Geomorph: anrpackage for the collection and analysis of geometric morphometric shape data

Vibrissae (whiskers) are important components of the mammalian tactile sensory system, and primarily function as detectors of vibrotactile information from the environment. Pinnipeds possess the largest vibrissae among mammals and their vibrissal hair shafts demonstrate a diversity of shapes. The vibrissae of most phocid seals exhibit a beaded morphology with repeating sequences of crests and troughs along their length. However, there are few detailed analyses of pinniped vibrissal morphology, and these are limited to a few species. Therefore, we comparatively characterized differences in vibrissal hair shaft morphologies among phocid species with a beaded profile, phocid species with a smooth profile, and otariids with a smooth profile using traditional and geometric morphometric methods. Traditional morphometric measurements (peak-to-peak distance, crest width, trough width and total length) were collected using digital photographs. Elliptic Fourier analysis (geometric morphometrics) was used to quantify the outlines of whole vibrissae. The traditional and geometric morphometric datasets were subsequently combined by mathematically scaling each to true rank, followed by a single eigendecomposition. Quadratic discriminant function analysis demonstrated that 79.3, 97.8 and 100% of individuals could be correctly classified to their species based on vibrissal shape variables in the traditional, geometric and combined morphometric analyses, respectively. Phocids with beaded vibrissae, phocids with smooth vibrissae, and otariids each occupied distinct morphospace in the geometric morphometric and combined data analyses. Otariids split into two groups in the geometric morphometric analysis and gray seals appeared intermediate between beaded- and smooth-whiskered species in the traditional and combined analyses. Vibrissal hair shafts modulate the transduction of environmental stimuli to the mechanoreceptors in the follicle-sinus complex (F-SC), which results in vibrotactile reception, but it is currently unclear how the diversity of shapes affects environmental signal modulation.

Improvements in three-dimensional imaging technologies have renewed interest in the study of functional and ecological morphology. Quantitative approaches to shape analysis are used increasingly to study form-function relationships. These methods are computationally intensive, technically demanding, and time-consuming, which may limit sampling potential. There have been few side-by-side comparisons of the effectiveness of such approaches relative to more traditional analyses using linear measurements and ratios. Morphological variation in the distal femur of mammals has been shown to reflect differences in locomotor modes across clades. Thus I tested whether a geometric morphometric analysis of surface shape was superior to a multivariate analysis of ratios for describing ecomorphological patterns in distal femoral variation. A sample of 164 mammalian specimens from 44 genera was assembled. Each genus was assigned to one of six locomotor categories. The same hypotheses were tested using two methods. Six linear measurements of the distal femur were taken with calipers, from which four ratios were calculated. A 3D model was generated with a laser scanner, and analyzed using three dimensional geometric morphometrics. Locomotor category significantly predicted variation in distal femoral morphology in both analyses. Effect size was larger in the geometric morphometric analysis than in the analysis of ratios. Ordination reveals a similar pattern with arboreal and cursorial taxa as extremes on a continuum of morphologies in both analyses. Discriminant functions calculated from the geometric morphometric analysis were more accurate than those calculated from ratios. Both analysis of ratios and geometric morphometric surface analysis reveal similar, biologically meaningful relationships between distal femoral shape and locomotor mode. The functional signal from the morphology is slightly higher in the geometric morphometric analysis. The practical costs of conducting these sorts of analyses should be weighed against potentially slight increases in power when designing protocols for ecomorphological studies.

Geometric morphometrics is the statistical analysis of form based on Cartesian landmark coordinates. After separating shape from overall size, position, and orientation of the landmark configurations, the resulting Procrustes shape coordinates can be used for statistical analysis. Kendall shape space, the mathematical space induced by the shape coordinates, is a metric space that can be approximated locally by a Euclidean tangent space. Thus, notions of distance (similarity) between shapes or of the length and direction of developmental and evolutionary trajectories can be meaningfully assessed in this space. Results of statistical techniques that preserve these convenient properties—such as principal component analysis, multivariate regression, or partial least squares analysis—can be visualized as actual shapes or shape deformations. The Procrustes distance between a shape and its relabeled reflection is a measure of bilateral asymmetry. Shape space can be extended to form space by augmenting the shape coordinates with the natural logarithm of Centroid Size, a measure of size in geometric morphometrics that is uncorrelated with shape for small isotropic landmark variation. The thin-plate spline interpolation function is the standard tool to compute deformation grids and 3D visualizations. It is also central to the estimation of missing landmarks and to the semilandmark algorithm, which permits to include outlines and surfaces in geometric morphometric analysis. The powerful visualization tools of geometric morphometrics and the typically large amount of shape variables give rise to a specific exploratory style of analysis, allowing the identification and quantification of previously unknown shape features.

