Sharing is caring? Measurement error and the issues arising from combining 3D morphometric datasets

Assessing brain neuroplasticity: Surface morphometric analysis of cortical changes induced by Quadrato motor training

Morphological markers for brain plasticity are still lacking and their findings are challenged by the extreme variability of cortical brain surface. Trying to overcome the "correspondence problem," we applied a landmark-free method (the generalized procrustes surface analysis (GPSA)) for investigating the shape variation of cortical surface in a group of 40 healthy volunteers (i.e., the practice group) subjected to daily motor training known as Quadrato motor training (QMT). QMT is a sensorimotor walking meditation that aims at balancing body, cognition, and emotion. More specifically, QMT requires coordination and attention and consists of moving in one of three possible directions on corners of a 50 × 50 cm2. Brain magnetic resonance images (MRIs) of practice group (acquired at baseline, as well as after 6 and 12 weeks of QMT), were 3D reconstructed and here compared with brain MRIs of six more volunteers never practicing the QMT (naïve group). Cortical regions mostly affected by morphological variations were visualized on a 3D average color-scaled brain surface indicating from higher (red) to lower (blue) levels of variation. Cortical regions interested in most of the shape variations were as follows: (1) the supplementary motor cortex; (2) the inferior frontal gyrus (pars opercolaris) and the anterior insula; (3) the visual cortex; (4) the inferior parietal lobule (supramarginal gyrus and angular gyrus). Our results show that surface morphometric analysis (i.e., GPSA) can be applied to assess brain neuroplasticity processes, such as those stimulated by QMT.

What we see is what we touch? Sex estimation on the pelvis in virtual anthropology

BACKGROUND

Computed tomography (CT) scans are a convenient means to study 3D reconstructions of bones. However, errors associated with the different nature of the observation, e.g. visual and tactile (on dry bone) versus visual only (on a screen) have not been thoroughly investigated.

MATERIALS AND METHODS

We quantified the errors between modalities for sex estimation protocols of nonmetric (categorical and ordinal) and metric data, using 200 dry pelves of archaeological origin and the CT reconstructions of the same bones. In addition, we 3D surface scanned a subsample of 39 pelves to compare observations with dry bone and CT data. We did not focus on the sex estimation accuracy but solely on the consistency of the scoring, hence, the interchangeability of the modalities.

RESULTS

Metric data yielded the most consistent results. Among the nonmetric protocols, ordinal data performed better than categorical data. We applied a slightly modified description for the trait with the highest errors and grouped the traits according to consistency and availability in good, intermediate, and poor.

DISCUSSION

The investigated modalities were interchangeable as long as the trait definition was not arbitrary. Dry bone (gold standard) performed well, and CT and 3D surface scans performed better. We recommend researchers test their affinity for using virtual modalities. Future studies could use our consistency analysis and combine the best traits, validating their accuracy on various modalities.

A landmark-free analysis of the pelvic girdle in Sulawesi ricefishes (Adrianichthyidae): How 2D and 3D geometric morphometrics can complement each other in the analysis of a complex structure

Geometric morphometrics (GM) enable the quantification of morphological variation on various scales. Recent technical advances allow analyzing complex three-dimensional shapes also in cases where landmark-based approaches are not appropriate. Pelvic girdle bones (basipterygia) of Sulawesi ricefishes are 3D structures that challenge traditional morphometrics. We hypothesize that the pelvic girdle of ricefishes experienced sex-biased selection pressures in species where females provide brood care by carrying fertilized eggs supported by elongated pelvic fins ("pelvic brooding"). We test this by comparing pelvic bone shapes of both sexes in species exhibiting pelvic brooding and the more common reproductive strategy "transfer brooding," by using landmark-free 2D and 3D GM, as well as qualitative shape descriptions. Both landmark-free approaches revealed significant interspecific pelvic bone variation in the lateral process, medial facing side of the pelvic bone, and overall external and internal wing shape. Within pelvic brooders, the three analyzed species are clearly distinct, while pelvic bones of the genus Adrianichthys are more similar to transfer brooding Oryzias. Female pelvic brooding Oryzias exhibit prominent, medially pointing tips extending from the internal wing and basipterygial plate that are reduced or absent in conspecific males, Adrianichthys and transfer brooding Oryzias, supporting our hypothesis that selection pressures affecting pelvic girdle shape are sex-biased in Sulawesi ricefishes. Furthermore, both sexes of pelvic brooding Oryzias have overall larger pelvic bones than other investigated ricefishes. Based on these differences, we characterized two reproductive strategy- and sex-dependent pelvic girdle types for Sulawesi ricefishes. Morphological differences between the investigated pelvic brooding genera Adrianichthys and Oryzias provide additional evidence for two independent origins of pelvic brooding. Overall, our findings add to a better understanding on traits related to pelvic brooding in ricefishes and provide a basis for upcoming studies on pelvic girdle function and morphology.

