Form, Function, and Geometric Morphometrics

The potential of statistical shape modelling for geometric morphometric analysis of human teeth in archaeological research

This paper introduces statistical shape modelling (SSM) for use in osteoarchaeology research. SSM is a full field, multi-material analytical technique, and is presented as a supplementary geometric morphometric (GM) tool. Lower mandibular canines from two archaeological populations and one modern population were sampled, digitised using micro-CT, aligned, registered to a baseline and statistically modelled using principal component analysis (PCA). Sample material properties were incorporated as a binary enamel/dentin parameter. Results were assessed qualitatively and quantitatively using anatomical landmarks. Finally, the technique’s application was demonstrated for inter-sample comparison through analysis of the principal component (PC) weights. It was found that SSM could provide high detail qualitative and quantitative insight with respect to archaeological inter- and intra-sample variability. This technique has value for archaeological, biomechanical and forensic applications including identification, finite element analysis (FEA) and reconstruction from partial datasets.

Development and Assessment of Fully Automated and Globally Transitive Geometric Morphometric Methods, With Application to a Biological Comparative Dataset With High Interspecific Variation

Automated geometric morphometric methods are promising tools for shape analysis in comparative biology, improving researchers' abilities to quantify variation extensively (by permitting more specimens to be analyzed) and intensively (by characterizing shapes with greater fidelity). Although use of these methods has increased, published automated methods have some notable limitations: pairwise correspondences are frequently inaccurate and pairwise mappings are not globally consistent (i.e., they lack transitivity across the full sample). Here, we reassess the accuracy of published automated methods-cPDist (Boyer et al. Proc Nat Acad Sci 108 () 18221-18226) and auto3Dgm (Boyer et al.: Anat Rec 298 () 249-276)-and evaluate several modifications to these methods. We show that a substantial percentage of alignments and pairwise maps between specimens of dissimilar geometries were inaccurate in the study of Boyer et al. (Proc Nat Acad Sci 108 () 18221-18226), despite a taxonomically partitioned variance structure of continuous Procrustes distances. We show these inaccuracies are remedied using a globally informed methodology within a collection of shapes, rather than relying on pairwise comparisons (c.f. Boyer et al.: Anat Rec 298 () 249-276). Unfortunately, while global information generally enhances maps between dissimilar objects, it can degrade the quality of correspondences between similar objects due to the accumulation of numerical error. We explore a number of approaches to mitigate this degradation, quantify their performance, and compare the generated pairwise maps (and the shape space characterized by these maps) to a "ground truth" obtained from landmarks manually collected by geometric morphometricians. Novel methods both improve the quality of the pairwise correspondences relative to cPDist and achieve a taxonomic distinctiveness comparable to auto3Dgm. Anat Rec, 301:636-658, 2018. © 2017 Wiley Periodicals, Inc.

Cranial Indicators Identified for Peak Incidence of Otitis Media

Acute otitis media (AOM) is one of the most common pediatric conditions worldwide. Peak age of occurrence for AOM has been identified within the first postnatal year and it remains frequent until approximately six postnatal years. Morphological differences between adults and infants in the cartilaginous Eustachian tube (CET) and associated structures may be responsible for development of this disease yet few have investigated normal growth trajectories. We tested hypotheses on coincidence of skeletal growth changes and known ages of peak AOM occurrence. Growth was divided into five dental eruption stages ranging from edentulous neonates (Stage 1) to adults with erupted third maxillary molars (Stage 5). A total of 32 three-dimensional landmarks were used and Generalized Procrustes Analysis was performed. Next, we performed principal components analysis and calculated univariate measures. It was found that growth change in Stage 1 was the most rapid and comprised the largest amount of overall growth in upper respiratory tract proportions (where time is represented by the natural logarithmic transformation of centroid size). The analysis of univariate measures showed that Stage 1 humans did indeed possess the relatively shortest and most horizontally oriented CET's with the greatest amount of growth change occurring at the transition to Stage 2 (eruption of deciduous dentition at five postnatal months, commencing peak AOM incidence) and ceasing by Stage 3 (approximately six postnatal years). Skeletal indicators appear related to peak ages of AOM incidence and may contribute to understanding of a nearly ubiquitous human disease. Anat Rec, 2017. © 2017 Wiley Periodicals, Inc. Anat Rec, 300:1721-1740, 2017. © 2017 Wiley Periodicals, Inc.

