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Fig. 5 in Landmark and outline-based geometric morphometrics analysis of three Stomoxys flies (Diptera: Muscidae)

Fig. 5. Centroid size variation of the wings between species and sexes, shown as quartile boxes. Each box shows the group median separating the 25th and 75th quartiles. Vertical bars under the boxes represent the wing (units as mm).

Fig. 1 in Landmark and outline-based geometric morphometrics analysis of three Stomoxys flies (Diptera: Muscidae)

Fig. 1. Morphological characters of palpi used to separate Stomoxys pullus Austen, 1909 (A), S. uruma Shinonaga et Kano, 1966 (B) and S. indicus Picard, 1908 (C).

Fig. 8 in Landmark and outline-based geometric morphometrics analysis of three Stomoxys flies (Diptera: Muscidae)

Fig. 8. Perimeter variation of the wings between species and sexes, shown as quartile boxes. Each box shows the group median sepa- rating the 25th and 75th quartiles. Vertical bars under the boxes represent the wing (units as mm).

Fig. 7 in Landmark and outline-based geometric morphometrics analysis of three Stomoxys flies (Diptera: Muscidae)

Fig. 7. Landmark-based discriminant analysis. Factor map of canonical variates resulting from comparison among the three species of Stomoxys Geoffroy, 1762, in males (A) and females (B).

Fig. 4 in Landmark and outline-based geometric morphometrics analysis of three Stomoxys flies (Diptera: Muscidae)

Fig. 4. Contour digitised on Stomoxys Geoffroy, 1762 flies wing for outline-based geometric morphometrics analysis. A short, artificial segment is computed by the digitising program to completely close the contour.

opencc-by-4.0Aug 2023View details →

Dataset of the Geometric Morphometric Analysis of the article "Blank predetermination in the Iberian Acheulean. Insight from the cleaver on flake assemblage from Casal do Azemel site (Leiria, Portugal) by a Geometric Morphometric approach"

Raw data and datasets of the Geometric Morphometric Analysis performed in the article "Blank predetermination in the Iberian Acheulean. Insight from the cleaver on flake assemblage from Casal do Azemel site (Leiria, Portugal) by a Geometric Morphometric approach". Contains the raw data, the Generalised Procrustes Analysis dataset, the Elliptic Fourier Analysis dataset and all the variables tested (on the EFA dataset).

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Gill morphology data and geometric morphometric data of Enteromius spp. in relation to dissolved oxygen gradients

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publicApr 2023View details →

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Using geometric morphometrics to determine the ‘fittest’ floral shape: a case study in large-flowered buzz-pollinated Melastomataceae

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publicMar 2023View details →

opencc-zeroMar 2020View details →

Categorical versus geometric morphometric approaches to characterising the evolution of morphological disparity in Osteostraci (Vertebrata, stem-Gnathostomata)

Morphological variation (disparity) is almost invariably characterised by two non-mutually exclusive approaches: (i) quantitatively, through geometric morphometrics, and (ii) in terms of discrete, 'cladistic', or categorical characters. Uncertainty over the comparability of these approaches diminishes the potential to obtain nomothetic insights into the evolution of morphological disparity and the few benchmarking studies conducted so far show contrasting results. Here, we apply both approaches to characterising morphology in the stem-gnathostome clade Osteostraci in order to assess congruence between these alternative methods as well as to explore the evolutionary patterns of the group in terms of temporal disparity and the influence of phylogenetic relationships and habitat on morphospace occupation. Our results suggest that both approaches yield similar results in morphospace occupation and clustering, but also some differences indicating that these metrics may capture different aspects of morphology. Phylomorphospaces reveal convergence towards a generalised 'horseshoe'-shaped cranial morphology and two strong trends involving major groups of osteostracans (benneviaspidids and thyestiids), which probably reflect adaptations to different lifestyles. Temporal patterns of disparity obtained from categorical and morphometric approaches appear congruent, however disparity maxima are recorded at very different times in the evolutionary history of the group when increasing the number of taxa and characters in the categorical dataset. The results of our analyses indicate that categorical and continuous datasets may characterize different patterns of morphological disparity and that discrepancies could reflect preservational limitations of morphometric data and differences in the potential of each data type for characterizing more or less inclusive aspects of overall phenotype.

opencc-zeroSep 2020View details →

Effects of taphonomic deformation on geometric morphometric analysis of fossils: a case study using the dicynodont Diictodon feliceps (Therapsida, Anomodontia)

