Optimizing digitalization effort in morphometrics

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.

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.

Thirty years of geometric morphometrics: Achievements, challenges, and the ongoing quest for biological meaningfulness

The foundations of geometric morphometrics were worked out about 30 years ago and have continually been refined and extended. What has remained as a central thrust and source of debate in the morphometrics community is the shared goal of meaningful biological inference through a tight connection between biological theory, measurement, multivariate biostatistics, and geometry. Here we review the building blocks of modern geometric morphometrics: the representation of organismal geometry by landmarks and semilandmarks, the computation of shape or form variables via superimposition, the visualization of statistical results as actual shapes or forms, the decomposition of shape variation into symmetric and asymmetric components and into different spatial scales, the interpretation of various geometries in shape or form space, and models of the association between shape or form and other variables, such as environmental, genetic, or behavioral data. We focus on recent developments and current methodological challenges, especially those arising from the increasing number of landmarks and semilandmarks, and emphasize the importance of thorough exploratory multivariate analyses rather than single scalar summary statistics. We outline promising directions for further research and for the evaluation of new developments, such as "landmark-free" approaches. To illustrate these methods, we analyze three-dimensional human face shape based on data from the Avon Longitudinal Study of Parents and Children (ALSPAC).

Quantifying the Selection of Maxillary Anterior Teeth Using Extraoral Anatomical Landmarks

Background: Regardless of skin color, age, sex, or other factors, all beautiful faces follow the divine proportion. Proportions of face components appear to play a role in facial attractiveness.

Aim: The study determines the correlation between the mesiodistal width of anterior maxillary teeth, inter-canthal distance, inter-alar distance, and inter-commissural distance as a criterion for selecting anterior maxillary teeth.

Material and Methods: A cross-sectional study was carried out at the institutional level with a sample size of 200 participants with 100 male and 100 female participants. Inter-canthal distance, inter-alar distance, and inter-commissural distance were measured using the digital caliper and a customized silver scale to measure the mesiodistal width of anterior maxillary teeth. The data obtained were analyzed using Statistical Package for Social Sciences (SPSS) version 24.0 (IBM Corporation, Chicago, USA). Pearson's correlation test calculated the correlation coefficient, and the level of significance was kept at p<0.05.

Result: The width of the maxillary anterior and the inter-canthal gap showed a strong positive correlation, the inter-alar difference and the mesiodistal width of anterior teeth showed a moderately positive correlation, and the estimated inter-commissural width and the mesiodistal width of anterior teeth showed a strong positive correlation (p<0.05).

Conclusion: These parameters are correlated to the dimensions of the tooth size and can act as a guide while selecting the teeth for future rehabilitation treatment when the natural teeth are lost.

Incongruences between morphology and molecular phylogeny provide an insight into the diversification of the Crocidura poensis species complex

Untangling the factors of morphological evolution has long held a central role in the study of evolutionary biology. Extant speciose clades that have only recently diverged are ideal study subjects, as they allow the examination of rapid morphological variation in a phylogenetic context, providing insights into a clade’s evolution. Here, we focus on skull morphological variability in a widely distributed shrew species complex, the Crocidura poensis species complex. The relative effects of taxonomy, size, geography, climate and habitat on skull form were tested, as well as the presence of a phylogenetic signal. Taxonomy was the best predictor of skull size and shape, but surprisingly both size and shape exhibited no significant phylogenetic signal. This paper describes one of the few cases within a mammal clade where morphological evolution does not match the phylogeny. The second strongest predictor for shape variation was size, emphasizing that allometry can represent an easily accessed source of morphological variability within complexes of cryptic species. Taking into account species relatedness, habitat preferences, geographical distribution and differences in skull form, our results lean in favor of a parapatric speciation model within this complex of species, where divergence occurred along an ecological gradient, rather than a geographic barrier.

Determination of Morphogeometric Patterns in Individuals with Total Mandibular Edentulism in the Interforaminal Region from Cone Beam Computed Tomography (CBCT) Scans: A Pilot Study

The aim of this study was to determine the morphogeometric patterns of the interforaminal region from cone beam computed tomography (CBCT) scans of individuals with total mandibular edentulism. CBCT images were obtained from 40 patients with total edentulism who are older (12 men and 28 women; average age of 69.5 ± 9.4 years) and who wore a non-implant-supported, lower, removable, total prosthesis. We conducted a two-dimensional (2D) morphogeometric analysis of the Digital Imaging and Communication in Medicine (DICOM) files from the CBCT scans, and five equidistant cross sections were planned. For the three-dimensional (3D) morphogeometric analysis, standard triangular language (STL) files were obtained after segmentation of the interforaminal mandibular region, and four anatomical landmarks and their respective curves were digitized. The patterns among the shapes were determined using principal component analysis (PCA) on MorphoJ software (version 1.07a). The results of the 2D morphogeometric analyses for PCA of the interforaminal mandibular paramedian region were PC1 or elongated drop shape, 54.78%; PC2 or wineskin shape, 17.65%; PC3 or pear shape, 11.77%; and PC4 or eggplant shape, 5.71%, and those for PCA of the symphyseal region were PC1 or elongated drop shape, 62.13%; PC2 or ovoid shape, 11.64%; PC3 or triangular shape, 9.71%; and PC4 or tuber shape, 4.96%. The results of the 3D morphogeometric analyses for the interforaminal hemimandibular region were PC1, 59.83%; PC2, 10.39%; PC3, 7.67%; and PC4, 5.09%. This study provides relevant information for future clinical guidelines on prosthetics and implants, in addition to proposing the use of new technologies that support diagnosis and treatment in patients with edentulism.

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.