A PCA-Based Method for Determining Craniofacial Relationship and Sexual Dimorphism of Facial Shapes

Previous studies have used principal component analysis (PCA) to investigate the craniofacial relationship, as well as sex determination using facial factors. However, few studies have investigated the extent to which the choice of principal components (PCs) affects the analysis of craniofacial relationship and sexual dimorphism. In this paper, we propose a PCA-based method for visual and quantitative analysis, using 140 samples of 3D heads (70 male and 70 female), produced from computed tomography (CT) images. There are two parts to the method. First, skull and facial landmarks are manually marked to guide the model’s registration so that dense corresponding vertices occupy the same relative position in every sample. Statistical shape spaces of the skull and face in dense corresponding vertices are constructed using PCA. Variations in these vertices, captured in every principal component (PC), are visualized to observe shape variability. The correlations of skull- and face-based PC scores are analysed, and linear regression is used to fit the craniofacial relationship. We compute the PC coefficients of a face based on this craniofacial relationship and the PC scores of a skull, and apply the coefficients to estimate a 3D face for the skull. To evaluate the accuracy of the computed craniofacial relationship, the mean and standard deviation of every vertex between the two models are computed, where these models are reconstructed using real PC scores and coefficients. Second, each PC in facial space is analysed for sex determination, for which support vector machines (SVMs) are used. We examined the correlation between PCs and sex, and explored the extent to which the choice of PCs affects the expression of sexual dimorphism. Our results suggest that skull- and face-based PCs can be used to describe the craniofacial relationship and that the accuracy of the method can be improved by using an increased number of face-based PCs. The results show that the accuracy of the sex classification is related to the choice of PCs. The highest sex classification rate is 91.43% using our method

exploring patterns of morphological integration in the crania of papio hamadryas ursinus and homo sapiens

A Theses submitted to the faculty of science, university of the Witwatersrand, Johannesburg, in fulfilment of the requirements for the degree of doctor of philosophyMorphological integration is the pattern of correlation or covariation among parts due to genetic, developmental and functional processes, and is essential for the viability of an organism. Integration among processes is not uniform but forms distinct modules allowing for their independent evolvability and is thus central to the study of biological evolution. The incongruence between phylogenies estimated using the genotype and the cranial morphology in both the Papionini primates as well as the Hominidae possibly result from the disregard of character integration. Regarding the degree of morphological integration humans display extremely low levels of integration among the primates, while the baboon possesses extremely high levels. This thesis set out to address three broad aims regarding integration of the baboon and human cranium; namely 1) to study the effect of allometry on measures of integration, and when allometry and sexual dimorphism had been accounted for, 2) to assess the patterning of morphological integration into morphological modules; and finally, 3) to assess differences in the pattern of covariation between the cranial base, cranial vault and facial skeleton in humans and baboons. Although allometric growth is divided into neural and somatic, the findings suggest that the effect of allometry conceals more detailed patterns of morphological integration likely resulting from genetic and developmental processes, and should therefore be accounted for in studies of morphological integration. It is unlikely that allometry among cranial regions constrains evolutionary diversity, but rather offers a path of least resistance. The second aim offered up novel methods of exploring the pattern of morphological covariation using clustering and network methods that supported current hypotheses and proposed that the oral and basicranial regions are comprised of additional modules; however, rigorous scientific scrutiny is required for its support. iv The third aim involved the analysis of integration between the cranial base, cranial vault, and facial skeleton. The results supported the proposal that humans and nonhuman primates share a similar pattern of integration likely reflecting shared developmental processes among the primates, but with key differences probably relating to functional demands. Integration between these three cranial regions primarily involve their relative positioning and proportions. The broad pattern of integration likely reflects the role of the cranium as the supporting framework around the organs and functional capsules, the “real” modules, which accommodate one another epigenetically as they develop. The recognition of both independent modules and their pervasive integration are important and depend primarily on the nature of the investigation.GR201