Taphonomic deformation, the distortion of fossils as a result of geological processes, poses problems for the use of geometric morphometrics in addressing paleobiological questions. Signal from biological variation, such as ontogenetic trends and sexual dimorphism, may be lost if variation from deformation is too high. Here, we investigate the effects of taphonomic deformation on geometric morphometric analyses of the abundant, well known Permian therapsid Diictodon feliceps. Distorted Diictodon crania can be categorized into seven typical styles of deformation: lateral compression, dorsoventral compression, anteroposterior compression, 'saddle-shape' deformation (localized collapse at cranial mid-length), anterodorsal shear, anteroventral shear, and right/left shear. In simulated morphometric datasets incorporating known 'biological' signals and subjected to uniform shear, deformation was typically the main source of variance but accurate 'biological' information could be recovered in most cases. However, in empirical datasets, not only was deformation the dominant source of variance, but little structure associated with allometry and sexual dimorphism was apparent, suggesting that the more varied deformation styles suffered by actual fossils overprint biological variation. In a principal component analysis of all anomodont therapsids, deformed Diictodon specimens exhibit significant dispersion around the 'true' position of this taxon in morphospace based on undistorted specimens. The overall variance associated with deformation for Anomodontia as a whole is minor, and the major axes of variation in the study sample show a strong phylogenetic signal instead. Although extremely problematic for studying variation in fossil taxa at lower taxonomic levels, the cumulative effects of deformation in this study are shown to be random, and inclusion of deformed specimens in higher-level analyses of morphological disparity are warranted. Mean morphologies of distorted specimens are found to approximate the morphology of undistorted specimens, so we recommend use of species-level means in higher-level analyses when possible.

opencc-zeroSep 2020View details →

AFLP and geometric morphometrics for Littorina fabalis

Low dispersal marine intertidal species facing strong divergent selective pressures associated with steep environmental gradients have a great potential to inform us about local adaptation and reproductive isolation. Among these, gastropods of the genus Littorina offer a unique system to study parallel phenotypic divergence resulting from adaptation to different habitats related with wave exposure. In this study, we focused on two Littorina fabalis ecotypes from Northern European shores and compared the patterns of habitat-related phenotypic and genetic divergence across three different geographic levels (local, regional and global). Geometric morphometric analyses revealed that individuals from habitats moderately exposed to waves usually present a larger shell size with a wider aperture than those from sheltered habitats. The phenotypic clustering of L. fabalis by habitat across most locations (mainly in terms of shell size) support an important role of ecology in morphological divergence. A genome scan based on amplified fragment length polymorphisms (AFLPs) revealed a heterogeneous pattern of differentiation across the genome between populations from the two different habitats, suggesting ecotype divergence in the presence of gene flow. The contrasting patterns of genetic structure between nonoutlier and outlier loci, and the decreased sharing of outlier loci with geographic distance among locations are compatible with parallel evolution of phenotypic divergence, with an important contribution of gene flow and/or ancestral variation. In the future, model-based inference studies based on sequence data across the entire genome will help unravelling these evolutionary hypotheses, improving our knowledge about adaptation and its influence on diversification within the marine realm.

opencc-zeroOct 2020View details →

Geometric morphometric wing analysis represents a robust tool to identify female mosquitoes (Diptera: Culicidae) in Germany

Accurate species identification is the prerequisite to assess the relevance of mosquito specimens, but is often hindered by missing or damaged morphological features. The present study analyses the applicability of wing geometric morphometrics as a low-cost and practical alternative to identify native mosquitoes in Germany. Wing pictures were collected for 502 female mosquitoes of five genera and 19 species from 80 sampling sites. The reliable species identification based on interspecific wing geometry of 18 landmarks per specimen was tested. Leave-one-out cross validation revealed an overall accuracy of 99% for the genus and 90% for the species identification. Misidentifications were mainly due to three pairings of Aedes species: Aedes annulipes vs. Aedes cantans, Aedes cinereus vs. Aedes rossicus and Aedes communis vs. Aedes punctor. Cytochrome oxidase subunit I (COI) gene region was sequenced to validate the morphological and morphometric identification. Similar to the results of the morphometric analysis, the same problematic three Aedes-pairs clustered, but most other species could be well separated. Overall, our study underpins that morphometric wing analysis is a robust tool for reliable mosquito identification, which reach the accuracy of COI barcoding.

opencc-zeroOct 2020View details →

Random forests for predicting species identity of forensically important blow flies (Diptera: Calliphoridae) and flesh flies (Sarcophagidae) using geometric morphometric data: proof of concept

