Phylogenetic analysis of the African papionin basicranium using 3-D geometric morphometrics: The need for improved methods to account for allometric effects

Geometric morphometrics approach for classifying children's nutritional status on out of sample data

Current alignment-based methods for classification in geometric morphometrics do not generally address the classification of new individuals that were not part of the study sample. However, in the context of infant and child nutritional assessment from body shape images this is a relevant problem. In this setting, classification rules obtained on the shape space from a reference sample cannot be used on out-of-sample individuals in a straightforward way. Indeed, a series of sample dependent processing steps, such as alignment (Procrustes analysis, for instance) or allometric regression, need to be conducted before the classification rule can be applied. This work proposes ways of obtaining shape coordinates for a new individual and analyzes the effect of using different template configurations on the sample of study as target for registration of the out-of-sample raw coordinates. Understanding sample characteristics and collinearity among shape variables is crucial for optimal classification results when evaluating children's nutritional status using arm shape analysis from photos. The SAM Photo Diagnosis App© Program's goal is to develop an offline smartphone tool, enabling updates of the training sample across different nutritional screening campaigns.

Developmental origin underlies evolutionary rate variation across the placental skull

The placental skull has evolved into myriad forms, from longirostrine whales to globular primates, and with a diverse array of appendages from antlers to tusks. This disparity has recently been studied from the perspective of the whole skull, but the skull is composed of numerous elements that have distinct developmental origins and varied functions. Here, we assess the evolution of the skull's major skeletal elements, decomposed into 17 individual regions. Using a high-dimensional morphometric approach for a dataset of 322 living and extinct eutherians (placental mammals and their stem relatives), we quantify patterns of variation and estimate phylogenetic, allometric and ecological signal across the skull. We further compare rates of evolution across ecological categories and ordinal-level clades and reconstruct rates of evolution along lineages and through time to assess whether developmental origin or function discriminate the evolutionary trajectories of individual cranial elements. Our results demonstrate distinct macroevolutionary patterns across cranial elements that reflect the ecological adaptations of major clades. Elements derived from neural crest show the fastest rates of evolution, but ecological signal is equally pronounced in bones derived from neural crest and paraxial mesoderm, suggesting that developmental origin may influence evolutionary tempo, but not capacity for specialisation. This article is part of the theme issue 'The mammalian skull: development, structure and function'.

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'.

A review of Theropithecus oswaldi with the proposal of a new subspecies

Theropithecus oswaldi darti, as currently understood, is the oldest Theropithecus taxon in the fossil record and the earliest subspecies in the Theropithecusoswaldi lineage. Theropithecus oswaldi darti is typified at the site of Makapansgat in South Africa, and a similar form (T. o. cf. darti) is usually recognized at Hadar, Dikika, some Middle Awash localities, and Woranso-Mille in Ethiopia. This taxon is also tentatively believed to occur in Kenya at Kanam and Koobi Fora and in Member C of the Shungura Formation in Ethiopia. While there is a general consensus that the East African 'darti' specimens are sufficiently similar to each other, there has always been a question of whether they are too distinct from the South African type material of T. o. darti to belong to the same subspecies. Here we conduct a morphological comparison of the different samples previously assigned to T. o. darti and T. o. cf. darti. The results of our analyses overwhelmingly support the hypothesis that the East African samples are distinct from the South African ones, and they are likely distinct in geological age as well. Therefore, we propose a new subspecies designation for the material previously termed T. o. cf. darti from East Africa: Theropithecus (Theropithecus) oswaldi ecki subsp. nov. We also formally recognize Theropithecus (Theropithecus) oswaldi serengetensis (Dietrich, 1942) for specimens from Laetoli, Woranso-Mille, and perhaps Galili.

Is the middle cranial fossa a reliable predictor of temporal lobe volume in extant and fossil anthropoids?

OBJECTIVES

We investigate the suitability of middle cranial fossa (MCF) size as a proxy for temporal lobe volume (TLV), examining the strength of the association between TLV and MCF metrics and assess the reliability predicting TLV in fossil anthropoids. The temporal lobe of the primate brain is a multimodal association cortex involved in long-term memory, auditory, and visual processing with unique specializations in modern humans for language comprehension. The MCF is the bony counterpart for the temporal lobe providing inferences for fossil hominin temporal lobe evolution. We now investigate whether the MCF is a suitable proxy for the temporal lobe.

METHODS

A sample of 23 anthropoid species (n = 232, including 13 fossil species) from computed tomography (CT) scans of ex vivo crania and magnetic resonance imaging (MRI) of the in vivo brain were generated into three-dimensional (3D) virtual models. Seven linear metrics were digitally measured on the right MCF with right TLV calculated from in vivo MRI.