Shape, size, and maturity trajectories of the human ilium

Morphological traits of the ilium have consistently been more successful for juvenile sex determination than have techniques applied to other skeletal elements, however relatively little is known about the ontogeny and maturation of size and shape dimorphism in the ilium. We use a geometric morphometric approach to quantitatively separate the ontogeny of size and shape of the ilium, and analyze interpopulation differences in the onset, rate and patterning of sexual dimorphism. We captured the shape of three traits for a total of 191 ilia from Lisbon (Portugal) and London (UK) samples of known age and sex (0-17 years). Our results indicate that a) there is a clear dissociation between the ontogeny of size and shape in males and females, b) the ontogeny of size and shape are each defined by nonlinear trajectories that differ between the sexes, c) there are interpopulation differences in ontogenetic shape trajectories, which point to population-specific patterning in the attainment of sexual dimorphism, and d) the rate of shape maturation and size maturation is typically higher for females than males. Male and female shape differences in the ilium are brought about by trajectory divergence. Differences in size and shape maturation between the sexes suggest that maturity may confound our ability to discriminate between the sexes by introducing variation not accounted for in age-based groupings. The accuracy of sex determination methods using the ilium may be improved by the use of different traits for particular age groups, to capture the ontogenetic development of shape in both sexes

The Taxonomic Status of the Middle Pleistocene Hominins: A 3D Geometric Morphometric Investigation of Variation in the Supraorbital Region

This study investigated the significance of variation in the supraorbital morphology of the Middle Pleistocene hominins (MPH), using 3D geometric morphometric methods and a comparative taxonomic framework. The morphology of the supraorbital and orbital region of fourteen MPH from Africa, Asia, and Europe was recorded using 230 3D landmarks and surface semilandmarks. A comparative sample of 460 primates (Pan, Gorilla, Papio and Macaca) and 237 hominins (Early Pleistocene to Holocene) were included to model supraorbital variation in groups of varying taxonomic classification, ecology, and geographic and temporal range. It was found that the fourteen MPH had relatively low morphological distinctiveness in relation to established species, although they did cluster together in most morphometric analyses. Nevertheless, the variation in the supraorbital and orbital region of the MPH was not larger than could be expected in a single, cross-continental species, and the validity of continental subgroups within the MPH could not be supported based on comparisons to established primate and hominin taxa. Instead, results indicated that some of the MPH may represent transitional specimens or members of other hominin lineages. Sex could not be reliably estimated for the MPH using patterns of sexual dimorphism in other groups of known sex, and while differences in size, allometry, and encephalisation were found to have significant effects on variation in the supraorbital region, geography and chronology did not have significant effects on variation within the MPH. Based on the application of a morphological species concept and comparative primate and hominin data on supraorbital variation, the existence of multiple MPH taxa is indicated by the results found here. It is therefore suggested that the term Homo heidelbergensis (sensu lato) be applied to a restricted, cross-continental group of MPH (Bodo, Kabwe, Saldanha, Petralona, Arago 21, Ceprano, Narmada, and possibly Eliye Springs)

Additive genetic variation in the craniofacial skeleton of baboons (genus Papio) and its relationship to body and cranial size

Objectives Determining the genetic architecture of quantitative traits and genetic correlations among them is important for understanding morphological evolution patterns. We address two questions regarding papionin evolution: (1) what effect do body and cranial size, age, and sex have on phenotypic (VP) and additive genetic (VA) variation in baboon crania, and (2) how might additive genetic correlations between craniofacial traits and body mass affect morphological evolution? Materials and Methods We use a large captive pedigreed baboon sample to estimate quantitative genetic parameters for craniofacial dimensions (EIDs). Our models include nested combinations of the covariates listed above. We also simulate the correlated response of a given EID to selection on body mass alone. Results Covariates account for 1.2%–91% of craniofacial VP. EID VA decreases across models as more covariates were included. The median genetic correlation estimate between each EID and body mass is 0.33. Analysis of the multivariate response to selection reveals that observed patterns of craniofacial variation in extant baboons cannot be attributed solely to correlated response to selection on body mass, particularly in males. Discussion Because a relatively large proportion of EID VA is shared with body mass variation, different methods of correcting for allometry by statistically controlling for size can alter residual VP patterns. This may conflate direct selection effects on craniofacial variation with those resulting from a correlated response to body mass selection. This shared genetic variation may partially explain how selection for increased body mass in two different papionin lineages produced remarkably similar craniofacial phenotypes