Geometric morphometrics is a new approach for shape identification in diagnosis of malocclusion. Lateral cephalogram is an X-ray that taken for diagnosing malocclusion in dental setting. The aim of this study was to determine the differences of craniofacial shape in malocclusion by application of two-dimensional geometric morphometrics and to compile the database of malocclusion in adult Malaysian population. Lateral cephalogram radiographs of 381 adults Malaysia (age 18–45) were retrieved retrospectively and assigned to three groups according to their occlusion: class I, class II, and class III. The geometric morphometric shape study incorporated nine landmarks and was analyzed in details using tpsUtil p software. Geometric morphometric analysis such was done using MorphoJ software. The results of the principal component's analysis (PCA) yielded 14 main components responsible for 100% of the variation exhibited by the malocclusion with three highly significant PCA. The highest Mahalanobis distances were exhibited by the malocclusion class II and III population. The Procrustes ANOVA showed that the shape effect was highly significant (P<0.01). The discriminant function analysis showed the high percentage of 80% discriminate among the malocclusions after cross-validation. There are significant differences for ANB angle (A point-Nasion-B point) in all malocclusion groups. Class II has the widest ANB angle while class III has the most acute ANB angle. Skeletal shape was clearly associated with dental malocclusion and showed considerable variation. Geometric morphometrics is an alternative research tool and can be used for diagnosing individual classification of malocclusion.

Breathing motion is based on the differential activity of the thoracic, diaphragmatic and abdominal muscles. Muscle contributions differ between rest and exercise conditions and depend on posture and other factors. Traditionally, these changes are investigated on volumetric data using optoelectronic plethysmography (OEP). OEP offers insight into size variations of different chest wall (CW) compartments but does not provide three-dimensional visualization methods of CW breathing kinematics. Here we explore the use of three-dimensional geometric morphometrics to analyse size and shape changes caused by spontaneous breathing motion during quiet (QB), and recovery breathing (REC, immediately after heavy exercise) in two different postures (SIT, sitting on cycle ergometer; STA, standing position). Our findings show that size and shape differ significantly between inspiration and expiration and that differences are greater in REC than in QB. However, this is achieved by stronger expiration in SIT but by greater expiratory and inspiratory movements in STA. Shape analysis suggests that these differences may be attributed to constrained mobility of the shoulder girdle and a minor thoracic spine extension during inspiration owing to position on the ergometer. Breathing motion in STA seems biomechanically less constrained. Geometric morphometrics analyses can provide additional insights into data obtained by OEP.

Sexual Dimorphism of Frontal Sinus: A 2-Dimensional Geometric Morphometric Analysis on Lateral Skull Radiographs

We present here a newly developed software package named Artifact GeoMorph Toolbox 3-D (AGMT3-D). It is intended to provide archaeologists with a simple and easy-to-use tool for performing 3-D landmarks-based geometric morphometric shape analysis on 3-D digital models of archaeological artifacts. It requires no prior knowledge of programming or proficiency in statistics. AGMT3-D consists of a data-acquisition procedure for automatically positioning 3-D models in space and fitting them with grids of 3-D semi-landmarks. It also provides a number of analytical tools and procedures that allow the processing and statistical analysis of the data, including generalized Procrustes analysis, principal component analysis, a warp tool, automatic calculation of shape variabilities and statistical tests. It provides an output of quantitative, objective and reproducible results in numerical, textual and graphic formats. These can be used to answer archaeologically significant questions relating to morphologies and morphological variabilities in artifact assemblages. Following the presentation of the software and its functions, we apply it to a case study addressing the effects of different types of raw material on the morphologies and morphological variabilities present in an experimentally produced Acheulian handaxe assemblage. The results show that there are statistically significant differences between the mean shapes and shape variabilities of handaxes produced on flint and those produced on basalt. With AGMT3-D, users can analyze artifact assemblages and address questions that are deducible from the morphologies and morphological variabilities of material culture assemblages. These questions can relate to issues of, among others, relative chronology, cultural affinities, tool function and production technology. AGMT3-D is aimed at making 3-D landmarks-based geometric morphometric shape analysis more accessible to archaeologists, in the hope that this method will become a tool commonly used by archaeologists.

