RRmorph-a new R package to map phenotypic evolutionary rates and patterns on 3D meshes

The study of evolutionary rates and patterns is the key to understand how natural selection shaped the current and past diversity of phenotypes. Phylogenetic comparative methods offer an array of solutions to undertake this challenging task, and help understanding phenotypic variation in full in most circumstances. However, complex, three-dimensional structures such as the skull and the brain serve disparate goals, and different portions of these phenotypes often fulfil different functions, making it hard to understand which parts truly were recruited by natural selection. In the recent past, we developed tools apt to chart evolutionary rate and patterns directly on three-dimensional shapes, according to their magnitude and direction. Here, we present further developments of these tools, which now allow to restitute the mapping of rates and patterns with full biological realism. The tools are condensed in a new R software package.

Functional morphological integration related to feeding biomechanics in the hominine skull

Quantifying and characterizing the pattern of trait covariances is crucial for understanding how population-level patterns of integration might constrain or facilitate craniofacial evolution related to the feeding system. This study addresses an important gap in our knowledge by investigating magnitudes and patterns of morphological integration of biomechanically informative traits in the skulls of Homo sapiens, Pan troglodytes, and Gorilla gorilla. We predicted a lower magnitude of integration among human biomechanical traits since humans eat a softer, less biomechanically challenging diet than apes. Indeed, compared to African apes, the magnitudes of integration were lower in H. sapiens skulls for form data (raw dimensions) but were similar or higher for shape data (raw dimensions scaled by geometric mean). Patterns of morphological integration were generally similar, but not identical, across the three species, particularly for the form data compared to the shape data. Traits that load heavily on the primary axis of variation in morphospace are generally associated with size and/or shape of the temporalis and masseter muscles and with dimensions related to the constrained lever model of jaw biomechanics. Given the conserved nature of morphological integration, skull adaptations for food processing in African apes and humans may have been constrained to occur along certain paths of high evolvability. The conserved pattern of functional integration also indicates that extant hominine species can operate as reasonable analogues for extinct hominins in studies that require population-level patterns of trait variance/covariance.

A Comparison of Semilandmarking Approaches in the Analysis of Size and Shape

Often, few landmarks can be reliably identified in analyses of form variation and covariation. Thus, ‘semilandmarking’ algorithms have increasingly been applied to surfaces and curves. However, the locations of semilandmarks depend on the investigator’s choice of algorithm and their density. In consequence, to the extent that different semilandmarking approaches and densities result in different locations of semilandmarks, they can be expected to yield different results concerning patterns of variation and co-variation. The extent of such differences due to methodology is, as yet, unclear and often ignored. In this study, the performance of three landmark-driven semilandmarking approaches is assessed, using two different surface mesh datasets (ape crania and human heads) with different degrees of variation and complexity, by comparing the results of morphometric analyses. These approaches produce different semilandmark locations, which, in turn, lead to differences in statistical results, although the non-rigid semilandmarking approaches are consistent. Morphometric analyses using semilandmarks must be interpreted with due caution, recognising that error is inevitable and that results are approximations. Further work is needed to investigate the effects of using different landmark and semilandmark templates and to understand the limitations and advantages of different semilandmarking approaches.

A Comparison of Semilandmarking Approaches in the Visualisation of Shape Differences

In landmark-based analyses of size and shape variation and covariation among biological structures, regions lacking clearly identifiable homologous landmarks are commonly described by semilandmarks. Different algorithms may be used to apply semilandmarks, but little is known about the consequences of analytical results. Here, we assess how different approaches and semilandmarking densities affect the estimates and visualisations of mean and allometrically scaled surfaces. The performance of three landmark-driven semilandmarking approaches is assessed using two different surface mesh datasets with different degrees of variation and complexity: adult human head and ape cranial surfaces. Surfaces fitted to estimates of the mean and allometrically scaled landmark and semilandmark configurations arising from geometric morphometric analyses of these datasets are compared between semilandmarking approaches and different densities, as well as with those from warping to landmarks alone. We find that estimates of surface mesh shape (i.e., after re-semilandmarking and then re-warping) made with varying numbers of semilandmarks are generally consistent, while the warping of surfaces using landmarks alone yields surfaces that can be quite different to those based on semilandmarks, depending on landmark coverage and choice of template surface for warping. The extent to which these differences are important depends on the particular study context and aims.