RESULTS

Regression analyses produced statistically significant correlations between TLV and all MCF metrics (r ≥ 0.85; p ≤ 0.0009) with TLV predictions within ±1 standard error and three MCF metrics (posterior-width, mid-length, and mid-width) the most reliable predictors of TLV with only one metric weakly associated with TLV.

DISCUSSION

These findings indicate a strong association between the MCF and TLV, provide reliable predictors of fossil TLV that were previously unattainable, allow the inclusion of fragmentary fossil material, and enable inferences into the emergence of modern human temporal lobe morphology.

Normal and altered masticatory load impact on the range of craniofacial shape variation: An analysis of pre-Hispanic and modern populations of the American Southern Cone

The reduction of masticatory load intensity resulting from dietary changes in human evolution has been proposed as an important factor that alters craniofacial shape in past and current populations. However, its impact on craniofacial variation and on the perceived differences among populations is unclear. The maxillomandibular relationship, which alters masticatory force direction, is a factor often neglected but it can contribute to variation in craniofacial morphology, particularly among modern/urban populations where the prevalence of dental malocclusions is greater than in prehistoric populations. This study investigates the influence of masticatory load intensity and maxillomandibular relationship as a proxy for force direction on the human craniofacial skeleton. By using 3D imaging and geometric morphometrics, we analyzed craniofacial shape variation among 186 individuals from pre-Hispanic and modern Chilean and Argentinean populations that differ in diet consistency (a proxy for masticatory load intensity) and maxillomandibular relationship. We predicted that masticatory load would have a subtle effect on the upper craniofacial bones and that this would be more marked in the maxilla. Our results showed no clear influence of masticatory load on craniofacial shape, particularly in modern/urban populations. Allometry, on the contrary, shows a stronger effect. The degree of integration between the upper craniofacial bones and the load-bearing maxilla depends on masticatory load intensity, decreasing from high to low but showing a conservative pattern of covariation among the groups. The degree of variation in the shape of the maxilla is greater than the upper craniofacial bones. These results suggest that masticatory load has a limited effect in determining differences in craniofacial morphology among populations. This effect is slightly greater for the maxillary region of the face. We propose that the reduction of functional constraints is key to greater shape variation found in modern/urban populations.

Geometric morphometrics, homology and cladistics: review and recommendations

Geometric morphometric (GM) data has a long and contentious history in phylogenetic analyses. Often associated with phenetics, GM has been considered by many to be unable to provide meaningful information on phylogenetic relationships. However, the concepts of primary and secondary homology as developed for discrete characters can be readily extended to GM data: raw similarity in aligned landmark positions represents primary homology, and similarity ascribable to common ancestry represents secondary homology. We review fundamental concepts from the literature and provide a series of practical guidelines for the use of GM data in phylogenetics: (i) alignments that minimize linear distances between landmarks (or their approximation) perform better in highlighting apomorphic traits; (ii) Type I, Type II and linear semi-landmarks are preferable to Type III and surface semi-landmarks; (iii) excluding bilateral landmarks after, rather than before, alignment will prevent artefactual mediolateral displacement of midsagittal landmarks; (iv) phylogenetic analyses should employ linear rather than squared-change parsimony analysis of landmark displacements; (v) optimization of shape changes across a tree can be improved with methods that re-align the landmark configurations based on the results of the phylogenetic analysis; and (vi) GM data are no substitute for traditional morphological characters, but rather a complementary descriptor of shape diversity.

Phylogenetic relationship of a fossil macaque (Macaca cf. robusta) from the Korean Peninsula to extant species of macaques based on zygomaxillary morphology

Little is known about the biogeographical and evolutionary histories of macaques (Macaca spp.) in East Asia because the phylogenetic positions of fossil species remain unclear. Here we examined the zygomaxillary remains of a fossil macaque (M. cf. robusta) from the Durubong Cave Complex, South Korea, that dates back to the late Middle to Late Pleistocene, to infer its phylogenetic relationship to extant species. We took 195 fixed- and semi-landmarks from the zygomaxillary regions of the fossil specimen and from 147 specimens belonging to 14 extant species. We then conducted a generalized Procrustes analysis followed by a multivariate statistical analysis to evaluate the phenetic affinities of the fossil to the extant species and reconstructed the most parsimonious phylogenetic tree using a phylogenetic morphometric approach. We found that the fossil was most similar to Macaca fuscata (Japanese macaque) in the zygomaxillary morphospace although it was at the limit of the range of variation for this species. The second closest in the morphospace was the continental Macaca mulatta (rhesus macaque). Parsimonious reconstruction confirmed that the fossil was most closely related to M. fuscata, even after controlling for the effects of allometry. These findings suggest that in the late Middle to Late Pleistocene, close relatives of M. fuscata that looked like the extant species were distributed on the Korean Peninsula, where no species of macaques are found today. Thus, some morphological characteristics of M. fuscata may have developed before its ancestor dispersed into the Japanese archipelago.

