Three-dimensional Landmark Data Research Articles

Using two- and three-dimensional landmark data to examine the shape variation of Elliptio complanata from two heavily impounded rivers in northern New York (USA)

ABSTRACT Despite vast improvements in the quantification of shape variation with geometric morphometric methods, evaluating morphological variation in unionids has remained difficult due to the lack of measurable landmarks on shells and their overall morphological plasticity. In this study, we supplement traditional two-dimensional landmark data with three-dimensional landmark data. Using photogrammetry, we generate three-dimensional models that are landmarked. This approach adds a new, third dimension to capture shape changes, providing a more detailed understanding of the shell topography. With this method, we explore the differences in shell shape along river stretches of two heavily impounded rivers in northern New York (USA). We ask whether isolation by distance, presence of dams and/or difference in land use around sampling localities impact the shell morphologies of Elliptio complanata populations. Our data suggest that, although separated for almost a century, these unionid populations do not show a pattern of increased morphological difference with distance. But we find that broad, rounded morphs that are posteriorly extended occur more frequently in reservoir environments while unaltered river habitats have a higher number of slim and more elongated variants.

Systemic versus local patterns of limb joint articular morphology inferred from relative distances from morphological centroid.

Joint morphogenesis is a complex process known to require the interaction of developmental cascades and mechanical loading, yet many details of this interaction are incompletely understood. While prior work has established populational patterns of joint morphological (co)variance, exploring how these patterns manifest within the individual provides information on the deployment of morphogenic processes as either systemic or local influences on joint shape. To better identify the patterns of variance-generating morphogenic processes, this study investigates the degree to which individual joint shapes deviate from population averages systematically across the body. Using three-dimensional landmark data from 200 adult skeletons, we ranked individuals based on their distances from morphological centroids for eight major joints. Spearman correlations assessed associations between ranks across various articular pairings, testing hypotheses regarding systemic versus localized variance. Results reveal low coordination between deviations observed in conarticular surfaces, functional analogs, and same-bone surfaces; however strong associations exist between antimeres, suggesting the left-right deployment of variance-generating morphogenic patterns is highly consistent. These results support a model of localized rather than systemic processes driving variation in joint shape. While more remains to be elucidated about the specifics of articular surface morphogenesis, these findings advance our understanding of the systems of variance generation at play during development and growth of our definitive joint morphology.

Morphological trends in arcade shape and size in Middle Pleistocene Homo.

Middle Pleistocene fossil hominins, often summarized as Homo heidelbergensis sensu lato, are difficult to interpret due to a fragmentary fossil record and ambiguous combinations of primitive and derived characters. Here, we focus on one aspect of facial shape and analyze shape variation of the dental arcades of these fossils together with other Homo individuals. Three-dimensional landmark data were collected on computed tomographic scans and surface scans of Middle Pleistocene fossil hominins (n = 8), Homo erectus s.l. (n = 4), Homo antecessor (n = 1), Homo neanderthalensis (n = 13), recent (n = 52) and fossil (n = 19) Homo sapiens. To increase sample size, we used multiple multivariate regression to reconstruct complementary arches for isolated mandibles, and explored size and shape differences among maxillary arcades. The shape of the dental arcade in H. erectus s.l. and H. antecessor differs markedly from both Neanderthals and H. sapiens. The latter two show subtle but consistent differences in arcade length and width. Shape variation among Middle Pleistocene fossil hominins does not exceed the amount of variation of other species, but includes individuals with more primitive and more derived morphology, all more similar to Neanderthals and H. sapiens than to H. erectus s.l. Although our results cannot reject the hypothesis that the Middle Pleistocene fossil hominins belong to a single species, their shape variation comprises a more primitive morph that represents a likely candidate for the shape of the last common ancestor of Neanderthals and H. sapiens, and a more derived morph resembling Neanderthals. The arcade shape difference between Neanderthals and H. sapiens might be related to different ways to withstand mechanical stress.

