3D Geometric Morphometrics

This project investigates different aspects of craniofacial phenotypes exhibited in individuals with Down syndrome (DS), siblings of individuals with DS, and typically developing sibling pairs. A human sample (4-12 yrs.) consisting of 3D facial surface images (n = 55 for four separate samples: i.e. n = 220 overall) was used to explore developmental instability of the face and patterns of facial covariation between individuals with DS, their siblings, and typically developing sibling pairs. Morphometric analyses were used to infer how gene-dosage imbalance, caused by trisomy 21, is affecting DS craniofacial development. Overall we found increased fluctuating asymmetry in the faces of individuals with DS, which provides evidence for the "amplified developmental instability" model put forth by Shapiro (1975, 1983). However, the patterns of differences that we found suggest specific disruptions to regions of the face during craniofacial development rather than the generalized disruptions described by Shapiro under the amplified developmental instability model. Additionally, the results of our investigation found that covariation of facial metrics is different in DS individuals and in DS siblings relative to typically developing siblings. Based on differences in the pattern and strength of integration within and between facial regions in the DS and DS sibling samples, we put forth an "aneuploid conception model" to explain why facial integration is lowest in DS siblings and strengthened in DS relative to DS siblings.

In addition to the human-based analyses, micro-computed tomography (µCT) scans and morphometric analysis were employed to evaluate a complete genetic mouse model for DS - the Ts1Yey mouse. Morphometric comparison of craniofacial measures for Ts1Yey mice and euploid littermates (n = 12 for each sample) was done to determine if this model exhibits craniofacial differences similar to differences seen in humans with DS and in previously established DS mouse models. Overall, our results validate this mouse model for use in craniofacial DS investigations.

The timing and geographic origin of the common ancestor of modern humans and Neandertals remain controversial. A poor Pleistocene hominin fossil record and the evolutionary complexities introduced by dispersals and regionalisation of lineages have fuelled taxonomic uncertainty, while new ancient genomic data have raised completely new questions. Here, we use maximum likelihood and 3D geometric morphometric methods to predict possible morphologies of the last common ancestor of modern humans and Neandertals from a simplified, fully resolved phylogeny. We describe the fully rendered 3D shapes of the predicted ancestors of humans and Neandertals, and assess their similarity to individual fossils or populations of fossils of Pleistocene age. Our results support models of an Afro-European ancestral population in the Middle Pleistocene (Homo heidelbergensis sensu lato) and further predict an African origin for this ancestral population.

After viewing this presentation, attendees will gain a greater understanding of the morphological differences seen between male and female modern pubic bones and how those shape differences can be captured using a 3D geometric morphometric approach.

This presentation will impact the forensic science community by quantifying nonmetric shape analyses that are widely used in sexing human pubic bones through a 3D geometric morphometric approach for analysis. Using a 3D geometric morphometric approach allows for the utilization of landmarks and semi-landmarks to accurately capture the slight shape differences that nonmetric observations are not able to obtain.

Sex estimation methods for human skeletal remains have been a highly researched and debated topic in biological anthropology. A plethora of studies have been performed using various statistical methods, in part because os coxae variation spans a large spectrum and does not always fit into distinct nonmetric categories. Growing in popularity is the utilization of 3D geometric morphometric techniques; studies have been performed using landmarks and semi-landmarks to sex os coxae with a high degree of accuracy.

Generally, it is believed that male pubic bones tend to be shorter and triangular in shape, while females have a longer and squarer shape. Previous studies acknowledge the need to quantify nonmetric methods while sexing os coxae, but do not specifically test the widely used nonmetric visual method of sexing males on the basis of short or triangular pubic bones and females on the basis of long or square pubic bones.