Morphology of the Bony Labyrinth Supports the Affinities of Paradolichopithecus with the Papionina

Discoveries in recent decades indicate that the large papionin monkeys Paradolipopithecus and Procynocephalus are key members of the Late Pliocene - Early Pleistocene mammalian faunas of Eurasia. However, their taxonomical status, phylogenetic relationships, and ecological profile remain unclear. Here we investigate the two latter aspects through the study of the inner ear anatomy, as revealed by applying micro-CT scan imaging techniques on the cranium LGPUT DFN3-150 of Paradolichopithecus from the lower Pleistocene (2.3 Ma) fossil site Dafnero-3 in Northwestern Greece. Using geometric morphometric methods, we quantified shape variation and the allometric and phylogenetic signals in extant cercopithecines (n = 80), and explored the morphological affinities of the fossil specimen with extant taxa. LGPUT DFN3-150 has a large centroid size similar to that of baboons and their relatives. It shares several shape features with Macacina and Cercopithecini, which we interpret as probable retention of a primitive morphology. Overall, its inner ear morphology is more consistent with a stem Papionini more closely related to Papionina than Macacina, or to a basal crown Papionina. Our results, along with morphometrical and ecological features from previous studies, call into question the traditional hypothesis of a Paradolichopithecus-Macacina clade, and provide alternative perspectives in the study of Eurasian primate evolution during the late Neogene-Quaternary.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10764-022-00329-4.

Sexual Dimorphism of Cranial Morphological Traits in an Italian Sample: A Population-Specific Logistic Regression Model for Predicting Sex

Simple Summary

Despite the fact that sex estimation methods from crania are very popular in forensic anthropology, few validation studies have verified their accuracy and reliability in different populations. Different from craniometrics, for which validation studies have remarkably increased lately, the methods based on cranial morphology still need to be thoroughly investigated, even if a large consensus exists on the effects of population variability on sexual cranial dimorphism. When dealing with forensic contexts, appropriately-validated methods should be applied for building accurate biological profiles. Since the possible sexual dimorphism variation of cranial morphological traits needs to be evaluated properly in various populations, in this study, we analyzed the accuracy of existing regression models for predicting sex from cranial morphological traits in an Italian contemporary/modern population. In addition, we propose new logistic regression models that are more accurate and specific for our sample. The results also update the reference standards for populations of this geographical area and provide an additional important warning on sexual dimorphism to anthropologists working in forensic contexts.

Abstract

Although not without subjectivity, the cranial trait scoring method is an easy visual method routinely used by forensic anthropologists in sex estimation. The revision presented by Walker in 2008 has introduced predictive models with good accuracies in the original populations. However, such models may lead to unsatisfactory performances when applied to populations that are different from the original. Therefore, this study aimed to test the sex predictive equations reported by Walker on a contemporary Italian population (177 individuals) in order to evaluate the reliability of the method and to identify potential sexual dimorphic differences between American and Italian individuals. In order to provide new reference data to be used by forensic experts dealing with human remains of modern/contemporary individuals from this geographical area, we designed logistic regression models specific to our population, whose accuracy was evaluated on a validation sample from the same population. In particular, we fitted logistic regression models for all possible combinations of the five cranial morphological traits (i.e., nuchal crest, mastoid process, orbital margin, glabella, and mental eminence). This approach provided a comprehensive set of population-specific equations that can be used in forensic contexts where crania might be retrieved with severe taphonomic damages, thus limiting the application of the method only to a few morphological features. The results proved once again that the effects of secular changes and biogeographic ancestry on sexual dimorphism of cranial morphological traits are remarkable, as highlighted by the low accuracy (from 56% to 78%) of the six Walker’s equations when applied to our female sample. Among our fitted models, the one including the glabella and mastoid process was the most accurate since these features are more sexually dimorphic in our population. Finally, our models proved to have high predictive performances in both training and validation samples, with accuracy percentages up to 91.7% for Italian females, which represents a significant success in minimizing the potential misclassifications in real forensic scenarios.