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.

A deep learning approach for morphological feature extraction based on variational auto-encoder: an application to mandible shape

Shape measurements are crucial for evolutionary and developmental biology; however, they present difficulties in the objective and automatic quantification of arbitrary shapes. Conventional approaches are based on anatomically prominent landmarks, which require manual annotations by experts. Here, we develop a machine-learning approach by presenting morphological regulated variational AutoEncoder (Morpho-VAE), an image-based deep learning framework, to conduct landmark-free shape analysis. The proposed architecture combines the unsupervised and supervised learning models to reduce dimensionality by focusing on morphological features that distinguish data with different labels. We applied the method to primate mandible image data. The extracted morphological features reflected the characteristics of the families to which the organisms belonged, despite the absence of correlation between the extracted morphological features and phylogenetic distance. Furthermore, we demonstrated the reconstruction of missing segments from incomplete images. The proposed method provides a flexible and promising tool for analyzing a wide variety of image data of biological shapes even those with missing segments.

The relative performance of geometric morphometrics and linear‐based methods in the taxonomic resolution of a mammalian species complex

Morphology-based taxonomic research frequently applies linear morphometrics (LMM) in skulls to quantify species distinctions. The choice of which measurements to collect generally relies on the expertise of the investigators or a set of standard measurements, but this practice may ignore less obvious or common discriminatory characteristics. In addition, taxonomic analyses often ignore the potential for subgroups of an otherwise cohesive population to differ in shape purely due to size differences (or allometry). Geometric morphometrics (GMM) is more complicated as an acquisition technique but can offer a more holistic characterization of shape and provides a rigorous toolkit for accounting for allometry. In this study, we used linear discriminant analysis (LDA) to assess the discriminatory performance of four published LMM protocols and a 3D GMM dataset for three clades of antechinus known to differ subtly in shape. We assessed discrimination of raw data (which are frequently used by taxonomists); data with isometry (i.e., overall size) removed; and data after allometric correction (i.e., with nonuniform effects of size removed). When we visualized the principal component analysis (PCA) plots, we found that group discrimination among raw data was high for LMM. However, LMM datasets may inflate PC variance accounted in the first two PCs, relative to GMM. GMM discriminated groups better after isometry and allometry were removed in both PCA and LDA. Although LMM can be a powerful tool to discriminate taxonomic groups, we show that there is substantial risk that this discrimination comes from variation in size, rather than shape. This suggests that taxonomic measurement protocols might benefit from GMM-based pilot studies, because this offers the option of differentiating allometric and nonallometric shape differences between species, which can then inform on the development of the easier-to-apply LMM protocols.

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.

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.

Their young bite better: On- and off-host selection pressure as drivers for evolutionary-developmental modification in Rhipicephalus ticks

