyses
No full text<p>Tools for Geometric Morphometrics</p>
Arothron: R Functions for Geometric Morphometrics Analyses
No full text<p>Tools for Geometric Morphometrics</p>
A Comparison of Semilandmarking Approaches in the Analysis of Size and Shape
Get PDFOften, few landmarks can be reliably identified in analyses of form variation and covariation. Thus, ‘semilandmarking’ algorithms have increasingly been applied to surfaces and curves. However, the locations of semilandmarks depend on the investigator’s choice of algorithm and their density. In consequence, to the extent that different semilandmarking approaches and densities result in different locations of semilandmarks, they can be expected to yield different results concerning patterns of variation and co-variation. The extent of such differences due to methodology is, as yet, unclear and often ignored. In this study, the performance of three landmark-driven semilandmarking approaches is assessed, using two different surface mesh datasets (ape crania and human heads) with different degrees of variation and complexity, by comparing the results of morphometric analyses. These approaches produce different semilandmark locations, which, in turn, lead to differences in statistical results, although the non-rigid semilandmarking approaches are consistent. Morphometric analyses using semilandmarks must be interpreted with due caution, recognising that error is inevitable and that results are approximations. Further work is needed to investigate the effects of using different landmark and semilandmark templates and to understand the limitations and advantages of different semilandmarking approaches
Surface smoothing, decimation, and their effects on 3D biological specimens
No full textObjective
Smoothing and decimation filters are commonly used to restore the realistic appearance of virtual biological specimens, but they can cause a loss of topological information of unknown extent. In this study, we analyzed the effect of smoothing and decimation on a 3D mesh to highlight the consequences of an inappropriate use of these filters.
Materials and methods
Topological noise was simulated on four anatomical regions of the virtual reconstruction of an orangutan cranium. Sequential levels of smoothing and decimation were applied, and their effects were analyzed on the overall topology of the 3D mesh and on linear and volumetric measurements.
Results
Different smoothing algorithms affected mesh topology and measurements differently, although the influence on the latter was generally low. Decimation always produced detrimental effects on both topology and measurements. The application of smoothing and decimation, both separate and combined, is capable of recovering topological information.
Conclusion
Based on the results, objective guidelines are provided to minimize information loss when using smoothing and decimation on 3D meshes
) 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
Arothron: R Functions for Geometric Morphometrics Analyses
No full textTools for Geometric Morphometric
Maxillary sinus growth and development in Neanderthals and H. sapiens
No full textWe investigate and compare facial and maxillary sinus ontogeny among Neanderthals and H. sapiens to understand the extent of any differences and to investigate if these might arise through differences in developmental interactions. 3D facial and sinus landmarks were acquired from virtual reconstructions of H. sapiens and Neanderthals (H. sapiens N=60, Neanderthals=5). Geometric morphometric analyses compared ontogenetic trajectories of size and shape as well as patterns of covariation among the maxillary sinuses, facial skeleton and its sub-regions. Our results show that facial ontogeny diverges and that maxillary sinuses develop divergently among Neanderthals and modern humans. In both, maxillary sinus, facial and maxillary form are strongly associated. Further, PLS analyses indicate that the ontogeny of maxillary sinus form is strongly associated with that of several facial regions in infancy but becomes most closely associated with the form of the maxilla and nasal cavity in older individuals. In part, this is because the great changes in size that occur in the first few years of life dominate the analyses. However when shape alone is considered a similar shift in patterns of association is observed, albeit with lower correlations indicating that ontogenetic size changes alone do not explain the observed interactions. These findings suggest that despite differences in facial form and ontogenetic trajectories between modern humans and Neanderthals, their maxillary sinuses develop similarly, showing similar patterns of interaction with other facial components, but attaining larger sizes, consistent with the greater space available or expansion provided by the larger maxilla of Neanderthals
A Comparison of Semilandmarking Approaches in the Visualisation of Shape Differences
Get PDFIn 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
Advances in virtual morphometrics: a new approach to generate 2D and 3D surface outlines on virtual specimens
No full textPalaeoanthropology and Bioarchaeology make extensive use of outline-based morphometrics and this approach can be used to ex-tract information from several sources. 2D outlines are usually generated from teeth or lithic tools, as well as from skulls or longbones profiles, and this method is widespread in the study of human evolution [1, 2]. In many cases, the generation of outlines is avaluable alternative to traditional linear measurements or 2D landmark-based geometric morphometrics. 2D outlines are conven-tionally acquired through photography, a procedure prone to parallax errors . In recent years, the use of virtual collections increasedremarkably due to the availability of novel imaging techniques, such as CT-scanning, laser scanning and photogrammetry. anksto these new virtual environments, current methodological approaches can be improved and new techniques can be developed. Wepresent here a method to generate 2D and 3D outlines of complex specimens from a 3D surface model. e 3D contours recreatethe patterns of maximal breadth of the object outline. e procedure has been developed in the R statistical environment and usesα-shape approach and Bézier curves to generate the outlines. α-shape formalises the concept of “shape” for spatial point sets in com-putational geometry : a α-shape is built by connecting all the pairs of points lying on a circle which is not touching or overlappingany other point of the set. Bézier curves are used to approximate curves by generating a set of points through a polynomial fitting.Only three landmarks are needed to apply the method: these points define a reference plane to project all the vertices of the 3Dmodel onto. A α-shape is then obtained from the projected vertices and a Bézier approximation is used to generate evenly spacedlandmarks lying on the outline. e 3D outline is generated by bringing each point of the α-shape back on the surface model; aBézier curve is then calculated. is method allows high precision and reproducibility in outline generation and can be applied onboth skeletal and lithic material. 3D contours generated with this method consent to address new questions on functional trendsin skeletal morphology or in material culture, enhancing the morphometric approach on the study of human evolution
- …