Covariation between the cranium and the cervical vertebrae in hominids

The analysis of patterns of integration is crucial for the reconstruction and understanding of how morphological changes occur in a taxonomic group throughout evolution. These patterns are relatively constant; however, both patterns and the magnitudes of integration may vary across species. These differences may indicate morphological diversification, in some cases related to functional adaptations to the biomechanics of organisms. In this study, we analyze patterns of integration between two functional and developmental structures, the cranium and the cervical spine in hominids, and we quantify the amount of divergence of each anatomical element through phylogeny. We applied these methods to three-dimensional data from 168 adult hominid individuals, summing a total of more than 1000 cervical vertebrae. We found the atlas (C1) and axis (C2) display the lowest covariation with the cranium in hominids (Homo sapiens, Pan troglodytes, Pan paniscus, Gorilla gorilla, Gorilla beringei, Pongo pygmaeus). H. sapiens show a relatively different pattern of craniocervical correlation compared with chimpanzees and gorillas, especially in variables implicated in maintaining the balance of the head. Finally, the atlas and axis show lower magnitude of shape change during evolution than the rest of the cervical vertebrae, especially those located in the middle of the subaxial cervical spine. Overall, results suggest that differences in the pattern of craniocervical correlation between humans and gorillas and chimpanzees could reflect the postural differences between these groups. Also, the stronger craniocervical integration and larger magnitude of shape change during evolution shown by the middle cervical vertebrae suggests that they have been selected to play an active role in maintaining head balance.

Morphological integration of the canine region within the hominine alveolar arch

The early hominin record is characterized by numerous shifts in dental proportions (e.g., canine reduction and megadontia) linked to changes in diet and social behavior. Recent studies suggest that hominins exhibit a reduction in the magnitude of covariation between the anterior and posterior dental components compared with other extant great apes. They point toward, but do not directly test, the relative independence of canine morphology within the hominin alveolar arch. This study focuses specifically on the how the canine region covaries with other regions of the dental arch because the canine region has drastically reduced in size and changed in shape across human evolution. We examine extant primate species most commonly used as a comparative framework for fossil hominin morphology: Gorilla gorilla (n = 27), Pan troglodytes (n = 27), and Homo sapiens (n = 30). We used geometric morphometric methods to test for size and shape covariation between the canine region with other dental regions. We also examined the influence of sexual dimorphism and allometry on intraspecific and interspecific patterns of covariation. The analysis of size and shape covariation between the mandibular canine and other individual tooth regions elucidated complex, species-specific, and sex-specific morphological relationships in the mandibular alveolar arch. There was little evidence to support different patterns of morphological integration between humans on the one hand and nonhuman apes on the other. Canine region morphology was relatively independent from other dental regions across species based on shape and did not significantly covary more with either the incisor or postcanine region in any species. The size correlations between the canine and other dental regions were moderate to high. The species-specific results of this study question the ability to make a priori assumptions about morphological integration in the extant hominin mandibular alveolar arch and its application to the fossil record.

Sexual differences in human cranial morphology: Is one sex more variable or one region more dimorphic?