Rapid automated landmarking for morphometric analysis of three-dimensional facial scans.

Automated phenotyping is essential for the creation of large, highly standardized datasets from anatomical imaging data. Such datasets can support large-scale studies of complex traits or clinical studies related to precision medicine or clinical trials. We have developed a method that generates three-dimensional landmark data that meet the requirements of standard geometric morphometric analyses. The method is robust and can be implemented without high-performance computing resources. We validated the method using both direct comparison to manual landmarking on the same individuals and also analyses of the variation patterns andoutlier patterns in a large dataset of automated and manual landmark data. Direct comparison of manual and automated landmarks reveals that automated landmark data are less variable, but more highly integrated and reproducible. Automated data produce covariation structure that closely resembles that of manual landmarks. We further find that while our method does produce some landmarking errors, they tend to be readily detectable and can be fixed by adjusting parameters used in the registration and control-point steps. Data generated using the method described here have been successfully used to study the genomic architecture of facial shape in two different genome-wide association studies of facial shape.

Developmental Changes in Morphology of the Middle and Posterior External Cranial Base in Modern Homo sapiens.

The basicranium has been described as phylogenetically informative, developmentally stable, and minimally affected by external factors and consequently plays an important role in cranial size and shape in subadult humans. Here basicranial variation of subadults from several modern human populations was investigated and the impact of genetic relatedness on basicranial morphological similarities was investigated. Three-dimensional landmark data were digitized from subadult basicrania from seven populations. Published molecular data on short tandem repeats were statistically compared to morphological data from three ontogenetic stages. Basicranial and temporal bone morphology both reflect genetic distances in childhood and adolescence (5–18 years), but not in infancy (<5 years). The occipital bone reflects genetic distances only in adolescence (13–18 years). The sphenoid bone does not reflect genetic distances at any ontogenetic stage but was the most diagnostic region evaluated, resulting in high rates of correct classification among populations. These results suggest that the ontogenetic processes driving basicranial development are complex and cannot be succinctly summarized across populations or basicranial regions. However, the fact that certain regions reflect genetic distances suggests that the morphology of these regions may be useful in reconstructing population history in specimens for which direct DNA evidence is unavailable, such as archaeological sites.

Assessing the relationship between fluctuating asymmetry and cause of death in skeletal remains: A test of the developmental origins of health and disease hypothesis

This study examines the relationship between craniofacial fluctuating asymmetry and cause of death in an identified skeletal collection. This study tests the Developmental Origins of Health and Disease hypothesis using fluctuating asymmetry as the measure of developmental instability. The skeletal sample used in this study comes from Lisbon, Portugal, and individuals in the sample were born between 1806 and 1935. This represents a period during which Lisbon was beginning to undergo the modern health transition, in which mortality from infectious disease began to decline while mortality from degenerative diseases began to increase. Approximately equal numbers of individuals in the sample died from infectious diseases, such as tuberculosis, and from degenerative diseases. Fluctuating asymmetry is examined using three-dimensional landmark data collected from 392 individuals with documented causes of death. Landmark data may provide a more robust measure of fluctuating asymmetry, although it has not often been used in studies of fluctuating asymmetry in human skeletal samples. The results of the study show that individuals who died from degenerative diseases have higher rates of fluctuating asymmetry compared to individuals who died from infectious diseases. Males also exhibit higher rates of fluctuating asymmetry compared to females. The results of this study confirm earlier findings that early development has a significant impact on adult health outcomes. Furthermore, the results suggest that fluctuating asymmetry in skeletal samples may offer a means of testing the Developmental Origins of Health and Disease hypothesis.