Distinct life stages may experience different selection pressures influencing phenotypic evolution. Morphological evolution is also constrained by early phenotypes, since early development forms the phenotypic basis of later development. This work investigates evolutionary-developmental modification in three life stages and both sexes of 24 Rhipicephalus species using phylogenetic comparative methods for geometric morphometrics of basis capituli (basal mouthpart structure used for host attachment), and scutum or conscutum areas (proxy for overall body size). Findings indicate species using large hosts at early life stages have distinct basis capituli shapes, correlated with host size, enabling attachment to the tough skins of large hosts. Host-truncate species (one- and two-host) generally retain these adaptive features into later life stages, suggesting neoteny is linked to the evolution of host truncation. In contrast, species using small hosts at early life stages have lost these features. Developmental trajectories differ significantly between host-use strategies (niches), and correlate with distinct clades. In two-host and three-host species using large hosts at early life stages, developmental change is heterotopically accelerated (greater cell mass development) before the first off-host period where selection probably favours large individuals able to better resist dehydration when questing (waiting) for less abundant, less active hosts. In other species, development is heterotopically reduced (neotenic), possibly because dehydration risk is bypassed by prolonged host attachment (one-host species - heterotopic neoteny), or is allometrically repatterned possibly by using highly abundant and active hosts (three-host species using small hosts at early life stages - allometric repatterning). These findings highlight complex trade-offs between on- and off-host factors of free-living ectoparasite ecology, which mediate responses to diverse selection pressures varied by life stage and host-use strategy. It is proposed that these trade-offs shape evolutionary-developmental morphology and diversity of Rhipicephalus ticks.

One Genus or Two? Evaluating Whether Gracile and Robust Capuchin Monkeys are Validly Classified as Separate Genera Based on Craniofacial Shape

Assessments of whether closely related species should be classified into more than one genus have been a longstanding source of controversy in primatology. For example, researchers hold differing opinions about whether cebine species should be classified into one or two genera. In this study, we investigated whether craniofacial shape is a reliable taxonomic indicator among cebines and statistically evaluated whether the magnitude of craniofacial shape differences observed among gracile and robust capuchin species is consistent with a two-genus taxonomic framework. We quantify craniofacial shape using 3D landmark data taken from 72 surface models, representing five cebine species (Cebus albifrons, C. capucinus, C. olivaceus, C. (Sapajus) libidinosus, and C. (S.) macrocephalus). We find that although statistically significant shape differences exist between gracile and robust capuchins in all four craniofacial regions investigated (face and palate, basicranium, calvarium, and frontal region of the calvarium), the magnitude of shape differences between species pairs does not support gracile and robust species being classified into separate genera. The shape of the frontal region of the calvarium and the face and palate show the highest magnitude of shape differences between the gracile and robust capuchin groups, and both regions are good taxonomic predictors, showing correct classification rates of 97% and 96%, respectively. At the species-level, face and palate shape is the only craniofacial measure that consistently shows high classification rates among species (84-97% for combined-sex analyses). Our findings suggest that robust capuchin species that are often assigned to Sapajus may be more appropriately considered as Cebus under a single-genus framework for cebines based on craniofacial shape evidence.

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.

Evolution of the bovid cranium: morphological diversification under allometric constraint

The role of environmental selection in generating novel morphology is often taken for granted, and morphology is generally assumed to be adaptive. Bovids (antelopes and relatives) are widely differentiated in their dietary and climatic preferences, and presumably their cranial morphologies are the result of adaptation to different environmental pressures. In order to test these ideas, we performed 3D geometric morphometric analyses on 141 crania representing 96 bovid species in order to assess the influence of both extrinsic (e.g. diet, habitat) and intrinsic (size, modularity) factors on cranial shape. Surprisingly, we find that bovid crania are highly clumped in morphospace, with a large number of ecologically disparate species occupying a very similar range of morphology clustered around the mean shape. Differences in shape among dietary, habitat, and net primary productivity categories are largely non-significant, but we found a strong interaction between size and diet in explaining shape. We furthermore found no evidence for modularity having played a role in the generation of cranial differences across the bovid tree. Rather, the distribution of bovid cranial morphospace appears to be mainly the result of constraints imposed by a deeply conserved size-shape allometry, and dietary diversification the result of adaptation of existing allometric pathways.

Can morphotaxa be assessed with photographs? Estimating the accuracy of two-dimensional cranial geometric morphometrics for the study of threatened populations of African monkeys