The quantification of cranial sexual dimorphism (CSD) among modern humans is relevant in evolutionary studies of morphological variation and in a forensic context. Despite the abundance of quantitative studies of CSD, few have specifically examined intra-sex variability. Here we quantify CSD in a geographically homogeneous sample of adult crania, which includes Italian individuals from the 19th and 20th centuries. Cranial morphology is described with 92 3D landmarks analyzed using Procrustean geometric morphometrics (PGMM). Size and shape variables are used to compare morphological variance between sexes in the whole cranium and four individual regions. The same variables, plus Procrustes form, are used to quantify average sex differences and explore classification accuracy. Our results indicate that: (a) as predicted by Wainer's rule, males present overall more variance in size and shape, albeit this is statistically significant only for total cranial size; (b) differences between sexes are dominated by size and to a lesser extent by Procrustes form; (c) shape only accounts for a minor proportion of variance; (d) the cranial base shows almost no dimorphism for shape; and (e) facial Procrustes form is the most accurate predictor of skeletal sex. Overall, this study suggests developmental factors underlying differences in CSD among cranial regions; stresses the need for population-specific models that describe craniofacial variation as the basis for models that facilitate the estimation of sex in unidentified skeletal remains; and provides one of the first confirmations of "Wainer's rule" in relation to sexual dimorphism in mammals specific to the human cranium.

The role of developmental rate, body size, and positional behavior in the evolution of covariation and evolvability in the cranium of strepsirrhines and catarrhines

Recent studies on hominin craniofacial evolution have focused on phenotypic integration or covariation among traits. Covariation is thought to significantly affect evolutionary trajectories, shaping the ways in which hominins and other primates could have evolved. However, the ways in which covariation itself evolves are not well understood. This study aims to investigate the role of phylogeny, development, body size, and positional behavior in shaping the strength of covariation in strepsirrhine and catarrhine primate crania (n = 1009, representing 11 genera). These factors may have been catalysts for change in the magnitude of covariation, and they have changed significantly during primate evolution and particularly hominin evolution. Modern humans in particular have slow developmental trajectories, large bodies, and a unique form of locomotion in the form of orthograde bipedalism. Variance of eigenvalues, mean integration, mean evolvability, and mean conditional evolvability was estimated and their relationship to the various factors described earlier was assessed using phylogenetic and nonphylogenetic analyses. Results indicate that some phylogenetic signal is present, but it is not equivalent across integration statistics or cranial regions. In particular, these results suggest that closely related species are more similar than more distantly related species in evolvability of the cranial base and integration of the face. Two divergent patterns were also identified, in which covariation and evolvability of the cranial base are linked to developmental rate, but those of the face are linked to body size. Neither locomotion nor posture appears related to covariation or evolvability of the primate cranium. These results suggest that overall low covariation observed in the hominin cranium may be a result of separate trends in different cranial regions.

Assessing thoraco-pelvic covariation in Homo sapiens and Pan troglodytes: A 3D geometric morphometric approach

OBJECTIVES

Understanding thoraco-pelvic integration in Homo sapiens and their closest living relatives (genus Pan) is of great importance within the context of human body shape evolution. However, studies assessing thoraco-pelvic covariation across Hominoidea species are scarce, although recent research would suggest shared covariation patterns in humans and chimpanzees but also species-specific features, with sexual dimorphism and allometry influencing thoraco-pelvic covariation in these taxa differently.

MATERIAL AND METHODS

N = 30 adult H. sapiens and N = 10 adult Pan troglodytes torso 3D models were analyzed using 3D geometric morphometrics and linear measurements. Effects of sexual dimorphism and allometry on thoraco-pelvic covariation were assessed via regression analyses, and patterns of thoraco-pelvic covariation in humans and chimpanzees were computed via Two-Block Partial Least Squares analyses.

RESULTS

Results confirm the existence of common aspects of thoraco-pelvic covariation in humans and chimpanzees, and also species-specific covariation in H. sapiens that is strongly influenced by sexual dimorphism and allometry. Species-specific covariation patterns in chimpanzees could not be confirmed because of the small sample size, but metrics point to a correspondence between the most caudal ribs and iliac crest morphology that would be irrespective of sex.

CONCLUSIONS

This study suggests that humans and chimpanzees share common aspects of thoraco-pelvic covariation but might differ in others. In humans, torso integration is strongly influenced by sexual dimorphism and allometry, whilst in chimpanzees it may not be. This study also highlights the importance not only of torso widths but also of torso depths when describing patterns of thoraco-pelvic covariation in primates. Larger samples are necessary to support these interpretations.