Allometry and function of primate pelves

Functional inference of locomotion in fossil primate pelves is difficult due to the effects of body size, phylogeny, and other non‐locomotor functions on pelvic shape. This study examines size and scaling of pelvic anatomy using phylogenetic comparative methods to determine aspects of the pelvis that may be affected by the loading requirements of both locomotor mode and body size. Three‐dimensional landmark data were collected on 787 pelves from 40 taxa ranging in mean body size from 0.25 to 270 kg. Ten linear dimensions were calculated and phylogenetic reduced major axis regressions were performed for each pelvic dimension on overall pelvic size at several taxonomic levels. At the primate‐wide level, tests of the null hypothesis of isometric scaling of pelvic dimensions were rejected for some ilium dimensions and for the cross‐sectional areas of the ilium and ischium, dimensions that have been suggested to be strongly related to the effects of locomotor loading. The height of the lower ilium scales with negative allometry, while ilium width and the cross‐sectional area of the ilium and ischium all scale with strong positive allometry; tests for Catarrhini, Platyrrhini, Lemuriformes, and Lorisiformes support the primate‐wide results (all results significant at p&lt;0.05). These results suggest that as body size increases—and forces due to loading increase—the height of the ilium decreases to mitigate bending stresses, while the areas of the ilium and ischium increase to reduce bone strain. Primate pelvic anatomy is likely adapted to the combined effects of loading due to large body size and locomotion.Grant Funding Source: NSF‐BCS #075–2575, The Leakey Foundation

Evolvability of the Primate Pelvic Girdle

The ilium and ischiopubic bones of the pelvis arise from different regulatory pathways, and as a result, they may be modular in their organization such that features on one bone may be morphologically integrated with each other, but not with features on the other pelvic bone. Modularity at this gross level of organization can act to increase the ability of these structures to respond to selection pressures (i.e., their evolvability). Furthermore, recent work has suggested that the evolution of the human pelvis was facilitated by low levels of integration and high levels of evolvability relative to other African apes. However, the extent of morphological integration and modularity of the bones of the pelvic girdle is not well understood, especially across the entire order of primates. Therefore, the hypothesis that the ilium and ischiopubis constitute separate modules was tested using three-dimensional landmark data that were collected from 752 pelves from 35 primate species. In addition, the hypothesis that the human pelvis demonstrates greatest evolvability was tested by comparing it to all other primates. The results demonstrate that regardless of phylogeny and locomotor function, the primate pelvis as a whole is characterized by low levels of overall integration and high levels of evolvability. In addition, the results support the developmental hypothesis of separate ilium and ischiopubis modular units. Finally, all primates, including humans, apparently share a common pattern of integration, modularity, and evolvability in the pelvis.

Bootstrap inference for mean reflection shape and size-and-shape with three-dimensional landmark data

Working within the framework of a multi-dimensional scaling approach to shape analysis, we develop bootstrap methods for inference about mean reflection shape and size-and-shape based on labelled landmark data. The approach is developed in general dimensions though we focus on the three-dimensional case. We consider two pivotal statistics which we use to construct bootstrap confidence regions for the mean reflection shape or size-and-shape, and present simulation results which show that these statistics perform well in a variety of examples. We also suggest regularized versions of the test statistics that are suitable for more challenging cases where sample size is not sufficiently large in relation to the number of landmarks and present numerical results confirming that regularization indeed leads to better performance. An algorithm for producing a graphical representation of the confidence region for the mean reflection shape is presented and applied in an example involving molecular dynamics simulation data.

Phylogenetic morphometrics (II): algorithms for landmark optimization.

This paper describes algorithms for optimizing two- or three-dimensional landmark data onto trees directly. The method is based on a first approximation using grids, and subsequent iterative refinement of the initial point estimates. Details of the implementation are discussed, as well as an empirical example. © The Willi Hennig Society 2010.

