Error in geometric morphometric data collection: Combining data from multiple sources

Testing the reliability of the rearticulation of osteological primate pelves in comparative morphological studies

The evolution of human pelvic form is primarily studied using disarticulated osteological material of living and fossil primates that need rearticulation to approximate anatomical position. To test whether this technique introduces errors that impact biological signals, virtual rearticulations of the pelvis in anatomical position from computed tomography scans were compared with rearticulated models from the same individuals for one female and one male of Homo sapiens, Pan troglodytes, Macaca mulatta, Lepilemur mustelinus, Galago senegalensis, and Nycticebus pygmaeus. "Cadaveric" pelvic bones were first analyzed in anatomical position, then the three bones were segmented individually, intentionally scattered, and "rearticulated" to test for rearticulation error. Three-dimensional landmarks and linear measurements were used to characterize the overall pelvis shape. Cadaveric and rearticulated pelves were not identical, but inter-specific and intra-specific shape differences were higher than the landmarking error in the cadaveric individuals and the landmarking/rearticulation error in the rearticulated pelves, demonstrating that the biological signal is stronger than the noise introduced by landmarking and rearticulation. The rearticulation process, however, underestimates the medio-lateral pelvic measurements in species with a substantial pubic gap (e.g., G. senegalensis, N. pygmaeus) possibly because the greater contribution of soft tissue to the pelvic girdle introduces higher uncertainty during rearticulation. Nevertheless, this discrepancy affects only the caudal-most part of the pelvis. This study demonstrates that the rearticulation of pelvic bones does not substantially affect the biological signal in comparative 3D morphological studies but suggests that anatomically connected pelves of species with wide pubic gaps should be preferentially included in these studies.

Carpal kinematics and morphological correlates of wrist ulnar deviation mobility in nonhuman anthropoid primates

OBJECTIVES

Primates employ wrist ulnar deviation during a variety of locomotor and manipulative behaviors. Extant hominoids share a derived condition in which the ulnar styloid process has limited articulation or is completely separated from the proximal carpals, which is often hypothesized to increase ulnar deviation range of motion. Acute angulation of the hamate's triquetral facet is also hypothesized to facilitate ulnar deviation mobility and mechanics. In this study, we test these longstanding ideas.

METHODS

Three-dimensional (3D) carpal kinematics were examined using a cadaveric sample of Pan troglodytes, Pongo sp., and five monkey species. Ulnar styloid projection and orientation of the hamate's triquetral facet were quantified using 3D models.

RESULTS

Although carpal rotation patterns in Pan and Pongo were uniquely similar in some respects, P. troglodytes exhibited overall kinematic similarity with large terrestrial cercopithecoids (Papio and Mandrillus). Pongo, Macaca, and Ateles had high wrist ulnar deviation ranges of motion, but Pongo did this via a unique mechanism. In Pongo, the triquetrum functions as a distal carpal rather than part of the proximal row. Ulnar styloid projection and wrist ulnar deviation range of motion were not correlated but ulnar deviation range of motion and the triquetrohamate facet orientation were correlated.

CONCLUSIONS

Increased ulnar deviation mobility is not the function of ulnar styloid withdrawal in hominoids. Instead, this feature probably reduces stress on the ulnar side wrist or is a byproduct of adaptations that increase supination. Orientation of the hamate's triquetral facet offers some potential to reconstruct ulnar deviation mobility in extinct primates.

Morphological integration and shape covariation between the trapezium and first metacarpal among extant hominids

OBJECTIVES

The shape of the trapezium and first metacarpal (Mc1) markedly influence thumb mobility, strength, and the manual abilities of extant hominids. Previous research has typically focused solely on trapezium-Mc1 joint shape. Here we investigate how morphological integration and shape covariation between the entire trapezium (articular and non-articular surfaces) and the entire Mc1 reflect known differences in thumb use in extant hominids.

MATERIALS AND METHODS

We analyzed shape covariation in associated trapezia and Mc1s across a large, diverse sample of Homo sapiens (n = 40 individuals) and other extant hominids (Pan troglodytes, n = 16; Pan paniscus, n = 13; Gorilla gorilla gorilla, n = 27; Gorilla beringei, n = 6; Pongo pygmaeus, n = 14; Pongo abelii, n = 9) using a 3D geometric morphometric approach. We tested for interspecific significant differences in degree of morphological integration and patterns of shape covariation between the entire trapezium and Mc1, as well as within the trapezium-Mc1 joint specifically.

RESULTS

Significant morphological integration was only found in the trapezium-Mc1 joint of H. sapiens and G. g. gorilla. Each genus showed a specific pattern of shape covariation between the entire trapezium and Mc1 that was consistent with different intercarpal and carpometacarpal joint postures.

DISCUSSION

Our results are consistent with known differences in habitual thumb use, including a more abducted thumb during forceful precision grips in H. sapiens and a more adducted thumb in other hominids used for diverse grips. These results will help to infer thumb use in fossil hominins.

Investigating temporal bone variation of colonial populations from St-Lawrence Valley, Quebec: A 3D geometric morphometric approach

OBJECTIVES

In Quebec, genetic and genealogical research are used to document migratory events and family structures since colonial times, because bioarchaeological analysis is limited by poor skeletal preservation. This article aims to fill this gap by exploring past population structure in the St-Lawrence Valley from the French (1683-1760) and British (1760-1867) regimes using morphological variation of well-preserved temporal bones.

MATERIALS AND METHODS

3D geometric morphometrics shape data from seven populations (five Catholics of French descent and two Protestants of British descent; n = 214) were collected from temporal bones. Using Procrustes distances and both MANOVA and Discriminant Function Analysis, morphological differences were measured to calculate affinities patterns among populations. Shape variations were explored with between-group analysis, Mahalanobis distances and quantified by means of Fst estimates using Relethford-Blangero analysis.

RESULTS

Despite strong affinities between all Catholic cemeteries, all show divergent morphological regional diversity -especially Montreal and the fortified villages dedicated to its defense. Montreal exhibits low increase in morphological variance over three centuries. As our results show no morphological differences between the Catholic and the Protestant cemeteries in Montreal, this fact may highlight the potential presence of Irish or admixed individuals in Montreal cemeteries after the British takeover.

DISCUSSION

Patterns of morphological diversity highlighted that French colonists did not equally contribute to the descendant populations as reflected by significant interregional variation. Although historical records show that French and English-speaking populations did not tend to admix, morphological affinities between Protestants and Catholics in the beginning of the industrial era in Montreal could reflect the genetic contribution of Catholic Irish migrants.

RESEARCH HIGHLIGHTS

All Catholic cemeteries display distinct morphologies, highlighting differential contributions from French colonists and founder effects, which have increased regional differences. Montreal Catholic (French descent) and Protestant (English colonists) cemeteries show significant morphological affinities at the beginning of the industrial era. The Irish migration following the British conquest may explain morphological similarities observed between Catholic and Protestant cemeteries.

Factors influencing cranial variation between prehistoric Japanese forager populations

Understanding the factors shaping human crania has long been a goal of biological anthropology, and climate, diet, and population history are three of the most well-established influences. The effects of these factors are, however, rarely compared within a single, variable population, limiting interpretations of their relative contribution to craniofacial form. Jomon prehistoric foragers inhabited Japan throughout its climatic and ecological range and developed correspondingly varied modes of subsistence. We have previously demonstrated that a large sample of Jomon crania showed no clear climatic pattern; here, we examine variation in Jomon crania in more detail to determine if dietary factors and/or population history influence human intrapopulation variation at this scale. Based on well-established archaeological differences, we divide the Jomon into dietary groups and use geometric morphometric methods to analyse relationships between cranial shape, diet, and population history. We find evidence for diet-related influences on the shape of the neurocranium, particularly in the temporalis region. These shape differences may be interpreted in the context of regional variation in the biomechanical requirements of different diets. More experimental biomechanical and nutritional evidence is needed, however, to move suggested links between dietary content and cranial shape from plausible to well-supported. In contrast with the global scale of human variation, where neutral processes are the strongest influence on cranial shape, we find no pattern of population history amongst individuals from these Jomon sites. The determinants of cranial morphology are complex and the effect of diet is likely mediated by factors including sex, social factors, and chronology. Our results underline the subtlety of the effects of dietary variation beyond the forager/farmer dichotomy on cranial morphology and contribute to our understanding of the complexity of selective pressures shaping human phenotypes on different geographic scales.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12520-023-01901-6.

