Sample Size and Geometric Morphometrics Methodology Impact the Evaluation of Morphological Variation
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PROVIDER: S-EPMC10833145 | biostudies-literature | 2024 Jan
REPOSITORIES: biostudies-literature
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Project description:Background and aimsThe relative contributions of inter- and intraspecific variation to phytolith shape and size have only been investigated in a limited number of studies. However, a detailed understanding of phytolith variation patterns among populations or even within a single plant specimen is of key importance for the correct taxonomic identification of grass taxa in fossil samples and for the reconstruction of vegetation and environmental conditions in the past. In this study, we used geometric morphometric analysis for the quantification of different sources of phytolith shape and size variation.MethodsWe used landmark-based geometric morphometric methods for the analysis of phytolith shapes in two extant grass species (Brachypodium pinnatum and B. sylvaticum). For each species, 1200 phytoliths were analysed from 12 leaves originating from six plants growing in three populations. Phytolith shape and size data were subjected to multivariate Procrustes analysis of variance (ANOVA), multivariate regression, principal component analysis and linear discriminant analysis.Key resultsInterspecific variation largely outweighed intraspecific variation with respect to phytolith shape. Individual phytolith shapes were classified with 83 % accuracy into their respective species. Conversely, variation in phytolith shapes within species but among populations, possibly related to environmental heterogeneity, was comparatively low.ConclusionsOur results imply that phytolith shape relatively closely corresponds to the taxonomic identity of closely related grass species. Moreover, our methodological approach, applied here in phytolith analysis for the first time, enabled the quantification and separation of variation that is not related to species discrimination. Our findings strengthen the role of grass phytoliths in the reconstruction of past vegetation dynamics.
| S-EPMC7789106 | biostudies-literature
Project description:Traditional body measurement techniques are commonly used to assess physical health; however, these approaches do not fully represent the complex shape of the human body. Three-dimensional (3D) imaging systems capture rich point cloud data that provides a representation of the surface of 3D objects and have been shown to be a potential anthropometric tool for use within health applications. Previous studies utilising 3D imaging have only assessed body shape based on combinations and relative proportions of traditional body measures, such as lengths, widths and girths. Geometric morphometrics (GM) is an established framework used for the statistical analysis of biological shape variation. These methods quantify biological shape variation after the effects of non-shape variation-location, rotation and scale-have been mathematically held constant, otherwise known as the Procrustes paradigm. The aim of this study was to determine whether shape measures, identified using geometric morphometrics, can provide additional information about the complexity of human morphology and underlying mass distribution compared to traditional body measures. Scale-invariant features of torso shape were extracted from 3D imaging data of 9,209 participants form the LIFE-Adult study. Partial least squares regression (PLSR) models were created to determine the extent to which variations in human torso shape are explained by existing techniques. The results of this investigation suggest that linear combinations of body measures can explain 49.92% and 47.46% of the total variation in male and female body shape features, respectively. However, there are also significant amounts of variation in human morphology which cannot be identified by current methods. These results indicate that Geometric morphometric methods can identify measures of human body shape which provide complementary information about the human body. The aim of future studies will be to investigate the utility of these measures in clinical epidemiology and the assessment of health risk.
| S-EPMC8912174 | biostudies-literature
Project description:Psittacosaurus is one of the most abundant and speciose genera in the Dinosauria, with fifteen named species. The genus is geographically and temporally widespread with large sample sizes of several of the nominal species allowing detailed analysis of intra- and interspecific variation. We present a reanalysis of three separate, coeval species within the Psittacosauridae; P. lujiatunensis, P. major, and Hongshanosaurus houi from the Lujiatun beds of the Yixian Formation, northeastern China, using three-dimensional geometric morphometrics on a sample set of thirty skulls in combination with a reevaluation of the proposed character states for each species. Using these complementary methods, we show that individual and taphonomic variation are the joint causes of a large range of variation among the skulls when they are plotted in a morphospace. Our results demonstrate that there is only one species of Psittacosaurus within the Lujiatun beds and that the three nominal species represent different taphomorphotypes of P. lujiatunensis. The wide range of geometric morphometric variation in a single species of Psittacosaurus implies that the range of variation found in other dinosaurian groups may also be related to taphonomic distortion rather than interspecific variation. As the morphospace is driven primarily by variation resulting from taphonomic distortion, this study demonstrates that the geometric morphometric approach can only be used with great caution to delineate interspecific variation in Psittacosaurus and likely other dinosaur groups without a complementary evaluation of character states. This study presents the first application of 3D geometric morphometrics to the dinosaurian morphospace and the first attempt to quantify taphonomic variation in dinosaur skulls.
