Bolstering geometric morphometrics sample sizes with damaged and pathologic specimens: Is near enough good enough?

Assessing the application of landmark-free morphometrics to macroevolutionary analyses

The study of phenotypic evolution has been transformed in recent decades by methods allowing precise quantification of anatomical shape, in particular 3D geometric morphometrics. While this effectiveness of geometric morphometrics has been demonstrated by thousands of studies, it generally requires manual or semi-automated landmarking, which is time-consuming, susceptible to operator bias, and limits comparisons across morphologically disparate taxa. Emerging automated methods, particularly landmark-free techniques, offer potential solutions, but these approaches have thus far been primarily applied to closely related forms. In this study, we explore the utility of automated, landmark-free approaches for macroevolutionary analyses. We compare an application of Large Deformation Diffeomorphic Metric Mapping (LDDMM) known as Deterministic Atlas Analysis (DAA) with a high-density geometric morphometric approach, using a dataset of 322 mammals spanning 180 families. Initially, challenges arose from using mixed modalities (computed tomography (CT) and surface scans), which we addressed by standardising the data by using Poisson surface reconstruction that creates watertight, closed surfaces for all specimens. After standardisation, we observed a significant improvement in the correspondence between patterns of shape variation measured using manual landmarking and DAA, although differences emerged, especially for Primates and Cetacea. We further evaluated the downstream effects of these differences on macroevolutionary analyses, finding that both methods produced comparable but varying estimates of phylogenetic signal, morphological disparity and evolutionary rates. Our findings highlight the potential of landmark-free approaches like DAA for large scale studies across disparate taxa, owing to their enhanced efficiency. However, they also reveal several challenges that should be addressed before these methods can be widely adopted. In this context, we outline these issues, propose solutions based on existing literature, and identify potential avenues for further research. We argue that by incorporating these improvements, the application of landmark-free analyses could be expanded, thereby enhancing the scope of morphometric studies and enabling the analysis of larger and more diverse datasets.

Variation in Craniodental Pathologies Among Cercopithecoid Primates

Pathologies of the skull and teeth are well documented for many human populations, but there are fewer studies of other primates. We contrast lesion prevalence and patterning among cercopithecoid primates and map variation onto socioecological variables. We compare craniodental lesions in six species: Nasalis larvatus (n = 54), Colobus polykomos (n = 64), Cercopithecus mitis (n = 65), Macaca fascicularis (n = 109), Theropithecus gelada (n = 13), and Papio anubis (n = 76). One of us (C.A.K.) evaluated each adult skull for multiple lesion types using standard criteria. We also tested for a relationship between lesion prevalence and cranial suture fusion (age proxy). We used nonparametric tests for sex and species differences as well as pathology co-occurrence in SPSS. Socioecological data come from previous studies. Sex differences in lesion prevalence were only detected in P. anubis. Within taxa, some lesion types co-occurred. In Macaca, the presence of caries was associated with several other lesion types. Pulp cavity exposure co-occurred with TMJ osteoarthritis in multiple taxa. Among taxa, male P. anubis had higher lesion prevalences, particularly related to the anterior dentition and facial trauma. Because we did not detect a relationship between suture fusion and lesion prevalence, we propose that craniodental lesions may also be influenced by socioecological variables such as group composition and ratio of fruit to leaves in the diet. Our findings suggest that pain from pulp cavity exposure and related dental infections may alter chewing biomechanics and contribute to onset of TMJ osteoarthritis in nonhuman primates, as seen in humans. Further, we suggest that higher lesion prevalence in male baboons is likely related to male-male competition. Skeletal lesion analysis provides useful insight into primate socioecology, particularly for rare or difficult-to-observe phenomena, and provides additional biological context for our own species.