A geometric morphometric analysis of variation in Australian frog ilia and taxonomic interpretations

Anurans including frogs and toads exhibit an ilium that is often regarded as taxonomically diagnostic. The ilium, one of the three paired bones that make up the pelvic girdle, has been important in the fossil record for identifying anuran morphotypes. Osteological collections for Australian frogs are rare in herpetological museums, and skeletonizing whole-bodied specimens requires destroying soft tissue morphology which is valuable to anuran specialists working on living species. Computed tomography scans provide the opportunity to study anuran osteology without the loss of soft tissues. Our study, based on microcomputed tomography scans of extant Australian frogs from the public repository Morphosource and from museum collections focuses on the morphological differences between Australian frogs at the familial and generic levels using geometric morphometrics to compare the diagnostic shape of the ilium. Principal component analysis (PCA) and canonical variate analysis (CVA) were conducted to assess differences in the ilium between supraspecific groups of Australian frogs. The canonical variates analysis accurately predicted group membership (i.e., the correct family) with up to 76.2% success for cross-validated predictions and 100% of original group predictions. While the sample was limited to familial and generic level analyses, our research shows that ilial morphology in Australian frogs is taxonomically informative. This research provides a guide for identifying Australian anurans, including fossils, as well as new information relevant to considerations about their phylogenetic relationships, and the potential use of the fossil record to enhance efforts to conserve threatened living frog species.

Is shape in the eye of the beholder? Assessing landmarking error in geometric morphometric analyses on live fish

Geometric morphometrics is widely used to quantify morphological variation between biological specimens, but the fundamental influence of operator bias on data reproducibility is rarely considered, particularly in studies using photographs of live animals taken under field conditions. We examined this using four independent operators that applied an identical landmarking scheme to replicate photographs of 291 live Atlantic salmon (Salmo salar L.) from two rivers. Using repeated measures tests, we found significant inter-operator differences in mean body shape, suggesting that the operators introduced a systematic error despite following the same landmarking scheme. No significant differences were detected when the landmarking process was repeated by the same operator on a random subset of photographs. Importantly, in spite of significant operator bias, small but statistically significant morphological differences between fish from the two rivers were found consistently by all operators. Pairwise tests of angles of vectors of shape change showed that these between-river differences in body shape were analogous across operator datasets, suggesting a general reproducibility of findings obtained by geometric morphometric studies. In contrast, merging landmark data when fish from each river are digitised by different operators had a significant impact on downstream analyses, highlighting an intrinsic risk of bias. Overall, we show that, even when significant inter-operator error is introduced during digitisation, following an identical landmarking scheme can identify morphological differences between populations. This study indicates that operators digitising at least a sub-set of all data groups of interest may be an effective way of mitigating inter-operator error and potentially enabling data sharing.

An Open-Source Photogrammetry Workflow for Reconstructing 3D Models

Acquiring accurate 3D biological models efficiently and economically is important for morphological data collection and analysis in organismal biology. In recent years, structure-from-motion (SFM) photogrammetry has become increasingly popular in biological research due to its flexibility and being relatively low cost. SFM photogrammetry registers 2D images for reconstructing camera positions as the basis for 3D modeling and texturing. However, most studies of organismal biology still relied on commercial software to reconstruct the 3D model from photographs, which impeded the adoption of this workflow in our field due the blocking issues such as cost and affordability. Also, prior investigations in photogrammetry did not sufficiently assess the geometric accuracy of the models reconstructed. Consequently, this study has two goals. First, we presented an affordable and highly flexible SFM photogrammetry pipeline based on the open-source package OpenDroneMap (ODM) and its user interface WebODM. Second, we assessed the geometric accuracy of the photogrammetric models acquired from the ODM pipeline by comparing them to the models acquired via microCT scanning, the de facto method to image skeleton. Our sample comprised 15 Aplodontia rufa (mountain beaver) skulls. Using models derived from microCT scans of the samples as reference, our results showed that the geometry of the models derived from ODM was sufficiently accurate for gross metric and morphometric analysis as the measurement errors are usually around or below 2%, and morphometric analysis captured consistent patterns of shape variations in both modalities. However, subtle but distinct differences between the photogrammetric and microCT-derived 3D models could affect the landmark placement, which in return affected the downstream shape analysis, especially when the variance within a sample is relatively small. At the minimum, we strongly advise not combining 3D models derived from these two modalities for geometric morphometric analysis. Our findings can be indictive of similar issues in other SFM photogrammetry tools since the underlying pipelines are similar. We recommend that users run a pilot test of geometric accuracy before using photogrammetric models for morphometric analysis. For the research community, we provide detailed guidance on using our pipeline for building 3D models from photographs.

Testing different 3D techniques using geometric morphometrics: Implications for cranial fluctuating asymmetry in humans

This study aimed to test the performance of 3D digitizer, CT scanner, and surface scanner in detecting cranial fluctuating asymmetry. Sets of 32 landmarks (6 in the midline and 13 bilateral) were acquired from 14 archeological crania using a 3D digitizer, and from 3D models generated from a CT scanner and surface scanner using Viewbox 4. Levels of shape variation were analyzed in MorphoJ using Procrustes analysis of variance and Principal component analysis. Intra-observer error accounted for 1.7%, 1.8%, and 4.5% of total shape variation for 3D digitizer, CT scanner, and surface scanner respectively. Fluctuating asymmetry accounted for 15%-16% of total shape variation. Variation between techniques accounted for 18% of total shape variation. We found a higher level of missing landmarks in our surface scan data than for both 3D digitizer and CT scanner data, and both 3D model-based techniques sometimes obscured taphonomic damage. All three 3D techniques are appropriate for measuring cranial fluctuating asymmetry. We advise against combining data collected with different techniques.

Automated landmarking via multiple templates

Manually collecting landmarks for quantifying complex morphological phenotypes can be laborious and subject to intra and interobserver errors. However, most automated landmarking methods for efficiency and consistency fall short of landmarking highly variable samples due to the bias introduced by the use of a single template. We introduce a fast and open source automated landmarking pipeline (MALPACA) that utilizes multiple templates for accommodating large-scale variations. We also introduce a K-means method of choosing the templates that can be used in conjunction with MALPACA, when no prior information for selecting templates is available. Our results confirm that MALPACA significantly outperforms single-template methods in landmarking both single and multi-species samples. K-means based template selection can also avoid choosing the worst set of templates when compared to random template selection. We further offer an example of post-hoc quality check for each individual template for further refinement. In summary, MALPACA is an efficient and reproducible method that can accommodate large morphological variability, such as those commonly found in evolutionary studies. To support the research community, we have developed open-source and user-friendly software tools for performing K-means multi-templates selection and MALPACA.