Geometric morphometric analysis of mandibular morphology for age classification in Indonesian adolescents and adults

To study the intraspecies taxonomy of the Western honeybee (Apis mellifera), geometric morphometrics analyses can now replace the standard morphometry method, yet its availability for microtaxonomy of the Asian honeybee (Apis cerana F.) has not been reported. In order to assess effectiveness of geometric morphometrics analyses using the forewing in the microtaxonomy of the Asian honeybee, 180 individual worker bees were sampled from three sample sites, Jilin, Hainan, and Shaanxi, representing different habitats for A. cerana within China. Bees were analyzed by discrimination analysis using three methods: (1) standard morphometry method with 33 traditional characters, (2) simplified standard morphometry method with only 11 wing vein angles, and (3) geometric morphometrics analyses with 18 wing vein junctions. The results revealed that geometric morphometrics analyses could reflect the variability information of the forewing vein structures of A. cerana. Morphological differentiation at the three sample sites was identified. Cross-validation indicated the percentage of individuals falling into each sample site, were 98.3%, 95.0%, and 88.3% for Jilin, Hainan, and Shaanxi, respectively. Geometric morphometrics analyses produced classification results similar to those produced using the standard morphometry method, and it was superior for presenting the wing vein variability information compared to the simplified standard morphometry method. Therefore, we conclude that geometric morphometrics analyses could be efficient and effective in the microtaxonomy of A. cerana. Furthermore, geometric morphometrics is a potential method for resolving A. cerana subspecies classification issues.

Effect of Different Larval Rearing Temperatures on the Productivity (R_o) and Morphology of the Malaria Vector<i>Anopheles superpictus</i>Grassi (Diptera: Culicidae) Using Geometric Morphometrics

Geometric morphometric analysis reveals ethnic group related differences in the distal femur

Unsupervised machine learning and geometric morphometrics as tools for the identification of inter and intraspecific variations in the Anopheles Maculipennis complex

Geometric morphometric analysis of body shape and sexual dimorphism in Colossoma macropomum.

Forensic odontology is the field of dentistry that identifies human remains. The mandible is the strongest bone in the face and remains intact even in mass disasters. Geometric morphometrics is a shape analysis that uses landmark coordinates that can visualise the variation of the structure. A total of 305 DPT images of 159 male and 146 female Malay children were classified into two age groups: Group 1 (ages 3–7) and Group 2 (ages 8–12). These images were analysed using geometric morphometric analysis. Twenty landmarks were digitised using the tpsDig2 software. MorphoJ was used to perform discriminant function analysis (DFA), canonical variate analysis (CVA), principal component analysis (PCA), generalised Procrustes analysis (GPA), and Procrustes ANOVA. There were significant differences in mandible shape and size between the two age groups and sexes (p &lt; 0.05). The first five principal components (PC1–PC5) explained 75% of the shape variation. The DFA showed 82% accuracy in classifying children into age groups after cross-validation. However, the accuracy among males and females dropped to 62%, due to overlapping characteristics and the absence of secondary sexual traits in children under 12. Geometric morphometry can capture unique morphological shape variables, thus enabling the assessment of sexual dimorphism and age estimation using mandibles to aid forensic odontology. This research supports SDG 16: Peace, Justice and Strong Institutions, by enhancing scientific tools for victim identification and justice in the aftermath of disasters and crimes involving children.

Introduction: Virtual morphometric age assessment on the body of sternum and manubrium bones among the Malay population in Malaysia has never been conducted previously. Materials and methods: In this retrospective study, the morphological structures of the sternum and manubrium of 124 healthy individuals between the ages of 2 and 50 years old were analysed utilising geometric morphometrics. 37 landmark points were digitised on the body of the sternum and manubrium using IDAV software and the results were analysed in MorphoJ. Principal Component Analysis (PCA), Procrustes ANOVA, Discriminant Function Analysis (DFA) and regression on the centroid size to age were carried out to determine if sex and age affected the body of sternum morphology. Results: Geometric morphometric analysis indicates that age is the best method of classifying both body of sternum and manubrium. Regression analysis shows an increase in the size of the bones and reaching adult size before 20 years of age. Sexing is possible with DFA (cross-validation) and the effect is seen more on the sternum compared to the manubrium at 59.7%. Conclusion: The regression figure is useful as it provides a qualitative summary of the sternum and manubrium growth at different age ranges. This figure should be useful for forensic pathologists and medical practitioners who need to predict the age of the sternum body and manubrium by visual assessment.