A computerized craniofacial reconstruction method for an unidentified skull based on statistical shape models

Craniofacial reconstruction (CFR) has been widely used to produce the facial appearance of an unidentified skull in the realm of forensic science. Many studies have indicated that the computerized CFR approach is fast, flexible, consistent and objective in comparison to the traditional manual CFR approach. This paper presents a computerized CFR system called CFRTools, which features a CFR method based on a statistical shape model (SSM) of living human head models. Given an unidentified skull, a geometrically-similar template skull is chosen as a template, and a non-registration method is used to improve the accuracy of the construction of dense corresponding vertices through the alignment of the template and the unidentified skull. Generalized Procrustes analysis (GPA) and principal component analysis (PCA) are carried out to construct the skull and face SSMs. The sex of the unidentified skull is then predicted based on skull SSM and centroid size, rather than geometric measurements based on anatomical landmarks. Furthermore, a craniofacial morphological relationship which is learnt from the principal component (PC) scores of the skull and face dataset is used to produce a possible reconstructed face. Finally, multiple possible reconstructed faces for the same skull can further be recreated based on adjusting the PC coefficients. The experimental results show that the average rate of sex classification is 97.14% and the reconstructed face of the unidentified skull can be produced. In addition, experts’ understanding and experience can be harnessed in production of face variations for the same skull, which can further be used as a reference for portraiture creation

Number of Teeth Is Related to Craniofacial Morphology in Humans.

One of the most common dental anomalies in humans is the congenital absence of teeth, referred to as tooth agenesis. The association of tooth agenesis to craniofacial morphology has been previously investigated but remains unclear. We investigated this association by applying geometric morphometric methods in a large sample of modern humans. In line with previous studies, we report here that a reduced teeth number is linked to a less convex profile, as well as to a shorter face. The effects were similar for males and females; they increased as the severity of the tooth agenesis increased and remained unaltered by the inclusion of third molars and of allometry in the analysis. Furthermore, in cases with tooth agenesis only in the maxilla, there was no detectable effect in mandibular shape, whereas maxillary shape was affected independently of the location of missing teeth. The robustness of the present sample along with the shape analysis and the statistical approach applied, allowed for thorough testing of various contributing factors regarding the presence but also the magnitude of effects. The present findings suggest a relationship between number of teeth and overall craniofacial development and have evolutionary implications

Assessing the accuracy of the zygoma for estimating ancestry using geometric morphometrics in a South African sample

The large number of unidentified, decomposed and skeletonised remains found in South Africa (SA) necessitates relevant and reliable methods to assist in victim identification. Ancestry estimation from unknown skeletal remains is essential when reconstructing a demographic profile of a missing person. In the SA population, estimating ancestry is problematic as standards developed internationally rarely apply to the local, biologically heterogenous population. Craniofacial morphology is known to be ancestrally distinct and studies are yet to explore shape and size variation in the zygomatic bone of the SA population. The aim of this study was to assess ancestral variation in zygomatic shape and size in a SA population using three-dimensional geometric morphometric analyses. A sample of 158 individuals were analysed from Bantu-speaking (BA), European (EA) and Mixed Ancestral (MA) South African groups. Males were larger in size than females, but no size differences were observed between ancestral groups. Significant shape differences were observed between ancestral groups, while none were observed between males and females. BA and MA individuals had narrower, shorter and more anteriorly projecting zygomas than EA individuals. The zygoma was shown to accurately distinguish EA (84%) from BA (81%), and MA (80%) from EA (68%) individuals, but unreliably distinguished BA (60%) from MA (66%) individuals. This is likely correlated to the historical peopling of SA and historical forced racial classification. Age-related changes and antemortem tooth loss did not confound the ancestral variation in size, despite minor changes in zygomatic shape being associated with these two factors. These confounders did not impact ancestry estimation accuracies, further suggesting a minor impact on overall zygomatic shape. Furthermore, the patterning of ancestral variation in the zygoma revealed the need for further research to distinguish between the biologically heterogenous ancestral groups in SA