Testing inter-observer error under a collaborative research framework for studying lithic shape variability

Evaluating error that arises through the aggregation of data recorded by multiple observers is a key consideration in many metric and geometric morphometric analyses of stone tool shape. One of the most common approaches involves the convergence of observers for repeat trails on the same set of artefacts: however, this is logistically and financially challenging when collaborating internationally and/or at a large scale. We present and evaluate a unique alternative for testing inter-observer error, involving the development of 3D printed copies of a lithic reference collection for distribution among observers. With the aim of reducing error, clear protocols were developed for photographing and measuring the replicas, and inter-observer variability was assessed on the replicas in comparison with a corresponding data set recorded by a single observer. Our results demonstrate that, when the photography procedure is standardized and dimensions are clearly defined, the resulting metric and geometric morphometric data are minimally affected by inter-observer error, supporting this method as an effective solution for assessing error under collaborative research frameworks. Collaboration is becoming increasingly important within archaeological and anthropological sciences in order to increase the accessibility of samples, encourage dual-project development between foreign and local researchers and reduce the carbon footprint of collection-based research. This study offers a promising validation of a collaborative research design whereby researchers remotely work together to produce comparable data capturing lithic shape variability.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12520-022-01676-2.

Comparability of skeletal fibulae surfaces generated by different source scanning (dual-energy CT scan vs. high resolution laser scanning) and 3D geometric morphometric validation

This work aims to test accuracy and comparability of 3D models of human skeletal fibulae generated by clinical CT and laser scanner virtual acquisitions. Mesh topology, segmentation and smoothing protocols were tested to assess variation among meshes generated with different scanning methods and procedures, and to evaluate meshes‐interchangeability in 3D geometric morphometric analysis. A sample of 13 left human fibulae were scanned separately with Revolution Discovery CT dual energy (0.625 mm resolution) and ARTEC Space Spider 3D structured light laser scanner (0.1 mm resolution). Different segmentation methods, including half‐maximum height (HMH) and MIA‐clustering protocols, were compared to their high‐resolution standard generated with laser‐scanner by calculating topological surface deviations. Different smoothing algorithms were also evaluated, such as Laplacian and Taubin smoothing. A total of 142 semilandmarks were used to capture the shape of both proximal and distal fibular epiphyses. After Generalized Procrustes superimposition, the Procrustes coordinates of the proximal and distal fibular epiphyses were used separately to assess variation due to scanning methods and the operator error. Smoothing algorithms at low iteration do not provide significant variation among reconstructions, but segmentation protocol may influence final mesh quality (0.09–0.24 mm). Mean deviation among CT‐generated meshes that were segmented with MIA‐clustering protocol, and laser scanner‐generated ones, is optimal (0.42 mm, ranging 0.35–0.56 mm). Principal component analysis reveals that homologous samples scanned with the two methods cluster together for both the proximal and distal fibular epiphyses. Similarly, Procrustes ANOVA reveals no shape differences between scanning methods and replicates, and only 1.38–1.43% of shape variation is due to scanning device. Topological similarities support the comparability of CT‐ and laser scanner‐generated meshes and validate its simultaneous use in shape analysis with potential clinical relevance. We precautionarily suggest that dedicated trials should be performed in each study when merging different data sources prior to analyses.

A geometric morphometric approach to investigate primate proximal phalanx diaphysis shape

Current approaches to quantify phalangeal curvature assume that the long axis of the bone's diaphysis approximates the shape of a portion of a circle (included angle method) or a parabola (second-degree polynomial method). Here we developed, tested, and employed an alternative geometric morphometrics-based approach to quantify diaphysis shape of proximal phalanges in humans, apes and monkeys with diverse locomotor behaviors. 100 landmarks of the central longitudinal axis were extracted from 3D surface models and analyzed using 2DGM methods, including Generalized Procrustes Analyses. Principal components analyses were performed and PC1 scores (>80% of variation) represented the dorsopalmar shape of the bone's central longitudinal axis and separated taxa consistently and in accord with known locomotor behavioral profiles. The most suspensory taxa, including orangutans, hylobatids and spider monkeys, had significantly lower PC1 scores reflecting the greatest amounts of phalangeal curvature. In contrast, bipedal humans and the quadrupedal cercopithecoid monkeys sampled (baboons, proboscis monkeys) exhibited significantly higher PC1 scores reflecting flatter phalanges. African ape (gorillas, chimpanzees and bonobos) phalanges fell between these two extremes and were not significantly different from each other. PC1 scores were significantly correlated with both included angle and the a coefficient of a second-degree polynomial calculated from the same landmark dataset, but had a significantly higher correlation with included angles. Our alternative approach for quantifying diaphysis shape of proximal phalanges to investigate dorsopalmar curvature is replicable and does not assume a priori either a circle or parabola model of shape, making it an attractive alternative compared with existing methodologies.

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.

Using virtual reality for anatomical landmark annotation in geometric morphometrics

To study the shape of objects using geometric morphometrics, landmarks are oftentimes collected digitally from a 3D scanned model. The expert may annotate landmarks using software that visualizes the 3D model on a flat screen, and interaction is achieved with a mouse and a keyboard. However, landmark annotation of a 3D model on a 2D display is a tedious process and potentially introduces error due to the perception and interaction limitations of the flat interface. In addition, digital landmark placement can be more time-consuming than direct annotation on the physical object using a tactile digitizer arm. Since virtual reality (VR) is designed to more closely resemble the real world, we present a VR prototype for annotating landmarks on 3D models. We study the impact of VR on annotation performance by comparing our VR prototype to Stratovan Checkpoint, a commonly used commercial desktop software. We use an experimental setup, where four operators placed six landmarks on six grey seal (Halichoerus grypus) skulls in six trials for both systems. This enables us to investigate multiple sources of measurement error. We analyse both for the configuration and for single landmarks. Our analysis shows that annotation in VR is a promising alternative to desktop annotation. We find that annotation precision is comparable between the two systems, with VR being significantly more precise for one of the landmarks. We do not find evidence that annotation in VR is faster than on the desktop, but it is accurate.

Craniofacial fluctuating asymmetry in gorillas, chimpanzees, and macaques

OBJECTIVES

Craniofacial fluctuating asymmetry (FA) refers to the random deviations from symmetry exhibited across the craniofacial complex and can be used as a measure of developmental instability for organisms with bilateral symmetry. This article addresses the lack of data on craniofacial FA in nonhuman primates by analyzing FA magnitude and variation in chimpanzees, gorillas, and macaques. We offer a preliminary investigation into how FA, as a proxy for developmental instability, varies within and among nonhuman primates.

MATERIALS AND METHODS

We generated 3D surface models of 121 crania from Pan troglodytes troglodytes, Gorilla gorilla gorilla, and Macaca fascicularis fascicularis. Using geometric morphometric techniques, the magnitude of observed FA was calculated and compared for each individual, sex, and taxon, along with the variation of FA across cranial regions and for each bilateral landmark.

RESULTS

Gorillas and macaques exhibited higher and more similar magnitudes of FA to each other than either taxon did to chimpanzees; variation in magnitude of FA followed this same trend. No significant differences were detected between sexes using pooled data across species, but sex did influence FA magnitude within taxa in gorillas. Further, variation in FA variance across cranial regions and by landmark was not distributed in any particular pattern.

CONCLUSION

Possible environmentally induced causes for these patterns of FA magnitude include differences in growth rate and physiological stress experienced during life. Developmental stability may be greatest in chimpanzees in this sample. Additionally, these results point to appropriate landmarks for future FA analyses and may help suggest more urgent candidate taxa for conservation efforts.

Computational anatomy and geometric shape analysis enables analysis of complex craniofacial phenotypes in zebrafish

Due to the complexity of fish skulls, previous attempts to classify craniofacial phenotypes have relied on qualitative features or sparce 2D landmarks. In this work we aim to identify previously unknown 3D craniofacial phenotypes with a semiautomated pipeline in adult zebrafish mutants. We first estimate a synthetic ‘normative’ zebrafish template using microCT scans from a sample pool of wildtype animals using the Advanced Normalization Tools (ANTs). We apply a computational anatomy (CA) approach to quantify the phenotype of zebrafish with disruptions in bmp1a, a gene implicated in later skeletal development and whose human ortholog when disrupted is associated with Osteogenesis Imperfecta. Compared to controls, the bmp1a fish have larger otoliths, larger normalized centroid sizes, and exhibit shape differences concentrated around the operculum, anterior frontal, and posterior parietal bones. Moreover, bmp1a fish differ in the degree of asymmetry. Our CA approach offers a potential pipeline for high-throughput screening of complex fish craniofacial shape to discover novel phenotypes for which traditional landmarks are too sparce to detect. The current pipeline successfully identifies areas of variation in zebrafish mutants, which are an important model system for testing genome to phenome relationships in the study of development, evolution, and human diseases.