In this research, 35 known male and 35 known female specimens from the William M. Bass Donated Skeletal Collection at the University of Tennessee (UT) and 24 unknown specimens from the Forensic Anthropology Unit at the New York City Office of Chief Medical Examiner (NYC OCME), were scanned using a NextEngine 3D laser scanner. The os coxae were edited in Geomagic and 8 landmarks were placed on the left pubic bone. The landmarks were chosen to highlight the portion of the pubic bone associated with the triangular and rectangular shape differences between males and females. These points were placed on the dorsal aspect of the bone since there are fewer irregularities and span from the superior and inferior portions of the pubic symphysis, along the obturator foramen opposite the symphysis points, and up to the most superior point of the obturator foramen. The points were aligned using a Generalized Procrustes Analysis, and then a Principal Components (PC) analysis was employed to distinguish meaningful shape differences. A Discriminant Function Analysis (DFA) was then run on the PC scores to determine how accurate the captured portion of the pubic bone is in determining sex. The known specimens were placed in their proper sex categories for the DFA analysis, while the unknown specimens were left ungrouped to compare the nonmetric analyses of those os coxae found in their case reports versus their assigned group in the DFA analysis.

Using the 12 PC scores that contained significant shape information, the DFA analysis was able to classify 95.7% (94% males, 97% females) of the known UT pubic bones correctly into their skeletal sex groups with a 92.9% (91% males, 94% females) leave-one-out cross-validation accuracy. For the unknown NYC OCME specimens, 83.3% of the specimens matched their case reports. Intra-observer error was tested by placing the landmarks on the specimens a second time and running the same analyses. The results were an original classification accuracy of 97.1% (94% males, 100% females), a cross-validation accuracy of 91.4% (86% males, 97% females), with 87.5% of the unknown specimens matching their case reports. The differences in percentages between these two analyses are slight, and the changes were due to specimens that fell within the overlapping regions found on the PC plots.

The results capture the major morphological differences between male and female pubic bones. These differences match the nonmetric categories of a triangular shape in males and a square shape in females, which were found on the first PC, but it also captures 11 other significant PC variations that cannot be observed from visual assessments. This experiment has high accuracy results and can be a good categorization method for unknown specimens in future studies.

Bilateral cleft lip and palate (BCLP) is caused by a lack of merging of maxillary and nasal facial prominences during development and morphogenesis. BCLP is associated with congenital defects of the oronasal facial region that can impair ingestion, mastication, speech, and dentofacial development. Using cone beam computed tomography (CBCT) images, 7-18 yr. old individuals born with BCLP (n = 15) and age- and sex-matched controls (n = 15) were retrospectively assessed. Coordinate values of three-dimensional facial skeletal anatomical landmarks (n = 32) were measured from each CBCT image. Data were evaluated using principal coordinates analysis (PCOORD) and Euclidean Distance Matrix Analysis (EDMA). PCOORD axes 1-3 explain approximately 45% of the morphological variation between samples, and specific patterns of morphological differences were associated with each axis. Approximately 30% of facial skeletal measures significantly differ by confidence interval testing (α = 0.10) between samples. While significant form differences occur across the facial skeleton, strong patterns of differences are localized to the lateral and superioinferior aspects of the nasal aperture. In conclusion, the BCLP deformity significantly alters facial skeletal morphology of the midface and oronasal regions of the face, but morphological differences were also found in the upper facial skeleton and to a lesser extent, the lower facial skeleton. This pattern of strong differences in the oronasal region of the facial skeleton combined with differences across the rest of the facial complex underscores the idea that bones of the craniofacial skeleton are integrated.

Archaeological evidence shows that populations used to transverse the Sahara Desert throughout the Holocene despite the extreme temperatures and the rough physical terrain. The current paper examines whether the desert inhibited extended gene flow among populations by means of cranial morphology as captured by geometric morphometrics. The examined populations include the Garamantes, a group centered in Southwest Libya and largely controlling trans-Saharan trade, and various Egyptian, Tunisian and
Sudanese groups dating to the Middle and Late Holocene. The results showed that most inter-population comparisons were statistically significant and therefore all populations appear more or less distant to each other. The Mahalanobis biodistance measure identified four clusters. The first consists of the Garamantes alone, the second includes the populations from Kerma and Gizeh, the third includes the Badari and Naqada, while the fourth consists of the samples from Algeria, Carthago, Soleb and Alexandria. Moreover, the distance of the Garamantes to their neighbors was significantly high and the population appeared to be an outlier. This is attributed to the location of the Garamantes at the core of the desert, indicating that, despite the archaeological evidence, the Sahara Desert posed important limitations to gene flow between the Garamantes and other North African populations.