Evolution of the hominin knee and ankle

The dispersal of the genus Homo out of Africa approximately 1.8 million years ago (Ma) has been understood within the context of changes in diet, behavior, and bipedal locomotor efficiency. While various morphological characteristics of the knee and ankle joints are considered part of a suite of traits indicative of, and functionally related to, habitual bipedal walking, the timing and phylogenetic details of these morphological changes remain unclear. To evaluate the timing of knee and ankle joint evolution, we apply geometric morphometric methods to three-dimensional digital models of the proximal and distal tibiae of fossil hominins, Holocene Homo sapiens, and extant great apes. Two sets of landmarks and curve semilandmarks were defined on each specimen. Because some fossils were incomplete, digital reconstructions were carried out independently to estimate missing landmarks and semilandmarks. Group shape variation was evaluated through shape-and form-space principal component analysis and fossil specimens were projected to assess variation in the morphological space computed from the extant comparative sample. We show that a derived proximal tibia (knee) similar to that seen in living H. sapiens evolved with early Homo at ∼2 Ma. In contrast, derived characteristics in the distal tibia appear later, probably with the arrival of Homo erectus. These results suggest a dissociation of the morphologies of the proximal and distal tibia, perhaps indicative of divergent functional demands and, consequently, selective pressures at these joints. It appears that longer distance dispersals that delivered the Dmanisi hominins to Georgia by 1.8 Ma and H. erectus to east-southeast Asia by 1.6 Ma were facilitated by the evolution of a morphologically derived knee complex comparable to that of recent humans and an ankle that was morphologically primitive. This research sets the foundation for additional paleontological, developmental, and functional research to better understand the mechanisms underlying the evolution of bipedalism.

Trabecular mapping: Leveraging geometric morphometrics for analyses of trabecular structure

OBJECTIVES

Trabecular microstructure of limb bone epiphyses has been used to elucidate the relationship between skeletal form and behavior among mammals. Such studies have often relied on the analysis of a single volume of interest (VOI). Here we present a method for evaluating variation in bone microstructure across articular surfaces by leveraging sliding semilandmarks.

METHODS

Two samples were used to demonstrate the proposed methodology and test the hypothesis that microstructural variables are homogeneously distributed: tali from two ape genera (Pan and Pongo, n = 9) and modern human distal femora (n = 10). Sliding semilandmarks were distributed across articular surfaces and used to locate the position of multiple VOIs immediately deep to the cortical shell. Trabecular bone properties were quantified using the BoneJ plugin for ImageJ. Nonparametric MANOVA tests were used to make group comparisons and differences were explored using principal components analysis and visualized using color maps.

RESULTS

Tests reveal that trabecular parameters are not distributed homogeneously and identify differences between chimpanzee and orangutan tali with regards to trabecular spacing and degree of anisotropy, with chimpanzee tali being more anisotropic and having more uniformly spaced trabeculae. Human males and females differed in the pattern of trabecular spacing with males having more uniform trabecular spacing across the joint surface.

CONCLUSIONS

The proposed procedure quantifies variation in trabecular bone parameters across joint surfaces and allows for meaningful statistical comparisons between groups of interest. Consequently it holds promise to help elucidate links between trabecular bone structure and animal behavior.

Diachronic changes in size and shape of human proximal tibia in Central Europe during the latest 1200 years

During the past twelve centuries, the stature of Central European inhabitants has increased significantly with corresponding changes in the size of lower limb bones. The aim of our study was to determine whether these changes have occurred strictly in relation to size or if the shape of skeletal structures has been altered simultaneously. Diachronic size and shape changes in the proximal part of tibia in a Central European population (Czech Republic) were studied using geometric morphometrics (principal components analysis, Hotelling's test, linear discriminant analysis). The study sample consisted of 183 three-dimensional (3D) models of adult tibiae dating to the early Middle Ages (N=65), early 20th century (N=60), and from a modern Czech population (N=57). A positive secular trend in size manifested only between the two modern Czech populations (the 20th century vs. the 21st century), a time range shorter than one century. By contrast, landmark-based shape analyses revealed significant differences in tibial morphology over the three periods covered in the study. In particular, progressive changes were observed in the position of tibial tuberosity (shifted medially), the inclination of the line connecting tuberosity with anterior edge of the tibial plateau (sloped down), the reshaping of the lower back condyle boundary (shifted posteriorly), and reshaping of the medial contour of the medial condyle (shifted anteriorly). Changes in the shape of the proximal tibial extremity across the chronologically distinct groups indicated the existence of discreet but convincing microevolutionary trends involving this anatomical structure.