3D geometric morphometrics analysis of mandibular fragments of Ouranopithecus macedoniensis from the late Miocene deposits of Central Macedonia, Greece

OBJECTIVES

To explore mandibular shape differences between Ouranopithecus macedoniensis and a comparative sample of extant great apes using three-dimensional (3D) geometrics morphometrics. Other objectives are to assess mandibular shape variation and homogeneity within Ouranopithecus, explore the effects of size on mandibular shape, and explore the degree of mandibular sexual size dimorphism in Ouranopithecus.

MATERIALS AND METHODS

The comparative sample comprises digitized mandibles from adult extant great apes. The 3D analysis includes three datasets: one with landmarks registered on the mandibular corpus and symphysis of mandibles preserving both sides, one on hemimandibles only, and one focused on the ramus and gonial area. Multivariate statistical analyses were conducted, such as ordination analyses (PCA), intra-specific Procrustes distances pairs, pairwise male-female centroid size differences, and correlation analyses.

RESULTS

The male and female specimens of Ouranopithecus have mandibular shapes that are quite similar, although differences exist. The Procrustes distances results suggest more shape variation in Ouranopithecus than in the extant great apes. Ouranopithecus shows some similarities in mandibular shape to the larger great apes, Gorilla and Pongo. Moreover, the degree of sexual dimorphism in the small Ouranopithecus sample is greater than any of the great apes. Based on our correlation analyses of principal components (PC) with size, some PCs are significantly correlated with size, with correlation varying from moderate to substantial.

DISCUSSION

This study attempted to understand better the variation within the mandibles of O. macedoniensis and the expression of sexual dimorphism in this taxon in more detail than has been done previously. The overall mandibular morphology of Ouranopithecus shows some similarities to those of the larger great apes, which likely reflects similarities in size. Compared to Gorilla and Pongo, O. macedoniensis shows an elevated degree of morphological variation, although limitations relating to sample size apply. Sexual dimorphism in the mandibles of O. macedoniensis appears to be relatively high, seemingly greater than in Gorilla and high even in comparison to Pongo, but this again is possibly in part an artifact of a small sample size.

Landmark Data to Distinguish and Identify Morphologically Close Tabanus spp. (Diptera: Tabanidae)

Tabanus spp., also known as horse flies (Diptera: Tabanidae), are important vectors of several animal pathogens. Adult females of Tabanus megalops and Tabanus striatus, which are members of the T. striatus complex, are morphologically similar and hence difficult to distinguish using morphological characteristics. In addition, molecular identification by DNA barcoding is also unable to distinguish these species. These two species can occur sympatrically with Tabanus rubidus, which is morphologically similar to T. megalops and T. striatus. Wing geometric morphometrics has been widely used in various insects to distinguish morphologically similar species. This study explored the effectiveness of landmark-based geometrics at distinguishing and identifying T. megalops, T. rubidus, and T. striatus in Thailand. Specimens were collected from different geographical regions of Thailand, and only unambiguously identified specimens were used for geometric morphometric analyses. Left wings of females of T. megalops (n = 160), T. rubidus (n = 165), and T. striatus (n = 85) were photographed, and 22 wing landmarks were used for the analysis. Wing shape was able to distinguish among species with high accuracy scores, ranging from 94.38% to 99.39%. We showed that morphologically very close species of Tabanus can be reliably distinguished by the geometry of their wing venation, and we showed how our experimental material could be used as a reference to tentatively identify new field collected specimens.

Three-dimensional printed personalized drug devices with anatomical fit: a review

OBJECTIVES

Three-dimensional printing (3DP) has opened the era of drug personalization, promising to revolutionize the pharmaceutical field with improvements in efficacy, safety and compliance of the treatments. As a result of these investigations, a vast therapeutic field has opened for 3DP-loaded drug devices with an anatomical fit. Along these lines, innovative dosage forms, unimaginable until recently, can be obtained. This review explores 3DP-engineered drug devices described in recent research articles, as well as in patented inventions, and even devices already produced by 3DP with drug-loading potential.

KEY FINDINGS

3D drug-loaded stents, implants and prostheses are reviewed, along with devices produced to fit hard-to-attach body parts such as nasal masks, vaginal rings or mouthguards. The most promising 3DP techniques for such devices and the complementary technologies surrounding these inventions are also discussed, particularly the scanners useful for mapping body parts. Health regulatory concerns regarding the new use of such technology are also analysed.

SUMMARY

The scenario discussed in this review shows that for wearable 3DP drug devices to become a tangible reality to users, it will be necessary to overcome the existing regulatory barriers, create new interfaces with electronic systems and improve the mapping mechanisms of body surfaces.

Measurement error using a SeeMaLab structured light 3D scanner against a Microscribe 3D digitizer

Background

Geometric morphometrics is a powerful approach to capture and quantify morphological shape variation. Both 3D digitizer arms and structured light surface scanners are portable, easy to use, and relatively cheap, which makes these two capturing devices obvious choices for geometric morphometrics. While digitizer arms have been the “gold standard”, benefits of having full 3D models are manifold. We assessed the measurement error and investigate bias associated with the use of an open-source, high-resolution structured light scanner called SeeMaLab against the popular Microscribe 3D digitizer arm.

Methodology

The analyses were based on 22 grey seal (Halichoerus grypus) skulls. 31 fixed anatomical landmarks were annotated both directly using a Microscribe 3D digitizer and on reconstructed 3D digital models created from structured light surface scans. Each skull was scanned twice. Two operators annotated the landmarks, each twice on all the skulls and 3D models, allowing for the investigation of multiple sources of measurement error. We performed multiple Procrustes ANOVAs to compare the two devices in terms of within- and between-operator error, to quantify the measurement error induced by device, to compare between-device error with other sources of variation, and to assess the level of scanning-related error. We investigated the presence of general shape bias due to device and operator.

Results

Similar precision was obtained with both devices. If landmarks that were identified as less clearly defined and thus harder to place were omitted, the scanner pipeline would achieve higher precision than the digitizer. Between-operator error was biased and seemed to be smaller when using the scanner pipeline. There were systematic differences between devices, which was mainly driven by landmarks less clearly defined. The factors device, operator and landmark replica were all statistically significant and of similar size, but were minor sources of total shape variation, compared to the biological variation among grey seal skulls. The scanning-related error was small compared to all other error sources.

Conclusions

As the scanner showed precision similar to the digitizer, a scanner should be used if the advantages of obtaining detailed 3D models of a specimen are desired. To obtain high precision, a pre-study should be conducted to identify difficult landmarks. Due to the observed bias, data from different devices and/or operators should not be combined when the expected biological variation is small, without testing the landmarks for repeatability across platforms and operators. For any study necessitating the combination of landmark measurements from different operators, the scanner pipeline will be better suited. The small scanning-related error indicates that by following the same scanning protocol, different operators can be involved in the scanning process without introducing significant error.

ALPACA: A fast and accurate computer vision approach for automated landmarking of three‐dimensional biological structures

Landmark‐based geometric morphometrics has emerged as an essential discipline for the quantitative analysis of size and shape in ecology and evolution. With the ever‐increasing density of digitized landmarks, the possible development of a fully automated method of landmark placement has attracted considerable attention. Despite the recent progress in image registration techniques, which could provide a pathway to automation, three‐dimensional (3D) morphometric data are still mainly gathered by trained experts. For the most part, the large infrastructure requirements necessary to perform image‐based registration, together with its system specificity and its overall speed, have prevented its wide dissemination.