Relationship of cranial robusticity to cranial form, geography and climate in Homo sapiens

Variation in cranial robusticity among modern human populations is widely acknowledged but not well-understood. While the use of "robust" cranial traits in hominin systematics and phylogeny suggests that these characters are strongly heritable, this hypothesis has not been tested. Alternatively, cranial robusticity may be a response to differences in diet/mastication or it may be an adaptation to cold, harsh environments. This study quantifies the distribution of cranial robusticity in 14 geographically widespread human populations, and correlates this variation with climatic variables, neutral genetic distances, cranial size, and cranial shape. With the exception of the occipital torus region, all traits were positively correlated with each other, suggesting that they should not be treated as individual characters. While males are more robust than females within each of the populations, among the independent variables (cranial shape, size, climate, and neutral genetic distances), only shape is significantly correlated with inter-population differences in robusticity. Two-block partial least-squares analysis was used to explore the relationship between cranial shape (captured by three-dimensional landmark data) and robusticity across individuals. Weak support was found for the hypothesis that robusticity was related to mastication as the shape associated with greater robusticity was similar to that described for groups that ate harder-to-process diets. Specifically, crania with more prognathic faces, expanded glabellar and occipital regions, and (slightly) longer skulls were more robust than those with rounder vaults and more orthognathic faces. However, groups with more mechanically demanding diets (hunter-gatherers) were not always more robust than groups practicing some form of agriculture.

Genetic variation in baboon craniofacial sexual dimorphism.

Sexual dimorphism is a widespread phenomenon and contributes greatly to intraspecies variation. Despite a long history of active research, the genetic basis of dimorphism for complex traits remains unknown. Understanding the sex-specific differences in genetic architecture for cranial traits in a highly dimorphic species could identify possible mechanisms through which selection acts to produce dimorphism. Using distances calculated from three-dimensional landmark data from CT scans of 402 baboon skulls from a known genealogy, we estimated genetic variance parameters in both sexes to determine the presence of gene-by-sex (G x S) interactions and X-linked heritability. We hypothesize that traits exhibiting the greatest degree of sexual dimorphism (facial traits in baboons) will demonstrate either stronger G x S interactions or X-linked effects. We found G x S interactions and X-linked effects for a few measures that span the areas connecting the face to the neurocranium but for no traits restricted to the face. This finding suggests that facial traits will have a limited response to selection for further evolution of dimorphism in this population. We discuss the implications of our results with respect to the origins of cranial sexual dimorphism in this baboon sample, and how the genetic architecture of these traits affects their potential for future evolution.

Which cranial regions reflect molecular distances reliably in humans? Evidence from three‐dimensional morphology

Knowledge of the degree to which various subsets of morphological data reflect molecular relationships is crucial for studies attempting to estimate genetic relationships from patterns of morphological variation. This study assessed the phylogenetic utility of six different human cranial regions, plus the entire cranium. Three-dimensional landmark data were collected for 83 landmarks from samples of skulls from 14 modern human populations. The data were subsequently divided into anatomical regions: basicranium, upper face, mandible, temporal bone, upper jaw, cranial vault, and a subset of points from around the entire cranium. Depictions of population molecular distances were calculated using published data on microsatellites for the same or closely related populations. Distances based on morphological variation of each of the anatomical regions were compared with molecular distances, and the correlations assessed. The morphology of the basicranium, temporal bone, upper face, and entire cranium demonstrated the highest correlations with molecular distances. The morphology of the mandible, upper jaw, and cranial vault, as measured here, were not significantly correlated with molecular distances. As the three-dimensional morphology of the temporal bone, upper face, basicranium, and entire cranium appear to consistently reflect genetic relationships in humans, especially with more reliability than the cranial vault, it would be preferable to focus on these regions when attempting to determine the genetic relationships of human specimens with no molecular data.