The classification of most mammalian orders and families is under debate and the number of species is likely greater than currently recognized. Improving taxonomic knowledge is crucial, as biodiversity is in rapid decline. Morphology is a source of taxonomic knowledge, and geometric morphometrics applied to two dimensional (2D) photographs of anatomical structures is commonly employed for quantifying differences within and among lineages. Photographs are informative, easy to obtain, and low cost. 2D analyses, however, introduce a large source of measurement error when applied to crania and other highly three dimensional (3D) structures. To explore the potential of 2D analyses for assessing taxonomic diversity, we use patas monkeys (Erythrocebus), a genus of large, semi-terrestrial, African guenons, as a case study. By applying a range of tests to compare ventral views of adult crania measured both in 2D and 3D, we show that, despite inaccuracies accounting for up to one-fourth of individual shape differences, results in 2D almost perfectly mirror those in 3D. This apparent paradox might be explained by the small strength of covariation in the component of shape variance related to measurement error. A rigorous standardization of photographic settings and the choice of almost coplanar landmarks are likely to further improve the correspondence of 2D to 3D shapes. 2D geometric morphometrics is, thus, appropriate for taxonomic comparisons of patas ventral crania. Although it is too early to generalize, our results corroborate similar findings from previous research in mammals, and suggest that 2D shape analyses are an effective heuristic tool for morphological investigation of small differences.

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.

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.

Optimizing digitalization effort in morphometrics

Quantifying phenotypes is a common practice for addressing questions regarding morphological variation. The time dedicated to data acquisition can vary greatly depending on methods and on the required quantity of information. Optimizing digitization effort can be done either by pooling datasets among users, by automatizing data collection, or by reducing the number of measurements. Pooling datasets among users is not without risk since potential errors arising from multiple operators in data acquisition prevent combining morphometric datasets. We present an analytical workflow to estimate within and among operator biases and to assess whether morphometric datasets can be pooled. We show that pooling and sharing data requires careful examination of the errors occurring during data acquisition, that the choice of morphometric approach influences amount of error, and that in some cases pooling data should be avoided. The demonstration is based on a worked example (Sus scrofa teeth) using a combinations of 18 morphometric approaches and datasets for which we identified and quantified several potential sources of errors in the workflow. We show that it is possible to estimate the analytical power of a study using a small subset of data to select the best morphometric protocol and to optimize the number of variables necessary for analysis. In particular, we focus on semi-landmarks, which often produce an inflation of variables in contrast to the number of available observations use in statistical testing. We show how the workflow can be used for optimizing digitization efforts and provide recommendations for best practices in error management.

Australian Rodents Reveal Conserved Cranial Evolutionary Allometry across 10 Million Years of Murid Evolution

AbstractAmong vertebrates, placental mammals are particularly variable in the covariance between cranial shape and body size (allometry), with rodents being a major exception. Australian murid rodents allow an assessment of the cause of this anomaly because they radiated on an ecologically diverse continent notably lacking other terrestrial placentals. Here, we use 3D geometric morphometrics to quantify species-level and evolutionary allometries in 38 species (317 crania) from all Australian murid genera. We ask whether ecological opportunity resulted in greater allometric diversity compared with other rodents or whether conserved allometry suggests intrinsic constraints and/or stabilizing selection. We also assess whether cranial shape variation follows the proposed rule of craniofacial evolutionary allometry (CREA), whereby larger species have relatively longer snouts and smaller braincases. To ensure we could differentiate parallel versus nonparallel species-level allometric slopes, we compared the slopes of rarefied samples across all clades. We found exceedingly conserved allometry and CREA-like patterns across the 10-million-year split between Mus and Australian murids. This could support both intrinsic-constraint and stabilizing-selection hypotheses for conserved allometry. Large-bodied frugivores evolved faster than other species along the allometric trajectory, which could suggest stabilizing selection on the shape of the masticatory apparatus as body size changes.

Forensic sex estimation using the vertebrae: an evaluation on two European populations

Sex estimation is one of the primary steps for constructing the biological profile of skeletal remains leading to their identification in the forensic context. While the pelvis is the most sex diagnostic bone, the cranium and other post-cranial elements have been extensively studied. Earlier research has also focused on the vertebral column with varying results regarding its sex classification accuracy as well as the underlying population specificity. The present study focuses on three easily identifiable vertebrae, namely T1, T12, and L1, and utilizes two modern European populations, a Greek and a Danish, to evaluate their forensic utility in sex identification. To this end, 865 vertebrae from 339 individuals have been analyzed for sexual dimorphism by further evaluating the effects of age-at-death and population affinity on its expression. Our results show that T1 is the best sex diagnostic vertebra for both populations reaching cross-validated accuracy of almost 90%, while age-at-death has limited effect on its sexual dimorphism. On the contrary, T12 and L1 produced varying results ranging from 75 to 83% accuracy with the Greek population exhibiting distinctively more pronounced sexual dimorphism. Additionally, age-at-death had significant effect on sexual dimorphism of T12 and L1 and especially in the Greek female and Danish male groups. Our results on inter-population comparison suggest that vertebral sex discriminant functions, and especially those utilizing multiple measurements, are highly population specific and optimally suitable only for their targeted population. An open-source software tool to facilitate classifying new cases based on our results is made freely available to forensic researchers.

