Application Of Geometric Morphometrics Research Articles

Geometric Morphometric Analysis of Genus Chaetocnema (Coleoptera: Chrysomelidae: Alticini) with Insights on Its Subgenera Classification and Morphological Diversity

In taxonomy, qualitative methods are commonly used to analyze morphological characters, which can lead to dramatic changes in higher taxa. Geometric morphometrics (GM) has proven to be useful for discriminating species in various taxonomy groups. However, the application of geometric morphometrics in supraspecies classification is relatively scarce. In this study, we tested the controversial two subgenera classification of Chaetocnema with geometric morphometrics; a total of 203 Chaetocnema species representing 50% of all known species from around the world were selected for the analysis. We analyzed the shape of the pronotum, elytron, head, aedeagus, and spermatheca. The results showed that the two traditional subgenera distinctly differed from each other; therefore, we propose using two subgenera arrangements to facilitate the understanding and taxonomy of the Chaetocnema species (especially in the Oriental, Palearctic, and Nearctic regions). Additionally, the morphological diversity of the abovementioned structures of Chaetocnema was analyzed, and it was found that the highest morphological diversity was in the spermatheca, which was greater than that in the aedeagus. Our research demonstrated that GM could be useful for detecting morphological delimitation of the supraspecies taxa. It also showed that GM methods are applicable to insects as small as 2 mm in body size.

The Novel Application of Geometric Morphometrics with Principal Component Analysis to Existing G Protein-Coupled Receptor (GPCR) Structures.

The G protein-coupled receptor (GPCR) superfamily is a large group of membrane proteins which, because of their vast involvement in cell signalling pathways, are implicated in a plethora of disease states and are therefore considered to be key drug targets. Despite advances in techniques to study these receptors, current prophylaxis is often limited due to the challenging nature of their dynamic, complex structures. Greater knowledge and understanding of their intricate structural rearrangements will therefore undoubtedly aid structure-based drug design against GPCRs. Disciplines such as anthropology and palaeontology often use geometric morphometrics to measure variation between shapes and we have therefore applied this technique to analyse GPCR structures in a three-dimensional manner, using principal component analysis. Our aim was to create a novel system able to discriminate between GPCR structures and discover variation between them, correlated with a variety of receptor characteristics. This was conducted by assessing shape changes at the extra- and intracellular faces of the transmembrane helix bundle, analysing the XYZ coordinates of the amino acids at those positions. We have demonstrated that GPCR structures can be classified based on characteristics such as activation state, bound ligands and fusion proteins, with the most significant results focussed at the intracellular face. Conversely, our analyses provide evidence that thermostabilising mutations do not cause significant differences when compared to non-mutated GPCRs. We believe that this is the first time geometric morphometrics has been applied to membrane proteins on this scale, and believe it can be used as a future tool in sense-checking newly resolved structures and planning experimental design.

Technical note: A technique to mount Sarcophagidae and Calliphoridae (Diptera) larvae for forensic identification using geometric morphometrics

Geometric morphometric analyses use landmark coordinates from images of specific areas on specimens. Therefore, to minimize differences arising from human preparation, preparation of the specimen is crucial. The application of geometric morphometrics has been used in entomology for identifying adult dipteran species, however, applying this technique to larval specimens requires the production of standard protocols which would allow specimens to be compared equally. This proposed protocol consists of a two-step process:1. using 15% potassium hydroxide (KOH) to clear the specimen, followed by rinsing the specimen with 80% ethanol;2. removal and spreading of the mouthhooks on a slide for imaging and analysis.The goal of this work is to standardize specimen preparation, which would reduce human error and facilitate use of geometric morphometrics to identify dipteran larvae.