We compared the head skeleton (skull and lower jaw) of juvenile and adult specimens of five snake species [Anilios (=Ramphotyphlops) bicolor, Cylindrophis ruffus, Aspidites melanocephalus, Acrochordus arafurae, and Notechis scutatus] and two lizard outgroups (Ctenophorus decresii, Varanus gilleni). All major ontogenetic changes observed were documented both qualitatively and quantitatively. Qualitative comparisons were based on high-resolution micro-CT scanning of the specimens, and detailed quantitative analyses were performed using three-dimensional geometric morphometrics. Two sets of landmarks were used, one for accurate representation of the intraspecific transformations of each skull and jaw configuration, and the other for comparison between taxa. Our results document the ontogenetic elaboration of crests and processes for muscle attachment (especially for cervical and adductor muscles); negative allometry in the braincase of all taxa; approximately isometric growth of the snout of all taxa except Varanus and Anilios (positively allometric); and positive allometry in the quadrates of the macrostomatan snakes Aspidites, Acrochordus and Notechis, but also, surprisingly, in the iguanian lizard Ctenophorus. Ontogenetic trajectories from principal component analysis provide evidence for paedomorphosis in Anilios and peramorphosis in Acrochordus. Some primitive (lizard-like) features are described for the first time in the juvenile Cylindrophis. Two distinct developmental trajectories for the achievement of the macrostomatan (large-gaped) condition in adult snakes are documented, driven either by positive allometry of supratemporal and quadrate (in pythons), or of quadrate alone (in sampled caenophidians); this is consistent with hypothesised homoplasy in this adaptive complex. Certain traits (e.g. shape of coronoid process, marginal tooth counts) are more stable throughout postnatal ontogeny than others (e.g. basisphenoid keel), with implications for their reliability as phylogenetic characters.

This study aims to eliminate the labor-intensive target installation process and its associated costs and other issues commonly caused from the current practices of laser based as-built data collection and modeling process. In this study, a laser scan system was utilized with corresponding texture data simultaneously obtained from a digital camera. Based on identified common features in the texture data, an optimized transformation matrix for the point clouds is generated, then the point clouds are registered without using any physical external target. The proposed method was tested at an ongoing building construction project. The interrelationships among registration speed, registered accuracy, and size of overlapping area were examined. The field experimental results demonstrate that the proposed target-free geometric data registration method can significantly reduce the registration time without compromising the registration accuracy; thus simplifying and promoting the current laser scanning and registration processes for progressive as-built modeling of construction projects.

For centuries, reindeer herding has been an integral part of the subsistence and culture among the Sámi of northern Fennoscandia. Despite the importance of this husbandry in their history, the timing and details of early reindeer domestication are still highly debated. Indeed, identifying domesticated individuals in the archaeological record remains complicated because reindeer are still considered to be in the early phases of the domestication process. In this work, we propose solutions for identifying domestic individuals using 3D geometric morphometrics on isolated elements from the long bones of the hindlimb in modern reindeer populations. These bones are important for understanding both the mobility of reindeer and the effect of load carrying or draught. A good level of distinction between the size and shape variables of these bones was found among subspecies, sex and lifestyles. This demonstrates that the long bones of the hindlimb can provide information on changes in locomotor behaviour induced by the domestication process, such as control and reduction of reindeer mobility by humans. This also demonstrates that analysis in geometric morphometrics is useful for exploring the use of draught reindeer in early Sámi reindeer herding and the implications for understanding reindeer domestication and early reindeer herding strategies.