Do we need the third dimension? Quantifying the effect of the z-axis in 3D geometric morphometrics based on sailfin silversides (Telmatherinidae)

This study investigated the impact of the third dimension in geometric morphometrics (GM) using sailfin silversides (Telmatherinidae) from the Malili Lakes of Sulawesi (Indonesia). The three morphospecies of the monophyletic "roundfin" radiation are laterally compressed and vary in shape traits. The results of 2D and 3D GM were compared and quantified to discuss the advantages and disadvantages of both methods for closely related species and their sexes. This approach focused on the head because it is far more complex and three-dimensionally structured than the trunk or the caudal region. The results revealed no significant benefit concerning repeatability and measurement error in 3D GM compared to 2D GM. The z-axis contributed substantially to the variance of the 3D data set but was irrelevant for discrimination of species and sexes in the approach. Limited gain in information was contrasted by substantially higher effort for 3D compared to the 2D analyses. The study concluded that 2D GM is the more efficient shape analysis approach for discriminating roundfins. Broader studies are needed to test which of the two methods is more efficient in distinguishing laterally compressed fishes in general. For future studies, due to the high investment required, this study recommends carefully evaluating the necessity of 3D GM. If in doubt, this study suggests testing for congruence between 2D and 3D GM with a subsample and consequently applying 2D GM in the case of high congruence.

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.

Modern morphometrics and the study of population differences: Good data behind clever analyses and cool pictures?

The study of phenotypic variation in time and space is central to evolutionary biology. Modern geometric morphometrics is the leading family of methods for the quantitative analysis of biological forms. This set of techniques relies heavily on technological innovation for data acquisition, often in the form of 2D or 3D digital images, and on powerful multivariate statistical tools for their analysis. However, neither the most sophisticated device for computerized imaging nor the best statistical test can produce accurate, robust and reproducible results, if it is not based on really good samples and an appropriate use of the 'measurements' extracted from the data. Using examples mostly from my own work on mammal craniofacial variation and museum specimens, I will show how easy it is to forget these most basic assumptions, while focusing heavily on analytical and visualization methods, and much less on the data that generate potentially powerful analyses and visually appealing diagrams.

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.

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).

Deciphering African late middle Pleistocene hominin diversity and the origin of our species

The origin of Homo sapiens remains a matter of debate. The extent and geographic patterning of morphological diversity among Late Middle Pleistocene (LMP) African hominins is largely unknown, thus precluding the definition of boundaries of variability in early H. sapiens and the interpretation of individual fossils. Here we use a phylogenetic modelling method to predict possible morphologies of a last common ancestor of all modern humans, which we compare to LMP African fossils (KNM-ES 11693, Florisbad, Irhoud 1, Omo II, and LH18). Our results support a complex process for the evolution of H. sapiens, with the recognition of different, geographically localised, populations and lineages in Africa - not all of which contributed to our species' origin. Based on the available fossils, H. sapiens appears to have originated from the coalescence of South and, possibly, East-African source populations, while North-African fossils may represent a population which introgressed into Neandertals during the LMP.

Tissue preservation can affect geometric morphometric analyses: a case study using fish body shape

In geometric morphometrics, the extent of variation attributable to non-biological causes (i.e. measurement error) is sometimes overlooked. The effects of this variation on downstream statistical analyses are also largely unknown. In particular, it is unclear whether specimen preservation induces substantial variation in shape and whether such variation affects downstream statistical inference. Using a combination of empirical fish body shape data and realistic simulations, we show that preservation introduces substantial artefactual variation and significant non-random error (i.e. bias). Most changes in shape occur when fresh fish are frozen and thawed, whereas a smaller change in shape is observed when frozen and thawed fish are fixed in formalin and transferred to ethanol. Surprisingly, we also show that, in our case, preservation produces only minor effects on three downstream analyses of shape variation: classification using canonical variate analysis, permutation tests of differences in means and computations of differences in mean shape between groups. Even mixing of differently preserved specimens has a relatively small effect on downstream analyses. However, we suggest that mixing fish with different preservation should still be avoided and discuss the conditions in which this practice might be justified.