Behind the steps of ancient sheep mobility in Iberia: new insights from a geometric morphometric approach

In Western Europe, the transition from the middle Iron Age to the early Roman period implied changes in livestock practices, with the emergence of a specialized and selective animal husbandry. These changes have been related in Italy and south of France with changes in livestock management involving their mobility between ecologically complementary areas. The study of this question in the Iberian Peninsula has only been partially investigated through palaeoenvironmental analyses, and the information about the origin and significance of this phenomenon is very scarce. To shed new light on this topic we used an archaeozoological approach, with the application of geometric morphometrics. They were used to study size and shape variability in sheep astragali from 9 sites dating from the middle Iron Age to the early Roman period (5th c. BC–3rd c. AD) and located on the Pyrenees and on the north-eastern Iberian coast as a case study. The results we obtained, combined with Number of Identified Specimens (NISP) and kill-off patterns, showed local specificities in terms of breeding methods and sheep morphologies between the two areas during the middle Iron Age. On the contrary, sheep with similar size and the implementation and development of similar sheep husbandry practices in the Pyrenees and the north-eastern Iberian coast were documented during the early Roman period. These results suggest the existence of livestock links between these two areas during the Roman period, that could be involved a possible movement of sheep between the lowlands and the Pyrenees for the first time.

3d point cloud model of human bio form created by the application of geometric morphometrics and method of anatomical features: human tibia example

Morphometrics refers to the quantitative analysis of a biological form and it can be used to describe its shape. Common types of geometric morphometrics are Landmark-based Geometric Morphometrics which describe shape by using anatomical landmarks (e.g. points), and Outline-based geometric morphometrics which uses envelope curves to describe shape of the biological form (e.g. bone), and they are not absolutely exclusive. Geometric morphometrics can be used for the creation of statistical models which represent shape variation of specific bio form. In this paper, novel application of geometric morphometrics for the creation of personalized models of unique bio-forms, i.e. models which are created for the specific patient is presented. Personalized model is defined as 3D point cloud model of biological form (in this case human tibia). Positions of points in 3D space are determined by using set of parametric functions defined by applying geometrical morphometrics, morphology properties and statistical analysis on the input set of human tibia samples. By using this technique, anatomically correct and geometrically accurate personalized models of bio forms can be created and used in pre, intra, and post-operative procedures in clinical practice.

On the shape of things: A geometric morphometrics approach to investigate Aurignacian group membership

The manufacture of composite projectile technology requires the production and assemblage of tightly fitted parts designed to fulfill a number of distinct functions. Each part combines a number of techno-functional units, and various processes may be responsible for the shape variability of these units. In order to investigate the relative contribution of each process to the overall variability of a projectile implement, one must identify the point of demarcation between its techno-functional units. In the present paper, the concept of shape modularity is introduced to precisely identify this locus. The application of geometric morphometrics and shape modularity to the study of two Aurignacian osseous projectile point types, i.e., split- and massive-based points, reveals interesting patterns. On both types, the maximum width delimits the distal and proximal techno-functional units of these objects. When focusing on the morphometric variability and the geographic distribution of the implements' proximal unit, the eight shapes identified for split-based points are found over vast regions of Europe. On the other hand, the two proximal shapes defined for massive-based points show a pattern of local, or regional, aggregation. These proximal shapes were likely considered fit for hafting and hunting by the prehistoric populations who reproduced them, and they are interpreted as a proxy for the socially shared rules of production that guided the manufacture of these tool types. They could therefore be used in future studies that aim to identify group membership amongst the Aurignacian metapopulation and the extent of their interactions.

Species identification of the psammophilous tenebrionid beetles Phaleria acuminata Küster, 1852 and Phaleria bimaculata (Linnaeus, 1767) from central Mediterranean beaches: geometric morphometrics and molecular insights from species to population level

Dominating global arid environments, from desert to coastal dunes, most Tenebrionidae are highly specific in their habitat preferences and display limited dispersal potential, thus exhibiting a remarkable degree of regional genetic and morphological differentiation. The tenebrionid genus Phaleria is speciose and widely distributed, with P. acuminata and P. bimaculata having a wide Mediterranean distribution, with numerous morphological differentiations at population level, often described as different taxa of doubtful taxonomical significance. In order to investigate the variability of the central Mediterranean populations of P. bimaculata and P. acuminata and to compare the results obtained with different identification techniques, these species were sampled on sandy beaches in Sicily (southern Italy) and on circum-Sicilian and Maltese islands. Collected samples were studied through the application of geometric morphometrics and the sequencing of a fragment of the mitochondrial COII gene. Geometric morphometrics and molecular analyses gave congruent results, allowing a sound separation of the two species. At the population level, the two species showed different patterns. P. acuminata showed a remarkable morphological and molecular homogeneity throughout the sampled area. Conversely, two well-characterized sub-clades were detected within P. bimaculata, and within the two lineages, a low-to-absent inter-populations differentiation was observed, in spite of the physical isolation of the sampled sandy beaches and of their geographical distance. These two P. bimaculata lineages, hereby named “Tyrrhenian sub-clade” and “Southern sub-clade,” might be compatible with the hypothesis of subspecific status already proposed for the populations from the Aeolian archipelago (as P. bimaculata marcuzzii Aliquò).