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Project description:The morphology of the skull contains considerable ecological information about a species, because the skull contains sensory organs that are used to look for food, compete for mates, or to migrate. Spotted seals (Phoca largha) and harbor seals (Phoca vitulina) are similar in body size and pelage color but differ in habitat use and reproductive biology. The current study aims to clarify differences in the shapes of skulls in the spotted and harbor seals using geometric morphometrics and to discuss whether ecological differences can explain morphological differences in skulls. First, we discovered that the age at which the shape of skulls stopped changing was 7 years in both species, using the linear-threshold model. Using a total of 75 landmarks, 54 individuals (25 spotted seals, 29 harbor seals) that were older than the age at which skulls stopped changing were correctly identified at a rate of 100%. The total of 75 landmarks was narrowed down to eight key landmarks that resulted in an identification accuracy rate of 100% using random forests. Of the eight landmarks, seven were related to feeding apparatus, indicated that the harbor seal had a broader mouth and mandible than the spotted seal. Because of both species were dietary generalists and classified as pierce feeders, we suggested that the different features in the shapes of their skulls were caused not only by differences in their feeding behavior but also other differences related to reproductive behavior.
| S-EPMC9290137 | biostudies-literature
Project description:Current alignment-based methods for classification in geometric morphometrics do not generally address the classification of new individuals that were not part of the study sample. However, in the context of infant and child nutritional assessment from body shape images this is a relevant problem. In this setting, classification rules obtained on the shape space from a reference sample cannot be used on out-of-sample individuals in a straightforward way. Indeed, a series of sample dependent processing steps, such as alignment (Procrustes analysis, for instance) or allometric regression, need to be conducted before the classification rule can be applied. This work proposes ways of obtaining shape coordinates for a new individual and analyzes the effect of using different template configurations on the sample of study as target for registration of the out-of-sample raw coordinates. Understanding sample characteristics and collinearity among shape variables is crucial for optimal classification results when evaluating children's nutritional status using arm shape analysis from photos. The SAM Photo Diagnosis App© Program's goal is to develop an offline smartphone tool, enabling updates of the training sample across different nutritional screening campaigns.
| S-EPMC11785739 | biostudies-literature
Project description:Investigating the morphological differences of the calcaneus in humans and great apes is crucial for reconstructing locomotor repertories of fossil hominins. However, morphological variations in the calcaneus of the great apes (chimpanzees, gorillas, and orangutans) have not been sufficiently studied. This study aims to clarify variations in calcaneal morphology among great apes based on three-dimensional geometric morphometrics. A total of 556 landmarks and semilandmarks were placed on the calcaneal surface to calculate the principal components of shape variations among specimens. Clear interspecific differences in calcaneal morphology were extracted, corresponding to the degree of arboreality of the three species. The most arboreal orangutans possessed comparatively more slender calcaneal tuberosity and deeper pivot region of the cuboid articular surface than chimpanzees and gorillas. However, the most terrestrial gorillas exhibited longer lever arm of the triceps surae muscle, larger peroneal trochlea, more concave plantar surface, more inverted calcaneal tuberosity, more everted cuboid articular surface, and more prominent plantar process than the orangutans and chimpanzees. These interspecific differences possibly reflect the functional adaptation of the calcaneus to locomotor behavior in great apes. Such information might be useful for inferring foot functions and reconstructing the locomotion of fossil hominoids and hominids.
| S-EPMC8536676 | biostudies-literature
Project description:Recently, great technical progress has been achieved in the field of plant phenotyping. High-throughput platforms and the development of improved algorithms for rosette image segmentation make it possible to extract shape and size parameters for genetic, physiological, and environmental studies on a large scale. The development of low-cost phenotyping platforms and freeware resources make it possible to widely expand phenotypic analysis tools for Arabidopsis. However, objective descriptors of shape parameters that could be used independently of the platform and segmentation software used are still lacking, and shape descriptions still rely on ad hoc or even contradictory descriptors, which could make comparisons difficult and perhaps inaccurate. Modern geometric morphometrics is a family of methods in quantitative biology proposed to be the main source of data and analytical tools in the emerging field of phenomics studies. Based on the location of landmarks (corresponding points) over imaged specimens and by combining geometry, multivariate analysis, and powerful statistical techniques, these tools offer the possibility to reproducibly and accurately account for shape variations among groups and measure them in shape distance units. Here, a particular scheme of landmark placement on Arabidopsis rosette images is proposed to study shape variation in viral infection processes. Shape differences between controls and infected plants are quantified throughout the infectious process and visualized. Quantitative comparisons between two unrelated ssRNA+ viruses are shown, and reproducibility issues are assessed. Combined with the newest automated platforms and plant segmentation procedures, geometric morphometric tools could boost phenotypic features extraction and processing in an objective, reproducible manner.