Here, we propose and implement a general and lightweight point cloud‐based approach to automatically collect high‐dimensional landmark data in 3D surfaces (Automated Landmarking through Point cloud Alignment and Correspondence Analysis). Our framework possesses several advantages compared with image‐based approaches. First, it presents comparable landmarking accuracy, despite relying on a single, random reference specimen and much sparser sampling of the structure's surface. Second, it can be efficiently run on consumer‐grade personal computers. Finally, it is general and can be applied at the intraspecific level to any biological structure of interest, regardless of whether anatomical atlases are available.

Our validation procedures indicate that the method can recover intraspecific patterns of morphological variation that are largely comparable to those obtained by manual digitization, indicating that the use of an automated landmarking approach should not result in different conclusions regarding the nature of multivariate patterns of morphological variation.

The proposed point cloud‐based approach has the potential to increase the scale and reproducibility of morphometrics research. To allow ALPACA to be used out‐of‐the‐box by users with no prior programming experience, we implemented it as a SlicerMorph module. SlicerMorph is an extension that enables geometric morphometrics data collection and 3D specimen analysis within the open‐source 3D Slicer biomedical visualization ecosystem. We expect that convenient access to this platform will make ALPACA broadly applicable within ecology and evolution.

Homo naledi pollical metacarpal shaft morphology is distinctive and intermediate between that of australopiths and other members of the genus Homo

Homo naledi fossils from the Rising Star cave system provide important insights into the diversity of hand morphology within the genus Homo. Notably, the pollical (thumb) metacarpal (Mc1) displays an unusual suite of characteristics including a median longitudinal crest, a narrow proximal base, and broad flaring intrinsic muscle flanges. The present study evaluates the affinities of H. naledi Mc1 morphology via 3D geometric morphometric analysis of shaft shape using a broader comparative sample (n = 337) of fossil hominins, recent humans, apes, and cercopithecoid monkeys than in prior work. Results confirm that the H. naledi Mc1 is distinctive from most other hominins in being narrow at the proximal end but surmounted by flaring muscle flanges distally. Only StW 418 (Australopithecus cf. africanus) is similar in these aspects of shape. The gracile proximal shaft is most similar to cercopithecoids, Pan, Pongo, Australopithecus afarensis, and Australopithecus sediba, suggesting that H. naledi retains the condition primitive for the genus Homo. In contrast, Neandertal Mc1s are characterized by wide proximal bases and shafts, pinched midshafts, and broad distal flanges, while those of recent humans generally have straight shafts, less robust muscle flanges, and wide proximal shafts/bases. Although uncertainties remain regarding character polarity, the morphology of the H. naledi thumb might be interpreted as a retained intermediate state in a transformation series between the overall gracility of the shaft and the robust shafts of later hominins. Such a model suggests that the addition of broad medial and lateral muscle flanges to a primitively slender shaft was the first modification in transforming the Mc1 into the overall more robust structure exhibited by other Homo taxa including Neandertals and recent Homo sapiens in whose shared lineage the bases and proximal shafts became expanded, possibly as an adaptation to the repeated recruitment of powerful intrinsic pollical muscles.

Assessing the status of the KNM-ER 42700 fossil using Homo erectus neurocranial development

Based on ontogenetic data of endocranial shape, it has been proposed that a younger than previously assumed developmental status of the 1.5-Myr-old KNM-ER 42700 calvaria could explain why the calvaria of this fossil does not conform to the shape of other Homo erectus individuals. Here, we investigate (ecto)neurocranial ontogeny in H. erectus and assess the proposed juvenile status of this fossil using recent Homo sapiens, chimpanzees (Pan troglodytes), and Neanderthals (Homo neanderthalensis) to model and discuss changes in neurocranial shape from the juvenile to adult stages. We show that all four species share common patterns of developmental shape change resulting in a relatively lower cranial vault and expanded supraorbital torus at later developmental stages. This finding suggests that ectoneurocranial data from extant hominids can be used to model the ontogenetic trajectory for H. erectus, for which only one well-preserved very young individual is known. However, our study also reveals differences in the magnitudes and, to a lesser extent, directions of the species-specific trajectories that add to the overall shared pattern of neurocranial shape changes. We demonstrate that the very young H. erectus juvenile from Mojokerto together with subadult and adult H. erectus individuals cannot be accommodated within the pattern of the postnatal neurocranial trajectory for humans. Instead, the chimpanzee pattern might be a better 'fit' for H. erectus despite their more distant phylogenetic relatedness. The data are also compatible with an ontogenetic shape trajectory that is in some regards intermediate between that of recent H. sapiens and chimpanzees, implying a unique trajectory for H. erectus that combines elements of both extant species. Based on this new knowledge, neurocranial shape supports the assessment that KNM-ER 42700 is a young juvenile H. erectus if H. erectus followed an ontogenetic shape trajectory that was more similar to chimpanzees than humans.

A landmark-free morphometrics pipeline for high-resolution phenotyping: application to a mouse model of Down syndrome

Characterising phenotypes often requires quantification of anatomical shape. Quantitative shape comparison (morphometrics) traditionally uses manually located landmarks and is limited by landmark number and operator accuracy. Here, we apply a landmark-free method to characterise the craniofacial skeletal phenotype of the Dp1Tyb mouse model of Down syndrome and a population of the Diversity Outbred (DO) mouse model, comparing it with a landmark-based approach. We identified cranial dysmorphologies in Dp1Tyb mice, especially smaller size and brachycephaly (front-back shortening), homologous to the human phenotype. Shape variation in the DO mice was partly attributable to allometry (size-dependent shape variation) and sexual dimorphism. The landmark-free method performed as well as, or better than, the landmark-based method but was less labour-intensive, required less user training and, uniquely, enabled fine mapping of local differences as planar expansion or shrinkage. Its higher resolution pinpointed reductions in interior mid-snout structures and occipital bones in both the models that were not otherwise apparent. We propose that this landmark-free pipeline could make morphometrics widely accessible beyond its traditional niches in zoology and palaeontology, especially in characterising developmental mutant phenotypes.

How does scanner choice and 3D model resolution affect data accuracy?

Researchers using digital methods often collect data from 3D models at different resolutions, obtained using different scanning techniques. Although previous research has sought to understand whether scanning method and model resolution affect data accuracy, no study has systematically evaluated the sources of error associated with scanning method, data acquisition method and model resolution with the aim of providing practical recommendations about the model resolution required to yield sufficiently accurate data for specimens of given sizes. In this study, using data taken from primate specimens of three broad size categories, we test whether 3D models obtained using five different scanners (Breuckmann SmartSCAN, DAVID/HP 3D Pro S3, NextEngine 2020i, Creaform Go!Scan 20 and microCT/clinicalCT) yield accurate measurements. We assess whether caliper measurements can be used alongside measurements collected from 3D surface models, whether scanning resolution affects measurement accuracy, and how scan resolution, estimated using each scanner's proprietary software, compares to model resolution measured in a standardized way. Each scanner produces 3D models that yield accurate measurements for each size category, however, combining caliper data with those taken from digital models can be problematic. Our results indicate that the accuracy of measurements taken from 3D models depends on both object size and model resolution. Based on our findings, we recommend that small specimens should be scanned at <0.3 mm, medium specimens at 0.3-0.7 mm, and large specimens at 0.3-0.5 mm resolutions if data taken from 3D surface models are to be combined with caliper datasets. We further show, for the first time, that discrepancies in estimated final model resolution are frequently observed across software packages. We therefore recommend that researchers ensure that final model resolutions are adequate based on specimen size and are independently verified using a software package other than the scanner's proprietary software. Finally, we consider the implications of the findings that measurements obtained from surface models are variably consistent with those obtained using calipers.