Review and application of geometric morphometrics in aquatic animals

Geometric morphometrics( GM) originated from late 1980s to early 1990s in last century. It differed from the traditional measurement,mainly focusing on the variability of shape. With relative theory foundation,w e w ere separating shape from size,explaining the intrinsic results using multivariate analysis. This new method w as meaningful to the organism w ith fixed and stable shape,and also w idely used in many fields. Generally,aquatic animals w ere surrounded by hard structures w ith relatively invariable shape. Meanw hile,they played different important roles in diversified w aters. This paper review ed the shape analysis of aquatic animals w ith geometric morphometrics in the recent decades,briefly described the developing process of this new method,explained the principles of outline and landmark method,and introduced methodology and some relevant softw are. Then w e retrospected the application of invertebrate and vertebrate morphological shape in aquatic area. The result show ed that this new approach w as accepted by many researchers at home and abroad,but had a limitation in species identification and population division,so w e should use the hard structures to analyze the morphological variation,consider the implication of environmental change w ith the morphology of organism,and try to print out the original appearance in 3D and describe the shape variation w ith theoretical studies.

Geometric morphometric analyses of orbit shape in Asian, African, and European human populations

The variation of orbit shape has been investigated, especially its role in population classi- fication. However, previous studies that treated orbit shape as a linear metric or non-metric trait have not produced conclusive quantitative data to show whether orbit shape is an accurate reflection of population affinity. Thus, in this study in order to examine regional variation in the orbit shape of con- temporary Asian, African, and European populations we use geometric morphometrics with a novel standardization technique. A standardized orbital plane was obtained and each specimen was photo- graphed. The results from this study show that regional variation in orbit shape exists. The Asian orbital contour was generally tall, rounded, and its inferior contour was symmetrical. The European tended to be square and more inclined, with the African being shorter. Moreover, the orbit shape of some specimens from these three regions overlapped. The similarities between the Asian and European samples were much smaller than those between Africans and Asians, or Africans and Europeans. Ad- ditionally, intergroup variability was larger on the bones of the maxilla and zygoma which form the in- ferior contour of the orbit, compared with the frontal bone forming the superior contour. The most variable areas of the orbit concentrate on the internal aspect of the upper margin, on the contours near the frontomalare orbitale and zygomaxillare. The application of geometric morphometrics with the newly developed standardization protocol to examine orbit shape between individuals from different geographic areas, has demonstrated its use to measure quantitatively human orbit shape, variation, and population affinity.

The effects of the periodontal ligament on mandibular stiffness: a study combining finite element analysis and geometric morphometrics

It is generally accepted that the periodontal ligament (PDL) plays a crucial role in transferring occlusal forces from the teeth to the alveolar bone. Studies using finite element analysis (FEA) have helped to better understand this role and show that the stresses and strains in the alveolar bone are influenced by whether and how PDL is included in FE models. However, when the overall distribution of stresses and strains in crania and mandibles are of interest, PDL is often not included in FE models, although little is known about how this affects the results. Here we study the effect of representing PDL as a layer of solid material with isotropic homogeneous properties in an FE model of a human mandible using a novel application of geometric morphometrics. The results show that the modelling of the PDL affects the deformation and thus strain magnitudes not only of the alveolar bone around the biting tooth, but that the whole mandible deforms differently under load. As a result, the strain in the mandibular corpus is significantly increased when PDL is included, while the strain in the bone beneath the biting tooth is reduced. These results indicate the importance of the PDL in FE studies. Thus we recommend that the PDL should be included in FE models of the masticatory apparatus, with tests to assess the sensitivity of the results to changes in the Young’s modulus of the PDL material.