The multifactorial nature of beak and skull shape evolution in parrots and cockatoos (Psittaciformes)

Background

The Psittaciformes (parrots and cockatoos) are characterised by their large beaks, and are renowned for their ability to produce high bite forces. These birds also possess a suite of modifications to their cranial architecture interpreted to be adaptations for feeding on mechanically resistant foods, yet the relationship between cranial morphology and diet has never been explicitly tested. Here, we provide a three-dimensional geometric morphometric analysis of the developmental and biomechanical factors that may be influencing the evolution of psittaciformes’ distinctive cranial morphologies.

Results

Contrary to our own predictions, we find that dietary preferences for more- or less- mechanically resistant foods have very little influence on beak and skull shape, and that diet predicts only 2.4% of the shape variation in psittaciform beaks and skulls. Conversely, evolutionary allometry and integration together predict almost half the observed shape variation, with phylogeny remaining an important factor in shape identity throughout our analyses, particularly in separating cockatoos (Cacatuoidea) from the true parrots (Psittacoidea).

Conclusions

Our results are similar to recent findings about the evolutionary trajectories of skull and beak shape in other avian families. We therefore propose that allometry and integration are important factors causing canalization of the avian head, and while diet clearly has an influence on beak shape between families, this may not be as important at driving evolvability within families as is commonly assumed.

Electronic supplementary material

The online version of this article (10.1186/s12862-019-1432-1) contains supplementary material, which is available to authorized users.

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.

Effect of preservation on fish morphology over time: Implications for morphological studies

It has long been recognized that the process of preserving biological specimens results in alterations of body shape, though detailed studies examining the degree to which morphological changes occur throughout the preservation process are lacking. We utilize geometric morphometric analyses, an increasingly common tool for examining shape variation in a wide variety of biological disciplines, to examine the effects of formalin and ethanol preservation on the body shape of 10 freshwater fish species over time: from fresh specimens to eight weeks after preservation. We found significant changes in body shape among fresh and formalin fixed specimens. Furthermore, changes in body shape continue to occur after subsequent ethanol preservation. Two fish species collected at multiple localities show significant morphological differences for a limited number of morphometric characters. However, the significance, or lack thereof, often changed inconsistently from one stage of preservation to another. We conclude that morphometric analyses would ideally be performed on fresh specimens. However, recognizing that this is not always feasible, it is important to be aware of the morphometric changes that can occur during preservation.

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.

Procrustes-based geometric morphometrics on MRI images: An example of inter-operator bias in 3D landmarks and its impact on big datasets

Using 3D anatomical landmarks from adult human head MRIs, we assessed the magnitude of inter-operator differences in Procrustes-based geometric morphometric analyses. An in depth analysis of both absolute and relative error was performed in a subsample of individuals with replicated digitization by three different operators. The effect of inter-operator differences was also explored in a large sample of more than 900 individuals. Although absolute error was not unusual for MRI measurements, including bone landmarks, shape was particularly affected by differences among operators, with up to more than 30% of sample variation accounted for by this type of error. The magnitude of the bias was such that it dominated the main pattern of bone and total (all landmarks included) shape variation, largely surpassing the effect of sex differences between hundreds of men and women. In contrast, however, we found higher reproducibility in soft-tissue nasal landmarks, despite relatively larger errors in estimates of nasal size. Our study exemplifies the assessment of measurement error using geometric morphometrics on landmarks from MRIs and stresses the importance of relating it to total sample variance within the specific methodological framework being used. In summary, precise landmarks may not necessarily imply negligible errors, especially in shape data; indeed, size and shape may be differentially impacted by measurement error and different types of landmarks may have relatively larger or smaller errors. Importantly, and consistently with other recent studies using geometric morphometrics on digital images (which, however, were not specific to MRI data), this study showed that inter-operator biases can be a major source of error in the analysis of large samples, as those that are becoming increasingly common in the 'era of big data'.