Three-dimensional surface scanning methods in osteology: A topographical and geometric morphometric comparison

Objectives

Three‐dimensional (3D) data collected by structured light scanners, photogrammetry, and computed tomography (CT) scans are increasingly combined in joint analyses, even though the scanning techniques and reconstruction software differ considerably. The aim of the present study was to compare the quality and accuracy of surface models and landmark data obtained from modern clinical CT scanning, 3D structured light scanner, photogrammetry, and MicroScribe digitizer.

Material and methods

We tested 13 different photogrammetric software tools and compared surface models obtained by different methods for four articulated human pelves in a topographical analysis. We also measured a set of 219 landmarks and semilandmarks twice on every surface as well as directly on the dry bones with a MicroScribe digitizer.

Results

Only one photogrammetric software package yielded surface models of the complete pelves that could be used for further analysis. Despite the complex pelvic anatomy, all three methods (CT scanning, 3D structured light scanning, photogrammetry) yielded similar surface representations with average deviations among the surface models between 100 and 200 μm. A geometric morphometric analysis of the measured landmarks showed that the different scanning methods yielded similar shape variables, but data acquisition via MicroScribe digitizer was most prone to error.

Discussion

We demonstrated that three‐dimensional models obtained by different methods can be combined in a single analysis. Photogrammetry proved to be a cheap, quick, and accurate method to generate 3D surface models at useful resolutions, but photogrammetry software packages differ enormously in quality.

Obtaining new resolutions in carnivore tooth pit morphological analyses: A methodological update for digital taphonomy

Modern day investigation in fields of archaeology and palaeontology can be greatly characterised by an exponential growth of integrated new technologies, nevertheless, while these advances are of great significance to multiple lines of research, their evaluation and update over time is equally as important. Here we present an application of inter and intra-observer analysis in taphonomy based geometric morphometrics, employing robust non-parametric statistical analyses for the study of experimental carnivore tooth pit morphologies. To fully understand the influence of measurement errors in the collection of this data, our statistical assessment was performed on fully superimposed, partially superimposed and raw landmark coordinates collected from 3D surface scanning. Experimental samples used to assess these errors includes wolf and dog tooth pits used in modern day ecological livestock predation analysis. Results obtained from this study highlight the importance of landmark type in the assessment of error, emphasising the value of semi-landmark models over the use of ambiguous Type III landmarks. In addition to this, data also reveals the importance of observer experience for the collection of data alongside an interesting increase in error when working with fully superimposed landmarks due to the “Pinocchio Effect”. Through this study we are able to redefine the geometric morphometric models used for tooth pit morphological analyses. This final hybrid Type II fixed landmark and semi-landmark model presents a significant reduction in human induced error, generating a more metrically reliable and replicable method that can be used for data pooling in future inter-institutional research. These results can be considered a fundamental step forward for carnivore inspired studies, having an impact on archaeological, palaeontological, modern-day ecological research as well as applications in other forensic sciences.

Testing repeatability, measurement error and species differentiation when using geometric morphometrics on complex shapes: a case study of Patagonian lizards of the genus Liolaemus (Squamata: Liolaemini)

The repeatability of findings is the key factor behind scientific reliability, and the failure to reproduce scientific findings has been termed the ‘replication crisis’. Geometric morphometrics is an established tool in evolutionary biology. However, different operators (and/or different methods) could act as large sources of variation in the data obtained. Here, we investigated inter-operator error in geometric morphometric protocols on complex shapes of Liolaemus lizards, as well as measurement error in three taxa varying in their difficulty of digitalization. We also examined the potential for these protocols to discriminate among complex shapes in closely related species. We found a wide range of inter-operator error, contributing between 19.5% and 60% to the total variation. Moreover, measurement error increased with the complexity of the quantified shape. All protocols were able to discriminate between species, but the use of more landmarks did not imply better performance. We present evidence that complex shapes reduce repeatability, highlighting the need to explore different sources of variation that could lead to such low repeatability. Lastly, we suggest some recommendations to improve the repeatability and reliability of geometric morphometrics results.

Morphometric approach to 3D soft-tissue craniofacial analysis and classification of ethnicity, sex, and age

Background

The application of three-dimensional scan models offers a useful resource for studying craniofacial variation. The complex mathematical analysis for facial point acquisition in three-dimensional models has made many craniofacial assessments laborious.

Method

This study investigates three-dimensional (3D) soft-tissue craniofacial variation, with relation to ethnicity, sex and age variables in British and Irish white Europeans. This utilizes a geometric morphometric approach on a subsampled dataset comprising 292 scans, taken from a Liverpool-York Head Model database. Shape variation and analysis of each variable are tested using 20 anchor anatomical landmarks and 480 sliding semi-landmarks.

Results

Significant ethnicity, sex, and age differences are observed for measurement covering major aspects of the craniofacial shape. The ethnicity shows subtle significant differences compared to sex and age; even though it presents the lowest classification accuracy. The magnitude of dimorphism in sex is revealed in the facial, nasal and crania measurement. Significant shape differences are also seen at each age group, with some distinct dimorphic features present in the age groups.

Conclusions

The patterns of shape variation show that white British individuals have a more rounded head shape, whereas white Irish individuals have a narrower head shape. White British persons also demonstrate higher classification accuracy. Regarding sex patterns, males are relatively larger than females, especially in the mouth and nasal regions. Females presented with higher classification accuracy than males. The differences in the chin, mouth, nose, crania, and forehead emerge from different growth rates between the groups. Classification accuracy is best for children and senior adult age groups.

Are geometric morphometric analyses replicable? Evaluating landmark measurement error and its impact on extant and fossil Microtus classification

Geometric morphometric analyses are frequently employed to quantify biological shape and shape variation. Despite the popularity of this technique, quantification of measurement error in geometric morphometric datasets and its impact on statistical results is seldom assessed in the literature. Here, we evaluate error on 2D landmark coordinate configurations of the lower first molar of five North American Microtus (vole) species. We acquired data from the same specimens several times to quantify error from four data acquisition sources: specimen presentation, imaging devices, interobserver variation, and intraobserver variation. We then evaluated the impact of those errors on linear discriminant analysis-based classifications of the five species using recent specimens of known species affinity and fossil specimens of unknown species affinity. Results indicate that data acquisition error can be substantial, sometimes explaining >30% of the total variation among datasets. Comparisons of datasets digitized by different individuals exhibit the greatest discrepancies in landmark precision, and comparison of datasets photographed from different presentation angles yields the greatest discrepancies in species classification results. All error sources impact statistical classification to some extent. For example, no two landmark dataset replicates exhibit the same predicted group memberships of recent or fossil specimens. Our findings emphasize the need to mitigate error as much as possible during geometric morphometric data collection. Though the impact of measurement error on statistical fidelity is likely analysis-specific, we recommend that all geometric morphometric studies standardize specimen imaging equipment, specimen presentations (if analyses are 2D), and landmark digitizers to reduce error and subsequent analytical misinterpretations.

Phylogeny of Libellulidae (Odonata: Anisoptera): comparison of molecular and morphology-based phylogenies based on wing morphology and migration

Background

Establishing the species limits and resolving phylogenetic relationships are primary goals of taxonomists and evolutionary biologists. At present, a controversial question is about interspecific phylogenetic information in morphological features. Are the interspecific relationships established based on genetic information consistent with the traditional classification system? To address these problems, this study analyzed the wing shape structure of 10 species of Libellulidae, explored the relationship between wing shape and dragonfly behavior and living habits, and established an interspecific morphological relationship tree based on wing shape data. By analyzing the sequences of mitochondrial COI gene and the nuclear genes 18S, 28S rRNA and ITS in 10 species of dragonflies, the interspecific relationship was established.