Ontogenetic changes in magnitudes of integration in the macaque skull

OBJECTIVES

Magnitudes of morphological integration may constrain or facilitate craniofacial shape variation. The aim of this study was to analyze how the magnitude of integration in the skull of Macaca fascicularis changes throughout ontogeny in relation to developmental and/or functional modules.

MATERIALS AND METHODS

Geometric morphometric methods were used to analyze the magnitude of integration in the macaque cranium and mandible in 80 juvenile and 40 adult M. fascicularis specimens. Integration scores in skull modules were calculated using integration coefficient of variation (ICV) of eigenvalues based on a resampling procedure. Resultant ICV scores between the skull as a whole, and developmental and/or functional modules were compared using Mann-Whitney U tests.

RESULTS

Results showed that most skull modules were more tightly integrated than the skull as a whole, with the exception of the chondrocranium in juveniles without canines, the chondrocranium/face complex and the mandibular corpus in adults, and the mandibular ramus in all juveniles. The chondrocranium/face and face/mandibular corpus complexes were more tightly integrated in juveniles than adults, possibly reflecting the influences of early brain growth/development, and the changing functional demands of infant suckling and later masticatory loading. This is also supported by the much higher integration of the mandibular ramus in adults compared with juveniles.

DISCUSSION

Magnitudes of integration in skull modules reflect developmental/functional mechanisms in M. fascicularis. However, the relationship between "evolutionary flexibility" and developmental/functional mechanisms was not direct or simple, likely because of the complex morphology, multifunctionality, and various ossification origins of the skull.

Three-dimensional geometric morphometrics of thorax-pelvis covariation and its potential for predicting the thorax morphology: A case study on Kebara 2 Neandertal

The skeletal torso is a complex structure of outstanding importance in understanding human body shape evolution, but reconstruction usually entails an element of subjectivity as researchers apply their own anatomical expertise to the process. Among different fossil reconstruction methods, 3D geometric morphometric techniques have been increasingly used in the last decades. Two-block partial least squares analysis has shown great potential for predicting missing elements by exploiting the covariation between two structures (blocks) in a reference sample: one block can be predicted from the other one based on the strength of covariation between blocks. The first aim of this study is to test whether this predictive approach can be used for predicting thorax morphologies from pelvis morphologies within adult Homo sapiens reference samples with known covariation between the thorax and the pelvis. The second aim is to apply this method to Kebara 2 Neandertal (Israel, ∼60 ka) to predict its thorax morphology using two different pelvis reconstructions as predictors. We measured 134 true landmarks, 720 curve semilandmarks, and 160 surface semilandmarks on 60 3D virtual torso models segmented from CT scans. We conducted three two-block partial least squares analyses between the thorax (block 1) and the pelvis (block 2) based on the H. sapiens reference samples after performing generalized Procrustes superimposition on each block separately. Comparisons of these predictions in full shape space by means of Procrustes distances show that the male-only predictive model yields the most reliable predictions within modern humans. In addition, Kebara 2 thorax predictions based on this model concur with the thorax morphology proposed for Neandertals. The method presented here does not aim to replace other techniques, but to rather complement them through quantitative prediction of a virtual 'scaffold' to articulate the thoracic fossil elements, thus extending the potential of missing data estimation beyond the methods proposed in previous works.

Locomotion, posture, and the foramen magnum in primates: Reliability of indices and insights into hominin bipedalism