Discriminant function sexing of the mandible of Indigenous South Africans

South Africa currently has a high homicide rate. This results in a large number of unidentified bodies being recovered each year, many of which are referred to the forensic examiner. This situation has resulted in considerable growth of forensic anthropological research devoted to devising standards for specific application in South African medico-legal investigations. The standards suitable for Black South Africans now encompass a wide variety of skeletal elements (e.g. cranium, humerus, pelvis, femur, patella, talus, calcaneus), each with differing degrees of accuracy. Apart from a preliminary investigation of the Zulu local population, however, we note that there appears to be no established metric mandible discriminant function standards for sex determination in this population. The purpose of the present study is to undertake a comprehensive analysis of sexual dimorphism in the mandible of Black South Africans, incorporating individuals from a selection of the larger local population groupings; the primary aim is to produce a series of metrical standards for the determination of sex. The sample analyzed comprises 225 non-pathological mandibles of Black South African individuals drawn from the R.A. Dart Collection. Nine linear measurements, obtained from mathematically transformed three-dimensional landmark data, are analyzed using basic univariate statistics and discriminant function analyses. All of the measurements examined are found to be sexually dimorphic; the dimensions of the ramus and corpus lengths are most dimorphic. The sex classification accuracy of the discriminant functions ranged from 70.7 to 77.3% for the univariate method, 81.8% for the stepwise method, and 63.6 to 84% for the direct method. We conclude that the mandible is a very useful element for sex determination in this population.

Mandibular Morphology as an Indicator of Human Subadult Age: Interlandmark Approaches*

The dentition is widely recognized as the set of developmental markers that appear to show the least variability against chronological age; these markers are thus widely used in forensic anthropological investigations. As a possible alternative, we investigate here the potential of mandibular morphology as a developmental marker for estimating age at death in subadults. The sample analyzed comprises 79 known age and sex subadult individuals of South African Bantu and African American origin. Linear measurements of ramus height were obtained from the mathematical conversion of three-dimensional landmark data. A series of regression analyses were then performed to predict age by using the measurement of ramus height; results were cross-validated using a jackknife procedure. Our results show that ramus height can be used to predict age in the subadult skeleton with accuracy, closely approaching that of standards based on the dentition (standard error rates are between +/-1.1 years and +/-2.4 years).

Determination of sex in south african blacks by discriminant function analysis of mandibular linear dimensions : A preliminary investigation using the zulu local population.

The determination of sex is a critical component in forensic anthropological investigation. The literature attests to numerous metrical standards, each utilizing diffetent skeletal elements, for sex determination in South A frican Blacks. Metrical standards are popular because they provide a high degree of expected accuracy and are less error-prone than subjective nonmetric visual techniques. We note, however, that there appears to be no established metric mandible discriminant function standards for sex determination in this population.We report here on a preliminary investigation designed to evaluate whether the mandible is a practical element for sex determination in South African Blacks. The sample analyzed comprises 40 nonpathological Zulu individuals drawn from the R.A. Dart Collection. Ten linear measurements, obtained from mathematically trans-formed three-dimensional landmark data, are analyzed using basic univariate statistics and discriminant function analyses. Seven of the 10 measurements examined are found to be sexually dimorphic; the dimensions of the ramus are most dimorphic. The sex classification accuracy of the discriminant functions ranged from 72.5 to 87.5% for the univariate method, 92.5% for the stepwise method, and 57.5 to 95% for the direct method. We conclude that the mandible is an extremely useful element for sex determination in this population.

Three-dimensional technology for linear morphological studies: a re-examination of cranial variation in four southern African indigenous populations