Maxillary morphology of chimpanzees: Captive versus wild environments

Morphological studies typically avoid using osteological samples that derive from captive animals because it is assumed that their morphology is not representative of wild populations. Rearing environments indeed differ between wild and captive individuals. For example, mechanical properties of the diets provided to captive animals can be drastically different from the food present in their natural habitats, which could impact cranial morphology and dental health. Here, we examine morphological differences in the maxillae of wild versus captive chimpanzees (Pan troglodytes) given the prominence of this species in comparative samples used in human evolution research and the key role of the maxilla in such studies. Size and shape were analysed using three-dimensional geometric morphometric methods based on computed tomography scans of 94 wild and 30 captive specimens. Captive individuals have on average larger and more asymmetrical maxillae than wild chimpanzees, and significant differences are present in their maxillary shapes. A large proportion of these shape differences are attributable to static allometry, but wild and captive specimens still differ significantly from each other after allometric size adjustment of the shape data. Levels of shape variation are higher in the captive group, while the degree of size variation is likely similar in our two samples. Results are discussed in the context of ontogenetic growth trajectories, changes in dietary texture, an altered social environment, and generational differences. Additionally, sample simulations show that size and shape differences between chimpanzees and bonobos (Pan paniscus) are exaggerated when part of the wild sample is replaced with captive chimpanzees. Overall, this study confirms that maxillae of captive chimpanzees should not be included in morphological or taxonomic analyses when the objective is to characterise the species.

Shape variation and sex differences of the adult human mandible evaluated by geometric morphometrics

In cases of osseous defects, knowledge of the anatomy, and its age and sex-related variations, is essential for reconstruction of normal morphology. Here, we aimed at creating a 3D atlas of the human mandible in an adult sample using dense landmarking and geometric morphometrics. We segmented 50 male and 50 female mandibular surfaces from CBCT images (age range: 18.9-73.7 years). Nine fixed landmarks and 510 sliding semilandmarks were digitized on the mandibular surface, and then slid by minimizing bending energy against the average shape. Principal component analysis extracted the main patterns of shape variation. Sexes were compared with permutation tests and allometry was assessed by regressing on the log of the centroid size. Almost 49 percent of shape variation was described by the first three principal components. Shape variation was related to width, height and length proportions, variation of the angle between ramus and corpus, height of the coronoid process and inclination of the symphysis. Significant sex differences were detected, both in size and shape. Males were larger than females, had a higher ramus, more pronounced gonial angle, larger inter-gonial width, and more distinct antegonial notch. Accuracy of sexing based on the first two principal components in form space was 91 percent. The degree of edentulism was weakly related to mandibular shape. Age effects were not significant. The resulting atlas provides a dense description of mandibular form that can be used clinically as a guide for planning surgical reconstruction.

Facing the facts: adaptive trade-offs along body size ranges determine mammalian craniofacial scaling

The mammalian cranium (skull without lower jaw) is representative of mammalian diversity and is thus of particular interest to mammalian biologists across disciplines. One widely retrieved pattern accompanying mammalian cranial diversification is referred to as 'craniofacial evolutionary allometry' (CREA). This posits that adults of larger species, in a group of closely related mammals, tend to have relatively longer faces and smaller braincases. However, no process has been officially suggested to explain this pattern, there are many apparent exceptions, and its predictions potentially conflict with well-established biomechanical principles. Understanding the mechanisms behind CREA and causes for deviations from the pattern therefore has tremendous potential to explain allometry and diversification of the mammalian cranium. Here, we propose an amended framework to characterise the CREA pattern more clearly, in that 'longer faces' can arise through several kinds of evolutionary change, including elongation of the rostrum, retraction of the jaw muscles, or a more narrow or shallow skull, which all result in a generalised gracilisation of the facial skeleton with increased size. We define a standardised workflow to test for the presence of the pattern, using allometric shape predictions derived from geometric morphometrics analysis, and apply this to 22 mammalian families including marsupials, rabbits, rodents, bats, carnivores, antelopes, and whales. Our results show that increasing facial gracility with size is common, but not necessarily as ubiquitous as previously suggested. To address the mechanistic basis for this variation, we then review cranial adaptations for harder biting. These dictate that a more gracile cranium in larger species must represent a structural sacrifice in the ability to produce or withstand harder bites, relative to size. This leads us to propose that facial gracilisation in larger species is often a product of bite force allometry and phylogenetic niche conservatism, where more closely related species tend to exhibit more similar feeding ecology and biting behaviours and, therefore, absolute (size-independent) bite force requirements. Since larger species can produce the same absolute bite forces as smaller species with less effort, we propose that relaxed bite force demands can permit facial gracility in response to bone optimisation and alternative selection pressures. Thus, mammalian facial scaling represents an adaptive by-product of the shifting importance of selective pressures occurring with increased size. A reverse pattern of facial 'shortening' can accordingly also be found, and is retrieved in several cases here, where larger species incorporate novel feeding behaviours involving greater bite forces. We discuss multiple exceptions to a bite force-mediated influence on facial proportions across mammals which lead us to argue that ecomorphological specialisation of the cranium is likely to be the primary driver of facial scaling patterns, with some developmental constraints as possible secondary factors. A potential for larger species to have a wider range of cranial functions when less constrained by bite force demands might also explain why selection for larger sizes seems to be prevalent in some mammalian clades. The interplay between adaptation and constraint across size ranges thus presents an interesting consideration for a mechanistically grounded investigation of mammalian cranial allometry.