The position (FMP) and orientation (FMO) of the foramen magnum have been used as proxies for locomotion and posture in extant and extinct primates. Several indices have been designed to quantify FMP and FMO but their application has led to conflicting results. Here, we test six widely used indices and two approaches (univariate and multivariate) for their capability to discriminate between postural and locomotor types in extant primates and fossil hominins. We then look at the locomotion of australopithecines and Homo on the base of these new findings. The following measurements are used: the opisthocranion-prosthion (OP-PR) and the opisthocranion-glabella (OP-GL) indices, the basion-biporion (BA-BP) and basion-bicarotid chords, the foramen magnum angle (FMA), and the basion-sphenoccipital ratio. After exploring the indices variability using principal component analysis, pairwise comparisons are performed to test for the association between each index and the locomotor and postural habits. Cranial size and phylogeny are taken into account. Our analysis indicates that none of the indices or approaches provides complete discrimination across locomotor and postural categories, although some differences are highlighted. FMA and BA-BP distinguish respectively obligate and facultative bipeds from all other groups. For what concerns posture, orthogrades and pronogrades differ with respects to OP-PR, OP-GL, and FMA. Although the multivariate approach seems to have some discrimination power, the results are most likely driven by facial and neurocranial variability embedded in some of the indices. These results demonstrate that indices relying on the anteroposterior positioning of the foramen may not be appropriate proxies for locomotion among primates. The assumptions about locomotor and postural habits in fossil hominins based on foramen magnum indices should be revised in light of these new findings.

Patterns and magnitudes of craniofacial covariation in extant cercopithecids

The cranium contains almost all of the vertebrate sensory organs and plays an essential role in vertebrate evolution. Research on the primate cranium has revealed that it is both highly integrated and modular, but studies have historically focused on covariance between the neurocranium and facial skeleton rather than on bones specific to special senses such as vision. The goal of this work is to investigate patterns and magnitudes of craniofacial covariation in extant cercopithecids with particular attention to the orbits. This study takes a quantitative approach using data collected from 38 homologous cranial landmarks across 11 genera of cercopithecid monkeys (Cercopithecidae, N = 291). These data demonstrate that both patterns and magnitudes of craniofacial covariation differ across Cercopithecidae at subfamily, tribe, and genus levels, with the strongest integration in the papionins (and specifically Papio) and significantly weaker covariation in the colobines, particularly Presbytis. Orbital height does not covary with other measurements of the cranium to the same degree as other cranial traits in Cercopithecidae and is highly constrained across the family. This study has important implications for our understanding of the evolution and development of morphological diversity in the cercopithecid cranium and evolution of the primate eye. This study also highlights the potential error of broad assumptions about generalizing patterns and magnitudes of modularity and integration across primates. Additionally, these findings reiterate the importance of trait selection for interpreting fossil taxonomy, as craniofacial covariation may impact phenotypes commonly used to differentiate fossil primate species.

Morphological consequences of artificial cranial deformation: Modularity and integration

The cranium is an anatomically complex structure. One source of its complexity is due to its modular organization. Cranial modules are distinct and partially independent units that interact substantially during ontogeny thus generating morphological integration. Artificial Cranial Deformation (ACD) occurs when the human skull is intentionally deformed, through the use of different deforming devices applied to the head while it is developing. Hence, ACD provides an interesting example to assess the degree to which biomechanical perturbations of the developing neurocranium impact on the degree of morphological integration in the skull as a whole. The main objective of this study was to assess how ACD affects the morphological integration of the skull. This was accomplished by comparing a sample of non-deformed crania and two sets of deformed crania (i.e. antero-posterior and oblique). Both developmental and static modularity and integration were assessed through Generalized Procrustes Analysis by considering the symmetric and asymmetric components of variation in adults, using 3D landmark coordinates as raw data. The presence of two developmental modules (i.e. viscero and neurocranium) in the skull was tested. Then, in order to understand how ACD affects morphological integration, the covariation pattern between the neuro and viscerocranium was examined in antero-posterior, oblique and non-deformed cranial categories using Partial Least-Squares. The main objective of this study was to assess how ACD affects the morphological integration of the skull. This was accomplished by comparing a sample of deformed (i.e. antero-posterior and oblique) and non-deformed crania. Hence, differences in integration patterns were compared between groups. The obtained results support the modular organization of the human skull in the two analyzed modules. The integration analyses show that the oblique ACD style differentially affects the static morphological integration of the skull by increasing the covariance between neuro and viscerocranium in a more constrained way than in antero-posterior and non-deformed skulls. In addition, the antero-posterior ACD style seems to affect the developmental integration of the skull by directing the covariation pattern in a more defined manner as compared to the other cranial categories.