Method

The wing shape information of the male forewings and hindwings was obtained by the geometric morphometrics method. The inter-species wing shape relationship was obtained by principal component analysis (PCA) in MorphoJ1.06 software. The inter-species wing shape relationship tree was obtained by cluster analysis (UPGMA) using Mesquite 3.2 software. The COI, 18S, ITS and 28S genes of 10 species dragonfly were blasted and processed by BioEdit v6 software. The Maximum Likelihood(ML) tree was established by raxmlGUI1.5b2 software. The Bayes inference (BI) tree was established by MrBayes 3.2.6 in Geneious software.

Results

The main difference in forewings among the 10 species of dragonfly was the apical, radial and discoidal regions dominated by the wing nodus. In contrast, the main difference among the hindwings was the apical and anal regions dominated by the wing nodus. The change in wing shape was closely related to the ability of dragonfly to migrate. The interspecific relationship based on molecular data showed that the species of Orthetrum genus branched independently of the other species. Compared to the molecular tree of 10 species, the wing shape clustering showed some phylogenetic information on the forewing shape (with large differences on the forewing shape tree vs. molecular tree), and there was no interspecific phylogenetic information of the hindwing shape tree vs. molecular tree.

Conclusion

The dragonfly wing shape characteristics are closely related to its migration ability. Species with strong ability to migrate have the forewing shape that is longer and narrower, and have larger anal region, whereas the species that prefer short-distance hovering or standing still for a long time have forewing that are wider and shorter, and the anal region is smaller. Integrating morphological and molecular data to evaluate the relationship among dragonfly species shows there is some interspecific phylogenetic information in the forewing shape and none in the hindwing shape. The forewing and hindwing of dragonflies exhibit an inconsistent pattern of morphological changes in different species.

Assessing zygomatic shape and size for estimating sex and ancestry in a South African sample

Unidentified, decomposed and skeletonised human remains are frequently found in South Africa, therefore, standardised, reliable and relevant sex and ancestry estimation methods are required for forensic identification. This study assessed sex and ancestral variation in zygomatic size and shape in a South African population using geometric morphometric analyses. The zygoma of 158 South African individuals were sampled. Eight zygomatic landmarks were captured in 3-dimensions using a Microscribe G2 digitiser and assessed using procrustean geometric morphometrics. Shape and size differences were analysed using multivariate linear regression, discriminant function and canonical variate analyses. Males had significantly larger zygomas than females. Significant shape variation was found between ancestral groups. Bantu-speaking and Mixed ancestry individuals had narrower, shorter and more anteriorly projecting orbital margins, whilst Europeans had vertically elongated and receded orbital margins. European ancestral groups were most discernible from Bantu-speakers and Mixed ancestral groups. Ancestry estimation accuracies improved when ancestry was aggregated with sex. Pairwise ancestry-linked comparisons in females were as follows; Bantu-speakers (76%) from Europeans (72%), Bantu-speakers (71%) from Mixed ancestry (59%) and European (72%) from Mixed ancestry (63%). Similarly, ancestry-linked comparisons in males were as follows; Bantu-speakers (77%) from Europeans (81%), Bantu-speakers (53%) from Mixed ancestry (59%) and European (72%) from Mixed ancestry (82%). Size differences are putatively linked to variations in hormone-regulated growth and muscular robusticity between males and females. Shape variations between ancestral groups are likely attributable to the heterogenous genetic and ancestral origins of the South African population. It is challenging to distinguish between South Africa Bantu speakers and Mixed ancestry people due to Mixed ancestry individuals having variable genetic contributions from Khoesan, Bantu-speakers, Europeans and Asians. Bantu-speaking and Mixed ancestry people had zygomatic morphologies consistent with historical thermoregulatory adaptations to sub-Saharan climates, reported in African-descendants. Zygomatic morphology in European descendants suggests ancestral origins from colder climatic regions. This study demonstrated the utility of the zygoma in distinguishing between ancestral groups in South Africa, but further research is required to develop population-specific standards to distinguish between South African populations with shared African ancestry. The zygoma shows a promising ability to estimate sex and ancestry in South Africans, suggesting population specific standards for this bone may be of forensic interest.

Comparative analysis of femoral biomechanical neck length in primates

The unique abductor capability of the human lesser gluteal muscles among extant hominoids has been suggested to be associated, in part, with biomechanical neck length of the femur. Beyond the hominin lineage, the relationship between biomechanical neck length and locomotor performance remains unclear due, in part, to the limited number of primate taxa directly compared and the need to examine species characterized by a wider range of locomotor diversity. Measurements were taken on the proximal femora of 28 extant taxa, with each species being assigned to a locomotor and phylogenetic category. Pairwise comparisons and phylogenetic generalized least-squares analysis were performed to examine the impact of phylogeny and locomotor adaptation on relative biomechanical neck length. Arboreal quadrupeds that perform varying proportions of climbing/clambering versus leaping were characterized by different biomechanical neck lengths, whereas semi-terrestrial anthropoids that perform either knuckle-walking or palmigrade/digitigrade quadrupedalism were found to have similar relative neck lengths. Samples categorized as either orthograde clamberers or bipeds were distinct from all other anthropoid samples and characterized by the relatively shortest and longest biomechanical neck lengths, respectively. Results of additional analyses that included prosimian primates suggest that relatively long biomechanical necks characterize species adapted to hind limb-dominated forms of locomotion (e.g., vertical clinging and leaping and bipedalism). Thus, biomechanical neck length is useful for signaling reliance on bipedalism (as performed by humans) or leaping, including subtle variation in leaping performance among arboreal quadrupeds. Furthermore, this trait is informative regarding reliance on irregular gait clambering as performed by orangutans.

3D Digitization in Functional Morphology: Where is the Point of Diminishing Returns?

Modern computational and imaging methods are revolutionizing the fields of comparative morphology, biomechanics, and ecomorphology. In particular, imaging tools such as X-ray micro computed tomography (µCT) and diffusible iodine-based contrast enhanced CT allow observing and measuring small and/or otherwise inaccessible anatomical structures, and creating highly accurate three-dimensional (3D) renditions that can be used in biomechanical modeling and tests of functional or evolutionary hypotheses. But, do the larger datasets generated through 3D digitization always confer greater power to uncover functional or evolutionary patterns, when compared with more traditional methodologies? And, if so, why? Here, we contrast the advantages and challenges of using data generated via (3D) CT methods versus more traditional (2D) approaches in the study of skull macroevolution and feeding functional morphology in bats. First, we test for the effect of dimensionality and landmark number on inferences of adaptive shifts during cranial evolution by contrasting results from 3D versus 2D geometric morphometric datasets of bat crania. We find sharp differences between results generated from the 3D versus some of the 2D datasets (xy, yz, ventral, and frontal), which appear to be primarily driven by the loss of critical dimensions of morphological variation rather than number of landmarks. Second, we examine differences in accuracy and precision among 2D and 3D predictive models of bite force by comparing three skull lever models that differ in the sources of skull and muscle anatomical data. We find that a 3D model that relies on skull µCT scans and muscle data partly derived from diceCT is slightly more accurate than models based on skull photographs or skull µCT and muscle data fully derived from dissections. However, the benefit of using the diceCT-informed model is modest given the effort it currently takes to virtually dissect muscles from CT scans. By contrasting traditional and modern tools, we illustrate when and why 3D datasets may be preferable over 2D data, and vice versa, and how different methodologies can complement each other in comparative analyses of morphological function and evolution.