In order to compare linear dimensions made by traditional anthropometric techniques, and those obtained from three-dimensional coordinates, samples of four indigenous southern African populations were analysed. Linear measurements were obtained using mathematically transformed, three-dimensional landmark data on 207 male crania of Cape Nguni, Natal Nguni, Sotho and Shangaan. Univariate comparisons for accuracy of the transformed linear data were made with those in a traditional linear study by de Villiers (The Skull of the South African Negro: A Biometrical and Morphological Study. Witwatersrand University Press, Johannesburg) on similar samples and equivalent landmarks. Comparisons were not made with her Penrose (Ann Eugenics 18 (1954) 337) analysis as an apparently anomalous ‘shape’–‘size’ statistic was found. The univariate comparisons demonstrated that accurate linear measurements could be derived from three-dimensional data, showing that it is possible to simultaneously obtain data for three-dimensional geometric ‘shape’ and linear inter-landmark analyses. Using Penrose and canonical variates analyses of the transformed three-dimensional inter-landmark measurements, similar population distances were found for the four indigenous southern African populations. The inter-population distance relationships took the form of three separated pairs of distances, with the within-pair distances very similar in size. The cranial features of the four populations were found to be overall very similar morphometrically. However the populations were each shown by CVA to have population specific features, and using discriminant analyses 50% or more of the individual crania (with the exception of the Sotho) could be referred to their correct populations.

Computing the Uniform Component of Shape Variation

Any change in shape of a configuration of landmark points in two or three dimensions includes a uniform component, a component that is a wholly linear (affine) transformation. The formulas for estimating this component have been standardized for two-dimensional data but not for three-dimensional data. We suggest estimating the component by way of the complementarity between the uniform component and the space of partial warps. The component can be estimated by regression in either one space or the other: regression on the partial warps, followed by their removal, or regression on a basis for the uniform component itself. Either of the new methods can be used for both two- and three-dimensional landmark data and thus generalize Bookstein's (1996, pages 153–168 in Advances in morphometrics [L. F. Marcus et al., eds.], Plenum, New York) linearized Procrustes formula for estimating the uniform component in two dimensions.

Computing the uniform component of shape variation.

Any change in shape of a configuration of landmark points in two or three dimensions includes a uniform component, a component that is a wholly linear (affine) transformation. The formulas for estimating this component have been standardized for two-dimensional data but not for three-dimensional data. We suggest estimating the component by way of the complementarity between the uniform component and the space of partial warps. The component can be estimated by regression in either one space or the other: regression on the partial warps, followed by their removal, or regression on a basis for the uniform component itself. Either of the new methods can be used for both two- and three-dimensional landmark data and thus generalize Bookstein's (1996, pages 153-168 in Advances in morphometrics [L. F. Marcus et al., eds.], Plenum, New York) linearized Procrustes formula for estimating the uniform component in two dimensions.

Three-dimensional Bolton-Brush Growth Study landmark data: ontogeny and sexual dimorphism of the Bolton standards cohort.

The treatment of craniofacial reconstructive surgery patients may benefit from comparison to average referent three-dimensional landmark data. These data may be useful for diagnosis, treatment planning, prosthetic design, or outcomes assessment. With regard to subadult patients, we hypothesize that the pattern of ontogenetic shape change of same sex, same ethnicity, referent populations will show gross uniformity. We present a preliminary shape analysis of 50 three-dimensional landmarks derived from 317 Bolton-Brush Growth Study biorthogonal image pairs. We determine which landmarks can be collected from scanned radiographs reliably by four operators for the precisely locatable points, ontogenetic trends in landmark configuration shape change, and patterns of sexual dimorphism. Participants were Bolton standards individuals (16 male and 16 female) who contributed biplane cephalograms seven or more times with annual or greater spacing between ages 3 and 18 years. After removing outliers, we searched for ontogenetic heterogeneity, including sexual dimorphism and within sex-specific Procrustes coordinate shape spaces. A cut-off of 4.3-mm interoperator error left 32 landmarks in our analysis. Three different approaches (principal component analysis, age-trend analysis, and principal components of age residuals) all found no patterns of individual variation around sex-specific average trends of shape change. Male shape change peaks at age 15, a correlate of the growth spurt. Simultaneous frontal and lateral anatomic landmark identification improves three-dimensional localization reliability. Three-dimensional craniodental shape change from ages 8 to 18 within the Bolton standards presents little heterogeneity. Considerations of ethnicity aside, these may be initial grounds for use of these data as a normative referent.