Macroevolutionary trends of brain mass in Primates

A distinctive trait in primate evolution is the expansion in brain mass. The potential drivers of this trend and how and whether encephalization influenced diversification dynamics in this group are hotly debated. We assembled a phylogeny accounting for 317 primate species, including both extant and extinct taxa, to identify macroevolutionary trends in brain mass evolution. Our findings show that Primates as a whole follow a macroevolutionary trend for an increase in body mass, relative brain mass and speciation rate over time. Although the trend for increased encephalization (brain mass) applies to all Primates, hominins stand out for their distinctly higher rates. Within hominins, this unique trend applies linearly over time and starts with Australopithecus africanus. The increases in both speciation rate and encephalization begin in the Oligocene, suggesting the two variables are causally associated. The substitution of early, stem Primates belonging to plesiadapiforms with crown Primates seems to be responsible for these macroevolutionary trends. However, our findings also suggest that cognitive capacities favoured speciation in hominins.

Morphological integration affects the evolution of midline cranial base, lateral basicranium, and face across primates

OBJECTIVES

The basicranium and face are two integrated bony structures displaying great morphological diversity across primates. Previous studies in hominids determined that the basicranium is composed of two independent modules: the midline basicranium, mostly influenced by brain size, and the lateral basicranium, predominantly associated with facial shape. To better assess how morphological integration impacts the evolution of primate cranial shape diversity, we test to determine whether the relationships found in hominids are retained across the order.

MATERIALS AND METHODS

Three-dimensional landmarks (29) were placed on 143 computed tomography scans of six major clades of extant primate crania. We assessed the covariation between midline basicranium, lateral basicranium, face, and endocranial volume using phylogenetically informed partial least squares analyses and phylogenetic generalized least squares models.

RESULTS

We found significant integration between lateral basicranium and face and between midline basicranium and face. We also described a significant correlation between midline basicranium and endocranial volume but not between lateral basicranium and endocranial volume.

DISCUSSION

Our findings demonstrate a significant and pervasive integration in the craniofacial structures across primates, differing from previous results in hominids. The uniqueness of module organization in hominids may explain this distinction. We found that endocranial volume is significantly integrated to the midline basicranium but not to the lateral basicranium. This finding underlines the significant effect of brain size on the shape of the midline structures of the cranial base in primates. With the covariations linking the studied features defined here, we suggest that future studies should focus on determining the causal links between them.

Covariation of the endocranium and splanchnocranium during great ape ontogeny

That great ape endocranial shape development persists into adolescence indicates that the splanchnocranium succeeds brain growth in driving endocranial development. However, the extent of this splanchnocranial influence is unknown. We applied two-block partial least squares analyses of Procrustes shape variables on an ontogenetic series of great ape crania to explore the covariation of the endocranium (the internal braincase) and splanchnocranium (face, or viscerocranium). We hypothesized that a transition between brain growth and splanchnocranial development in the establishment of final endocranial form would be manifest as a change in the pattern of shape covariation between early and adolescent ontogeny. Our results revealed a strong pattern of covariation between endocranium and splanchnocranium, indicating that chimpanzees, gorillas, and orangutans share a common tempo and mode of morphological integration from the eruption of the deciduous dentition onwards to adulthood: a reflection of elongating endocranial shape and continuing splanchnocranial prognathism. Within this overarching pattern, we noted that species variation exists in magnitude and direction, and that the covariation between the splanchnocranium and endocranium is somewhat weaker in early infancy compared to successive age groups. When correcting our covariation analyses for allometry, we found that an ontogenetic signal remains, signifying that allometric variation alone is insufficient to account for all endocranial-splanchnocranial developmental integration. Finally, we assessed the influence of the cranial base, which acts as the interface between the face and endocranium, on the shape of the vault using thin-plate spline warping. We found that not all splanchnocranial shape changes during development are tightly integrated with endocranial shape. This suggests that while the developmental expansion of the brain is the main driver of endocranial shape during early ontogeny, endocranial development from infancy onwards is moulded by the splanchnocranium in conjunction with the neurocranium.