Multiple generalist morphs of Lake Trout: Avoiding constraints on the evolution of intraspecific divergence?

A generalist strategy, as an adaptation to environmental heterogeneity, is common in Arctic freshwater systems, often accompanied, however, by intraspecific divergence that promotes specialization in niche use. To better understand how resources may be partitioned in a northern system that supports intraspecific diversity of Lake Trout, trophic niches were compared among four shallow‐water morphotypes in Great Bear Lake (N65^° 56′ 39″, W120^° 50′ 59″). Bayesian mixing model analyses of stable isotopes of carbon and nitrogen were conducted on adult Lake Trout. Major niche overlap in resource use among four Lake Trout morphotypes was found within littoral and pelagic zones, which raises the question of how such polymorphism can be sustained among opportunistic generalist morphotypes. Covariances of our morphological datasets were tested against δ¹³C and δ¹⁵N values. Patterns among morphotypes were mainly observed for δ¹⁵N. This link between ecological and morphological differentiation suggested that selection pressure(s) operate at the trophic level (δ¹⁵N), independent of habitat, rather than along the habitat‐foraging opportunity axis (δ¹³C). The spatial and temporal variability of resources in Arctic lakes, such as Great Bear Lake, may have favored the presence of multiple generalists showing different degrees of omnivory along a weak benthic–pelagic gradient. Morphs 1–3 had more generalist feeding habits using both benthic and pelagic habitats than Morph 4, which was a top‐predator specialist in the pelagic habitat. Evidence for frequent cannibalism in Great Bear Lake was found across all four morphotypes and may also contribute to polymorphism. We suggest that the multiple generalist morphs described here from Great Bear Lake are a unique expression of diversity due to the presumed constraints on the evolution of generalists and contrast with the development of multiple specialists, the standard response to intraspecific divergence.

Surface Model and Tomographic Archive of Fossil Primate and Other Mammal Holotype and Paratype Specimens of the Ditsong National Museum of Natural History, Pretoria, South Africa

Nearly a century of paleontological excavation and analysis from the cave deposits of the Cradle of Humankind UNESCO World Heritage Site in northeastern South Africa underlies much of our understanding of the evolutionary history of hominins, other primates and other mammal lineages in the late Pliocene and early Pleistocene of Africa. As one of few designated fossil repositories, the Plio-Pleistocene Palaeontology Section of the Ditsong National Museum of Natural History (DNMNH; the former Transvaal Museum) curates much of the mammalian faunas recovered from the fossil-rich deposits of major South African hominin-bearing localities, including the holotype and paratype specimens of many primate, carnivore, and other mammal species (Orders Primates, Carnivora, Artiodactyla, Eulipotyphla, Hyracoidea, Lagomorpha, Perissodactyla, and Proboscidea). Here we describe an open-access digital archive of high-resolution, full-color three-dimensional (3D) surface meshes of all 89 non-hominin holotype, paratype and significant mammalian specimens curated in the Plio-Pleistocene Section vault. Surface meshes were generated using a commercial surface scanner (Artec Spider, Artec Group, Luxembourg), are provided in formats that can be opened in both open-source and commercial software, and can be readily downloaded either via an online data repository (MorphoSource) or via direct request from the DNMNH. In addition to providing surface meshes for each specimen, we also provide tomographic data (both computerized tomography [CT] and microfocus [microCT]) for a subset of these fossil specimens. This archive of the DNMNH Plio-Pleistocene collections represents the first research-quality 3D datasets of African mammal fossils to be made openly available. This simultaneously provides the paleontological community with essential baseline information (e.g., updated listing and 3D record of specimens in their current state of preservation) and serves as a single resource of high-resolution digital data that improves collections accessibility, reduces unnecessary duplication of efforts by researchers, and encourages ongoing imaging-based paleobiological research across a range of South African non-hominin fossil faunas. Because the types, paratypes, and key specimens include globally-distributed mammal taxa, this digital archive not only provides 3D morphological data on taxa fundamental to Neogene and Quaternary South African palaeontology, but also lineages critical to research on African, other Old World, and New World paleocommunities. With such a broader impact of the DNMNH 3D data, we hope that establishing open access to this digital archive will encourage other researchers and institutions to provide similar resources that increase accessibility to paleontological collections and support advanced paleobiological analyses.