Body size and allometric variation in facial shape in children

OBJECTIVES

Morphological integration, or the tendency for covariation, is commonly seen in complex traits such as the human face. The effects of growth on shape, or allometry, represent a ubiquitous but poorly understood axis of integration. We address the question of to what extent age and measures of size converge on a single pattern of allometry for human facial shape.

METHODS

Our study is based on two large cross-sectional cohorts of children, one from Tanzania and the other from the United States (N = 7,173). We employ 3D facial imaging and geometric morphometrics to relate facial shape to age and anthropometric measures.

RESULTS

The two populations differ significantly in facial shape, but the magnitude of this difference is small relative to the variation within each group. Allometric variation for facial shape is similar in both populations, representing a small but significant proportion of total variation in facial shape. Different measures of size are associated with overlapping but statistically distinct aspects of shape variation. Only half of the size-related variation in facial shape can be explained by the first principal component of four size measures and age while the remainder associates distinctly with individual measures.

CONCLUSIONS

Allometric variation in the human face is complex and should not be regarded as a singular effect. This finding has important implications for how size is treated in studies of human facial shape and for the developmental basis for allometric variation more generally.

Evaluating causes of error in landmark-based data collection using scanners

In this study, we assess the precision, accuracy, and repeatability of craniodental landmarks (Types I, II, and III, plus curves of semilandmarks) on a single macaque cranium digitally reconstructed with three different surface scanners and a microCT scanner. Nine researchers with varying degrees of osteological and geometric morphometric knowledge landmarked ten iterations of each scan (40 total) to test the effects of scan quality, researcher experience, and landmark type on levels of intra- and interobserver error. Two researchers additionally landmarked ten specimens from seven different macaque species using the same landmark protocol to test the effects of the previously listed variables relative to species-level morphological differences (i.e., observer variance versus real biological variance). Error rates within and among researchers by scan type were calculated to determine whether or not data collected by different individuals or on different digitally rendered crania are consistent enough to be used in a single dataset. Results indicate that scan type does not impact rate of intra- or interobserver error. Interobserver error is far greater than intraobserver error among all individuals, and is similar in variance to that found among different macaque species. Additionally, experience with osteology and morphometrics both positively contribute to precision in multiple landmarking sessions, even where less experienced researchers have been trained in point acquisition. Individual training increases precision (although not necessarily accuracy), and is highly recommended in any situation where multiple researchers will be collecting data for a single project.

Sharing is caring? Measurement error and the issues arising from combining 3D morphometric datasets

Geometric morphometrics is routinely used in ecology and evolution and morphometric datasets are increasingly shared among researchers, allowing for more comprehensive studies and higher statistical power (as a consequence of increased sample size). However, sharing of morphometric data opens up the question of how much nonbiologically relevant variation (i.e., measurement error) is introduced in the resulting datasets and how this variation affects analyses. We perform a set of analyses based on an empirical 3D geometric morphometric dataset. In particular, we quantify the amount of error associated with combining data from multiple devices and digitized by multiple operators and test for the presence of bias. We also extend these analyses to a dataset obtained with a recently developed automated method, which does not require human-digitized landmarks. Further, we analyze how measurement error affects estimates of phylogenetic signal and how its effect compares with the effect of phylogenetic uncertainty. We show that measurement error can be substantial when combining surface models produced by different devices and even more among landmarks digitized by different operators. We also document the presence of small, but significant, amounts of nonrandom error (i.e., bias). Measurement error is heavily reduced by excluding landmarks that are difficult to digitize. The automated method we tested had low levels of error, if used in combination with a procedure for dimensionality reduction. Estimates of phylogenetic signal can be more affected by measurement error than by phylogenetic uncertainty. Our results generally highlight the importance of landmark choice and the usefulness of estimating measurement error. Further, measurement error may limit comparisons of estimates of phylogenetic signal across studies if these have been performed using different devices or by different operators. Finally, we also show how widely held assumptions do not always hold true, particularly that measurement error affects inference more at a shallower phylogenetic scale and that automated methods perform worse than human digitization.