Additive genetic variation in the craniofacial skeleton of baboons (genus Papio) and its relationship to body and cranial size

OBJECTIVES

Determining the genetic architecture of quantitative traits and genetic correlations among them is important for understanding morphological evolution patterns. We address two questions regarding papionin evolution: (1) what effect do body and cranial size, age, and sex have on phenotypic (V_P ) and additive genetic (V_A ) variation in baboon crania, and (2) how might additive genetic correlations between craniofacial traits and body mass affect morphological evolution?

MATERIALS AND METHODS

We use a large captive pedigreed baboon sample to estimate quantitative genetic parameters for craniofacial dimensions (EIDs). Our models include nested combinations of the covariates listed above. We also simulate the correlated response of a given EID due to selection on body mass alone.

RESULTS

Covariates account for 1.2-91% of craniofacial V_P . EID V_A decreases across models as more covariates are included. The median genetic correlation estimate between each EID and body mass is 0.33. Analysis of the multivariate response to selection reveals that observed patterns of craniofacial variation in extant baboons cannot be attributed solely to correlated response to selection on body mass, particularly in males.

DISCUSSION

Because a relatively large proportion of EID V_A is shared with body mass variation, different methods of correcting for allometry by statistically controlling for size can alter residual V_P patterns. This may conflate direct selection effects on craniofacial variation with those resulting from a correlated response to body mass selection. This shared genetic variation may partially explain how selection for increased body mass in two different papionin lineages produced remarkably similar craniofacial phenotypes.

The relative correspondence of cranial and genetic distances in papionin taxa and the impact of allometric adjustments

The reconstruction of phylogenetic relationships in the primate fossil record is dependent upon a thorough understanding of the phylogenetic utility of craniodental characters. Here, we test three previously proposed hypotheses for the propensity of primate craniomandibular data to exhibit homoplasy, using a study design based on the relative congruence between cranial distance matrices and a consensus genetic distance matrix ("genetic congruence") for papionin taxa: 1) matrices based on cranial regions subjected to less masticatory strain are more genetically congruent than high-strain cranial matrices; 2) matrices based on cranial regions developing earlier in ontogeny are more genetically congruent than matrices based on regions that develop later; and 3) matrices based on cranial regions with greater anatomical/functional complexity are more genetically congruent than matrices based on anatomically simpler regions. Morphological distance matrices based on the shape of 15 different cranial regions, delineated on the basis of previous catarrhine studies, were statistically compared to a matrix of known genetic distances in papionins. Since sexual dimorphism and allometry are known to characterize this clade, several analytical iterations were conducted: 1) mixed-sex, male-only, and female-only analyses and 2) with and without an allometric scaling adjustment. Across all datasets, the chondrocranium matrix was the most consistently correlated with genetic distances, which is also consistent with previous studies of cercopithecoid taxa; however, there was no support for the internal predictions of the three hypotheses tested. Allometric scaling corrections had the largest impact on the genetic congruence of facial shape matrices, a result consistent with previous studies that have described facial homoplasy in papionin taxa. These findings differ from patterns described for hominoid taxa, suggesting that no single predictive criterion can explain phylogenetic utility of cranial datasets across catarrhine primate taxa. Many of the differences in morphological-genetic matrix correlations could result from different levels of phenotypic integration and evolvability in cercopithecoids and hominoids, suggesting that further study of these phenomena in extant primates is warranted.

The 'temporal effect' in hominids: Reinvestigating the nature of support for a chimp-human clade in bone morphology

In 2004, an analysis by Lockwood and colleagues of hard-tissue morphology, using geometric morphometrics on the temporal bone, succeeded in recovering the correct phylogeny of living hominids without resorting to potentially problematic methods for transforming continuous shape variables into meristic characters. That work has increased hope that by using modern analytical methods and phylogenetically informative anatomical data we might one day be able to accurately infer the relationships of hominins, including the closest extinct relatives of modern humans. In the present study, using 3D virtually generated models of the hominid temporal bone and a larger suite of geometric morphometric and comparative techniques, we have re-examined the evidence for a Pan-Homo clade. Despite differences in samples, as well as the type of raw data, the effect of measurement error (and especially landmark digitization by a different operator), but also a broader perspective brought in by our diverse set of approaches, our reanalysis largely supports Lockwood and colleagues' original results. However, by focusing not only mainly on shape (as in the original 2004 analysis) but also on size and 'size-corrected' (non-allometric) shape, we demonstrate that the strong phylogenetic signal in the temporal bone is largely related to similarities in size. Thus, with this study, we are not suggesting the use of a single 'character', such as size, for phylogenetic inference, but we do challenge the common view that shape, with its highly complex and multivariate nature, is necessarily more phylogenetically informative than size and that actually size and size-related shape variation (i.e., allometry) confound phylogenetic inference based on morphology. This perspective may in fact be less generalizable than often believed. Thus, while we confirm the original findings by Lockwood et al., we provide a deep reinterpretation of their nature and potential implications for hominid phylogenetics and we show how crucial it is not to overlook size in geometric morphometric analyses.