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Project description:The methods of geometric morphometrics are commonly used to quantify morphology in a broad range of biological sciences. The application of these methods to large datasets is constrained by manual landmark placement limiting the number of landmarks and introducing observer bias. To move the field forward, we need to automate morphological phenotyping in ways that capture comprehensive representations of morphological variation with minimal observer bias. Here, we present Morphological Variation Quantifier (morphVQ), a shape analysis pipeline for quantifying, analyzing, and exploring shape variation in the functional domain. morphVQ uses descriptor learning to estimate the functional correspondence between whole triangular meshes in lieu of landmark configurations. With functional maps between pairs of specimens in a dataset we can analyze and explore shape variation. morphVQ uses Consistent ZoomOut refinement to improve these functional maps and produce a new representation of shape variation, area-based and conformal (angular) latent shape space differences (LSSDs). We compare this new representation of shape variation to shape variables obtained via manual digitization and auto3DGM, an existing approach to automated morphological phenotyping. We find that LSSDs compare favorably to modern 3DGM and auto3DGM while being more computationally efficient. By characterizing whole surfaces, our method incorporates more morphological detail in shape analysis. We can classify known biological groupings, such as Genus affiliation with comparable accuracy. The shape spaces produced by our method are similar to those produced by modern 3DGM and to auto3DGM, and distinctiveness functions derived from LSSDs show us how shape variation differs between groups. morphVQ can capture shape in an automated fashion while avoiding the limitations of manually digitized landmarks, and thus represents a novel and computationally efficient addition to the geometric morphometrics toolkit.
| S-EPMC9970057 | biostudies-literature
Project description:In cases of osseous defects, knowledge of the anatomy, and its age and sex-related variations, is essential for reconstruction of normal morphology. Here, we aimed at creating a 3D atlas of the human mandible in an adult sample using dense landmarking and geometric morphometrics. We segmented 50 male and 50 female mandibular surfaces from CBCT images (age range: 18.9-73.7 years). Nine fixed landmarks and 510 sliding semilandmarks were digitized on the mandibular surface, and then slid by minimizing bending energy against the average shape. Principal component analysis extracted the main patterns of shape variation. Sexes were compared with permutation tests and allometry was assessed by regressing on the log of the centroid size. Almost 49 percent of shape variation was described by the first three principal components. Shape variation was related to width, height and length proportions, variation of the angle between ramus and corpus, height of the coronoid process and inclination of the symphysis. Significant sex differences were detected, both in size and shape. Males were larger than females, had a higher ramus, more pronounced gonial angle, larger inter-gonial width, and more distinct antegonial notch. Accuracy of sexing based on the first two principal components in form space was 91 percent. The degree of edentulism was weakly related to mandibular shape. Age effects were not significant. The resulting atlas provides a dense description of mandibular form that can be used clinically as a guide for planning surgical reconstruction.
| S-EPMC11014969 | biostudies-literature
Project description:The fish body shape is a key factor that influences multiple traits such as swimming, foraging, mating, migrations, and predator avoidance. The present study describes the body morphological changes and the growth trajectories during the transformation from 24 to 54 days post-hatching in the golden grey mullet, Chelon auratus, using geometric morphometric analysis (GMA). The results revealed a decrease in morphological variability (i.e., morphological disparity) with the somatic growth. The main changes affected head size, elongation, and widening of the body. Given that this variability could affect the metabolism, some individuals with different morphologies and in different ontogenetic developmental stages were selected to estimate their potential respiration rate using the Electron Transport System (ETS) analysis. Differences were detected depending on the developmental stage, and being significantly smaller after 54 days post-hatching. Finally, a multivariate linear regression indicated that the specific ETS activity was partially related to the fish length and body shape. Thus, our findings emphasized the relevance of larval morphological variability for understanding the physiological processes that occur during the development.
| S-EPMC9913231 | biostudies-literature