In the last decades competing hypotheses have been forwarded attempting to explain the behavioral factors governing the technological choices of Acheulian Large Cutting Tools (LCT) makers and how they may have affected the morphology of bifacial tools. Hypotheses run the gamut of expert cognition and imposition of pre-planned forms on a wide variety of raw materials (mental template hypotheses) to suggestions that the final shapes of LCT are the mechanical outcomes of reduction intensity and the impact of raw material size, form and quality. The Melka Wakena site complex, located on the eastern shoulder of the Main Ethiopian Rift at an elevation of 2300-2400 m.a.s.l, presents an opportunity to explore patterns in the technology of Acheulian LCT production. Here we focus on two types of LCT – handaxes and cleavers – to evaluate the competing hypotheses. We present a technological study of the two tool types in stratified assemblages, examining the shape, size and raw material trends through time (from 1.6 Ma to ~ 0.7 Ma) on inter-and intra-assemblage scales. We used a high-resolution 3D homologous landmark- based geometric morphometric shape analysis, applied to a sample of high resolution 3D models of handaxes and cleavers from the stratified localities- MW2, MW5, and MW1. The same artifacts have also undergone a technological attribute analysis. Results show that raw material selection for these tool types was nearly identical across time and space in the Melka Wakena localities. There is no clear association between technological characteristics (LCT blank preparation, selection and shaping), and tool morphology. Moreover, morphological homogeneity within each type appears to increase over time and is strongly correlated to the degree of tool shaping.

3D Data Acquisition for Bioarchaeology, Forensic Anthropology, and Archaeology serves as a handbook for the collection and processing of 3-D scanned data and as a tool for scholars interested in pursuing research projects with 3-D models. The book's chapters enhance the reader’s understanding of the technology by covering virtual model processing protocols, alignment methods, actual data acquisition techniques, basic technological protocols, and considerations of variation in research design associated with biological anthropology and archaeology.

This study quantifies the metacarpal 1 (MC 1) proximal articular surface using three-dimensional morphometrics in extant hominids and fossil hominins (SK 84, cf. Paranthropus robustus/Homo erectus and StW 418, Australopithecus africanus) to understand which characteristics of the proximal metacarpal 1 are potentially correlated with human manipulative abilities and if they can be used in a paleoanthropological setting. A principal components (PC) analysis was used to compare MC 1 proximal articular surface shape and ANOVA and Tukey’s HSD post hoc tests were conducted to determine differences among groups. Homo is significantly different from nonhuman hominids having a less radioulnarly and dorsovolarly curved articular surface. All nonhuman hominids have more curved articular surface with Gorilla showing the most curved joint. Moreover, this study highlights the presence of a radially extended surface in Homo that may be related to the greater thumb abduction in human manipulation activities. Both fossils analyzed show a great ape-like MC 1 proximal articular surface which, associated with recent trabecular and archaeological evidence, may indicate that the ability to make/use stone tools preceded the morphological adaptations associated today to such behavior.

A key feature of stone artefact morphology is the arrangement and patterning of negative flake scars left on flakes and cores. Scar patterning is often treated as a rough guide to identifying methods of core preparation and reduction and usually forms a key component of lithic typologies and other systems of analysis. However, scar patterns are often complex and difficult to capture using traditional measurement or classificatory techniques, particularly where flakes are thick and irregular, or where cores are flaked on many sides from a number of platforms. Three-dimensional analysis of flake scars is now more feasible using digital 3D surface scanning technologies, or using three-dimensional measurement tools such as the Microscribe-3DX which is now widely used in biological geometric morphometric studies more generally [D.C. Adams, F.J. Rohlf, D.E. Slice, Ital. J. Zool. 71 (2004) 5-16; F.J. Rohlf, L.F. Marcus, Trends Ecol. Evol. 8 (1993) 129-132]. This paper develops a mathematical formula for describing scar patterning using vectors calculated from the start and end points of flake scars recorded in three dimensions.