Burial, excavation, and preparation of primate skeletal material for morphological study

Inclusion of osteological material in primatological research has a long history, and use of skeletal remains continues to be important in anatomical and anthropological research. Here we report a set of proven methods, including equipment, protocol, and procedure, which enable relatively simple acquisition of skeletal material from naturally deceased animals in field sites and sanctuaries. Such skeletal material, often with extensive accompanying life-history data, is a unique and valuable source of data for both academic and conservation-based research.

A comparison of catarrhine genetic distances with pelvic and cranial morphology: implications for determining hominin phylogeny

Inferring the evolutionary history of the hominins is necessarily reliant on comparative analyses of fossilized skeletal anatomy. However, the reliability of different primate skeletal regions for recovering phylogenetic relationships is currently poorly understood. Historically, postcranial variation has largely been conceived of as reflecting locomotory and postural adaptation. The shape of the os coxae is central to such discussions given the divergent morphology displayed by the bipedal hominin pelvis relative to other primate taxa. While previous cladistic studies have suggested that postcranial and cranial datasets do not differ in terms of their propensity for homoplasy, methodological issues such as the numbers of characters and their quantification make it difficult to evaluate these findings. Here, we circumvent these problems by constructing morphological distance matrices based on cranial, mandibular and os coxae three-dimensional shape. Statistical comparisons of these morphological distance matrices against a single genetic distance matrix for 11 catarrhine taxa show that cranial and os coxae shape reflect genetic relationships better than the mandible when humans are included, and that the cranium and os coxae do not differ statistically in terms of their genetic correlations. When humans were excluded from the analyses, all three anatomical regions were equally strongly correlated with genetic distance. Moreover, a second analysis focusing solely on os coxae variation of 16 taxa demonstrated that os coxae shape correctly recovers catarrhine taxonomic relationships at the sub-family level, even when humans are included. Taken together, our results suggest that there is no a priori reason to favor cranial shape data over os coxae morphology when inferring the genetic relationships of extant or extinct primate taxa. Morphological similarities between humans and other primates differ depending on the skeletal element, suggesting that combining skeletal elements into a single analysis may provide more accurate reconstructions of genetic relationships.

A calcaneus attributable to the primitive late Eocene anthropoid Proteopithecus sylviae: phenetic affinities and phylogenetic implications

A well-preserved calcaneus referrable to Proteopithecus sylviae from the late Eocene Quarry L-41 in the Fayum Depression, Egypt, provides new evidence relevant to this taxon's uncertain phylogenetic position. We assess morphological affinities of the new specimen using three-dimensional geometric morphometric analyses with a comparative sample of primate calcanei representing major extinct and extant radiations (n = 58 genera, 106 specimens). Our analyses reveal that the calcaneal morphology of Proteopithecus is most similar to that of the younger Fayum parapithecid Apidium. Principal components analysis places Apidium and Proteopithecus in an intermediate position between primitive euprimates and crown anthropoids, based primarily on landmark configurations corresponding to moderate distal elongation, a more distal position of the peroneal tubercle, and a relatively "unflexed" calcaneal body. Proteopithecus and Apidium are similar to cercopithecoids and some omomyiforms in having an ectal facet that is more tightly curved, along with a larger degree of proximal calcaneal elongation, whereas other Fayum anthropoids, platyrrhines and adapiforms have a more open facet with less proximal elongation. The similarity to cercopithecoids is most plausibly interpreted as convergence given the less tightly curved ectal facets of stem catarrhines. The primary similarities between Proteopithecus and platyrrhines are mainly in the moderate distal elongation and the more distal position of the peroneal tubercle, both of which are not unique to these groups. Proteopithecus and Apidium exhibit derived anthropoid features, but also a suite of primitive retentions. The calcaneal morphology of Proteopithecus is consistent with our cladistic analysis, which places proteopithecids as a sister group of Parapithecoidea.