A statistical shape analysis of the neurocranium and long bones

Morphological variation of skeletal elements, and the potential use of such variation in distinguishing among demographic groups, is often investigated using traditional metric or non-metric assessments. Traditional approaches, however, often fail to sufficiently capture the "true" shape of features, thus also failing to identify potentially important feature characteristics. The development of geometric morphometrics has allowed more comprehensive and accurate three-dimensional data capture which maintains the geometric properties of an object while isolating the effect of size from the data. The aim of this study was to employ the geometric morphometric approach to a 3D digitized sample of 1132 South African individuals from the skeletal collections of the Universities of Cape Town, Stellenbosch, Witwatersrand and Pretoria. Morphological variation among demographic groups was assessed using Generalized Procrustes Analyses applied to the individual bones of the neurocranium and the long bones of the limbs. The ability to distinguish groups based on the detected variation was assessed using Discriminant Function Analysis. The results show that, when size is isolated from the data, only a few elements show sexual dimorphism, while all examined elements show high accuracy in distinguishing among ancestry groups (>74%). When variation is assessed using both parameters, classification accuracies of 70-83% are obtained. Comparison of the different elements shows that the best classification accuracies are based on the frontal bone (84% average) and the humerus (81% average). This study shows that the morphologies of the neurocranium and long bones vary among sex and ancestry groups. This allows assessment of how the combination of variable intrinsic and extrinsic influences can manifest on different parts of the skeleton. In a population as genetically and historically complex as that of South Africa, understanding of the impact of such influences may inform forensic assessments of skeletal material, which is especially valuable considering the high rate of violent crimes and increasing number of unidentified remains being discovered in the country

Early recognition of mandibular growth pattern using geometric morphometrics

OBJECTIVE: The objective of this study is to determine the earliest time point in growth when a difference in mandibular shape of dolichocephalic and brachycephalic subjects is distinguishable. MATERIALS & METHODS: 11 dolichocephalic and 14 brachycephalic subjects were selected using lateral cephalograms from the Forsyth/Moorrees Twin Study using a method described by Rocky Mountain Orthodontics. 23 landmarks outlining the mandible were identified on the lateral cephalograms of each subject from their earliest age (5-8 years) to their latest (16-18 years) using TPSdig software. The 2 dimensional coordinates for each landmark were then exported to TPSUtil. From TPSUtil, the TPS data was then converted to a .csv file in Microsoft Excel and imported into MorphoJ for analysis. Primary morphometric analysis consisted of generalized Procrustes analysis, principal component analysis, and discriminant function analysis. RESULTS: The first 5 principal components for both facial types accounted for the majority of the variance. Discriminant function analyses were not significant for any phenotype or age group pairing, suggesting that the overall shape difference was too small to be detected between groups and over time starting at age 7. A plot of the Procrustes coordinates for the brachycephalic group versus the dolichocephalic group revealed that there were differences in shape between the two phenotypes, but this difference was statistically insignificant. CONCLUSIONS: The mandible increases in size with age, with minimal change in shape. Mandibular shape is established by the age of 7. The difference in mandibular shapes of the two phenotypes was not statistically significant