Landmark-based homologous multi-point warping approach to 3D facial recognition using multiple datasets

Over the years, neuroscientists and psychophysicists have been asking whether data acquisition for facial analysis should be performed holistically or with local feature analysis. This has led to various advanced methods of face recognition being proposed, and especially techniques using facial landmarks. The current facial landmark methods in 3D involve a mathematically complex and time-consuming workflow involving semi-landmark sliding tasks. This paper proposes a homologous multi-point warping for 3D facial landmarking, which is verified experimentally on each of the target objects in a given dataset using 500 landmarks (16 anatomical fixed points and 484 sliding semi-landmarks). This is achieved by building a template mesh as a reference object and applying this template to each of the targets in three datasets using an artificial deformation approach. The semi-landmarks are subjected to sliding along tangents to the curves or surfaces until the bending energy between a template and a target form is minimal. The results indicate that our method can be used to investigate shape variation for multiple datasets when implemented on three databases (Stirling, FRGC and Bosphorus).

Evidence of different climatic adaptation strategies in humans and non-human primates

To understand human evolution it is critical to clarify which adaptations enabled our colonisation of novel ecological niches. For any species climate is a fundamental source of environmental stress during range expansion. Mammalian climatic adaptations include changes in size and shape reflected in skeletal dimensions and humans fit general primate ecogeographic patterns. It remains unclear however, whether there are also comparable amounts of adaptation in humans, which has implications for understanding the relative importance of biological/behavioural mechanisms in human evolution. We compare cranial variation between prehistoric human populations from throughout Japan and ecologically comparable groups of macaques. We compare amounts of intraspecific variation and covariation between cranial shape and ecological variables. Given equal rates and sufficient time for adaptation for both groups, human conservation of non-human primate adaptation should result in comparable variation and patterns of covariation in both species. In fact, we find similar amounts of intraspecific variation in both species, but no covariation between shape and climate in humans, contrasting with strong covariation in macaques. The lack of covariation in humans may suggest a disconnect in climatic adaptation strategies from other primates. We suggest this is due to the importance of human behavioural adaptations, which act as a buffer from climatic stress and were likely key to our evolutionary success.

Measurement error in μCT-based three-dimensional geometric morphometrics introduced by surface generation and landmark data acquisition

Computed-tomography-derived (CT-derived) polymesh surfaces are widely used in geometric morphometric studies. This approach is inevitably associated with decisions on scanning parameters, resolution, and segmentation strategies. Although the underlying processing steps have been shown to potentially contribute artefactual variance to three-dimensional landmark coordinates, their effects on measurement error have rarely been assessed systematically in CT-based geometric morphometric studies. The present study systematically assessed artefactual variance in landmark data introduced by the use of different voxel sizes, segmentation strategies, surface simplification degrees, and by inter- and intra-observer differences, and compared their magnitude to true biological variation. Multiple CT-derived surface variants of the anuran (Amphibia: Anura) pectoral girdle were generated by systematic changes in the factors that potentially influence the surface geometries. Twenty-four landmarks were repeatedly acquired by different observers. The contribution of all factors to the total variance in the landmark data was assessed using random-factor nested permanovas. Selected sets of Euclidean distances between landmark sets served further to compare the variance among factor levels. Landmark precision was assessed by landmark standard deviation and compared among observers and days. Results showed that all factors, except for voxel size, significantly contributed to measurement error in at least some of the analyses performed. In total, 6.75% of the variance in landmark data that mimicked a realistic biological study was caused by measurement error. In this landmark dataset, intra-observer error was the major source of artefactual variance followed by inter-observer error; the factor segmentation contributed < 1% and slight surface simplification had no significant effect. Inter-observer error clearly exceeded intra-observer error in a different landmark dataset acquired by six partly inexperienced observers. The results suggest that intra-observer error can potentially be reduced by including a training period prior to the actual landmark acquisition task and by acquiring landmarks in as few sessions as possible. Additionally, the application of moderate and careful surface simplification and, potentially, also the use of case-specific optimal combinations of automatic local thresholding algorithms and parameters for segmentation can help reduce intra-observer error. If landmark data are to be acquired by several observers, it is important to ensure that all observers are consistent in landmark identification. Despite the significant amount of artefactual variance, we have shown that landmark data acquired from microCT-derived surfaces are precise enough to study the shape of anuran pectoral girdles. Yet, a systematic assessment of measurement error is advisable for all geometric morphometric studies.

Developmental stability and environmental stress: A geometric morphometrics analysis of asymmetry in the human femur

OBJECTIVES

The evaluation of developmental stability (DS) by measuring fluctuating asymmetry (FA), a bioindicator of general cumulative stress, is an approach that has often been used to characterize health status in past populations. New techniques of geometric morphometrics now enable a better appreciation of FA than before, with a more refined quantification of variation. The aim of our study is to determine the effectiveness of geometric morphometrics analyses of asymmetry in the human femur for the study of individual DS and inferring health status of human populations.

MATERIALS AND METHODS

We conducted a comparative analysis between two diachronic populations of distinct and known health status. Two samples of 70 pairs of adult femurs from individuals of comparable age range and sex were selected and CT-scanned. For each 3D reconstruction, two sets of 27 landmarks were digitized to quantify and minimize the effect of measurement error on the evaluation of FA.

RESULTS

While the measurement of FA in femoral centroid size seemed comparable between the samples, the amount of FA in femoral shape differed. Individuals who experienced high levels of environmental stress presented higher intra-individual variation. In parallel, results did not reveal any significant differences in DS between sexes or age groups.

DISCUSSION

The geometric morphometrics analysis of femoral asymmetry was effective for distinguishing two populations. After considering various factors of influence, genetics and biomechanics seem to have a limited impact on the results. Expressing FA appears to be normal but dependent on the disturbances of DS produced by environmental stress.

Low resolution scans can provide a sufficiently accurate, cost- and time-effective alternative to high resolution scans for 3D shape analyses

Background

Advances in 3D shape capture technology have made powerful shape analyses, such as geometric morphometrics, more feasible. While the highly accurate micro-computed tomography (µCT) scanners have been the "gold standard," recent improvements in 3D surface scanners may make this technology a faster, portable, and cost-effective alternative. Several studies have already compared the two devices but all use relatively large specimens such as human crania. Here we perform shape analyses on Australia's smallest rodent to test whether a 3D scanner produces similar results to a µCT scanner.

Methods

We captured 19 delicate mouse (Pseudomys delicatulus) crania with a µCT scanner and a 3D scanner for geometric morphometrics. We ran multiple Procrustes ANOVAs to test how variation due to scan device compared to other sources such as biologically relevant variation and operator error. We quantified operator error as levels of variation and repeatability. Further, we tested if the two devices performed differently at classifying individuals based on sexual dimorphism. Finally, we inspected scatterplots of principal component analysis (PCA) scores for non-random patterns.

Results

In all Procrustes ANOVAs, regardless of factors included, differences between individuals contributed the most to total variation. The PCA plots reflect this in how the individuals are dispersed. Including only the symmetric component of shape increased the biological signal relative to variation due to device and due to error. 3D scans showed a higher level of operator error as evidenced by a greater spread of their replicates on the PCA, a higher level of multivariate variation, and a lower repeatability score. However, the 3D scan and µCT scan datasets performed identically in classifying individuals based on intra-specific patterns of sexual dimorphism.

Discussion

Compared to µCT scans, we find that even low resolution 3D scans of very small specimens are sufficiently accurate to classify intra-specific differences. We also make three recommendations for best use of low resolution data. First, we recommend that extreme caution should be taken when analyzing the asymmetric component of shape variation. Second, using 3D scans generates more random error due to increased landmarking difficulty, therefore users should be conservative in landmark choice and avoid multiple operators. Third, using 3D scans introduces a source of systematic error relative to µCT scans, therefore we recommend not combining them when possible, especially in studies expecting little biological variation. Our findings support increased use of low resolution 3D scans for most morphological studies; they are likely also applicable to low resolution scans of large specimens made in a medical CT scanner. As most vertebrates are relatively small, we anticipate our results will bolster more researchers in designing affordable large scale studies on small specimens with 3D surface scanners.