Multiple modes of inference reveal less phylogenetic signal in marsupial basicranial shape compared with the rest of the cranium

Incorporating morphological data into modern phylogenies allows integration of fossil evidence, facilitating divergence dating and macroevolutionary inferences. Improvements in the phylogenetic utility of morphological data have been sought via Procrustes-based geometric morphometrics (GMM), but with mixed success and little clarity over what anatomical areas are most suitable. Here, we assess GMM-based phylogenetic reconstructions in a heavily sampled source of discrete characters for mammalian phylogenetics-the basicranium-in 57 species of marsupial mammals, compared with the remainder of the cranium. We show less phylogenetic signal in the basicranium compared with a 'Rest of Cranium' partition, using diverse metrics of phylogenetic signal (Kmult, phylogenetically aligned principal components analysis, comparisons of UPGMA/neighbour-joining/parsimony trees and cophenetic distances to a reference phylogeny) for scaled, Procrustes-aligned landmarks and allometry-corrected residuals. Surprisingly, a similar pattern emerged from parsimony-based analyses of discrete cranial characters. The consistent results across methods suggest that easily computed metrics such as Kmult can provide good guidance on phylogenetic information in a landmarking configuration. In addition, GMM data may be less informative for intricate but conservative anatomical regions such as the basicranium, while better-but not necessarily novel-phylogenetic information can be expected for broadly characterized shapes such as entire bones. This article is part of the theme issue 'The mammalian skull: development, structure and function'.

Temporomandibular joint shape in anthropoid primates varies widely and is patterned by size and phylogeny

The temporomandibular joint is the direct interface between the mandible and the cranium and is critical for transmitting joint reaction forces and determining mandibular range of motion. As a consequence, understanding variation in the morphology of this joint and how it relates to other aspects of craniofacial form is important for better understanding masticatory function. Here, we present a detailed three-dimensional (3D) geometric morphometric analysis of the cranial component of this joint, the glenoid fossa, across a sample of 17 anthropoid primates, and we evaluate covariation between the glenoid and the cranium and mandible. We find high levels of intraspecific variation in glenoid shape that is likely linked to sexual dimorphism and joint remodeling, and we identify differences in mean glenoid shape across taxonomic groups and in relation to size. Analyses of covariation reveal strong relationships between glenoid shape and a variety of aspects of cranial and mandibular form. Our findings suggest that intraspecific variation in glenoid shape in primates could further be reflective of high levels of functional flexibility in the masticatory apparatus, as has also been suggested for primate jaw kinematics and muscle activation patterns. Conversely, interspecific differences likely reflect larger scale differences between species in body size and/or masticatory function. Results of the covariation analyses dovetail with those examining covariation in the cranium of canids and may be indicative of larger patterns across mammals.