Wing shape variation has been shown to be useful for delineating forensically important fly species in two Diptera families: Calliphoridae and Sarcophagidae. Compared to DNA-based identification, the cost of geometric morphometric data acquisition and analysis is relatively much lower because the tools required are basic, and stable softwares are available. However, to date, an explicit demonstration of using wing geometric morphometric data for species identity prediction in these two families remains lacking. Here, geometric morphometric data from 19 homologous landmarks on the left wing of males from seven species of Calliphoridae (n=55), and eight species of Sarcophagidae (n=40) were obtained and processed using Generalized Procrustes Analysis. Allometric effect was removed by regressing centroid size (in log10) against the Procrustes coordinates. Subsequently, principal component analysis of the allometry-adjusted Procrustes variables was done, with the first 15 principal components used to train a random forests model for species prediction. Using a real test sample consisting of 33 male fly specimens collected around a human corpse at a crime scene, the estimated percentage of concordance between species identities predicted using the random forests model and those inferred using DNA-based identification was about 80.6% (approximate 95% confidence interval = [68.9%, 92.2%]). In contrast, baseline concordance using naive majority class prediction was 36.4%. The results provide proof of concept that geometric morphometric data has good potential to complement morphological and DNA-based identification of blow flies and flesh flies in forensic work.

opencc-by-4.0Dec 2017View details →

Figure 1. Landmarks head selection. A. Rhodnius prolixus. B in Head geometric morphometrics of two Chagas disease vectors from Venezuela

Figure 1. Landmarks head selection. A. Rhodnius prolixus. B. Triatoma maculata. Scale bar = 1 mm.

opencc-zeroDec 2022View details →

Using geometric wing morphometrics to distinguish Aedes japonicus japonicus and Aedes koreicus

Background: Aedes japonicus japonicus (Theobald, 1901) and Aedes koreicus (Edwards, 1917) have rapidly spread in Europe over the last decades. Both species are very closely related and occur in sympatry. Females are difficult to distinguish, and no distinctive morphological characters are known for males. However, accurate species discrimination is important as both species may differ in their vectorial capacity and spreading behaviour. In this study, we assessed the potential of geometric wing morphometrics as an alternative to distinguish the two species. Methods: A total of 147 Ae. japonicus specimens (77 females and 70 males) and 124 Ae. koreicus specimens (67 females and 57 males) were collected in South-West Germany. The left wing of each specimen was removed, mounted and photographed. The coordinates of 18 landmarks on the vein crosses were digitalised by a single observer. The resulting two-dimensional dataset was used to analyse the differences in the wing size (i.e., centroid size) and wing shape between Ae. japonicus and Ae. koreicus by means of geometric morphometrics. To analyse the reproducibility of the analysis, the landmark collection was repeated for 20 specimens per sex and species by two additional observers. Results: The wing size in female Ae. koreicus was significantly greater than in Ae. japonicus but did not differ significantly for males. However, the strong overlap in wing size for the females would not allow for discriminating the two species. In contrast, the wing shape clustered species-specific and a leave-one-out validation resulted in a reclassification accuracy of 95% for the females and 91% for the males. The data collected by different observers resulted in a similar accuracy, indicating a low observer bias for the landmark collection. Conclusions: Geometric wing morphometrics provide a reliable and robust tool to distinguish female and male specimens of Ae. japonicus and Ae. koreicus.

opencc-zeroDec 2023View details →

Data from: facial growth and development trajectories based on 3D images: geometric morphometrics with a deformation perspective

Developmental changes of facial shape are commonly investigated through geometric morphometrics. A limitation with this approach is the inability to investigate patterns of morphological changes at local scale. This could be addressed through quantifying the deformation required to deform one shape to another. This study aimed to investigate changes in mean, rate, and variance of facial shape at local scale using geometric morphometrics through deformation perspective. 2112 Europeans 3 to 40 years-old from the 3D Facial Norms project were included. Shape and rate trajectories from partial least-squares regressions revealed that the developmentally protrusive nasal bridge was due to local expansion in surrounding tissues as opposed to shape changes in nasal bridge per-ser. Local expansion of the supraorbital region, in particular the medial part in males, resulted in the sloping forehead and deep-situated eyes with development. Facial shape variation increased non-linearly with age (p < 0.05), with features having larger rate of change becoming more developmentally diversified. In summary, our deformation perspective facilitates unravelling morphogenetic processes underlying shape changes. Our extended analytical scope inspires novel measures worthy of consideration while establishing facial growth charts. The analytical framework in this study is broadly applicable for analysis of shape changes in general.

opencc-zeroJan 2024View details →

Wing geometric morphometrics and COI barcoding of Culex pipiens subgroup in the Republic of Korea

Two members of the Culex pipiens subgroup, Culex pallens and Culex pipiens f. molestus, are known to occur in the Republic of Korea (ROK). These species exhibit morphologically similar features and are challenging to distinguish below the species level. Therefore, this study utilized wing geometric morphometrics (GM) on the right wing of the Culex pipiens subgroup, alongside sequencing of the cytochrome c oxidase subunit I (COI) region. Mosquitoes were collected from 11 locations between June and October to minimize regional and seasonal variations. Additionally, Culex pipiens f. pipiens, which is not native to the ROK, was included in the analysis. Culex tritaeniorhynchus, Aedes albopictus, and Anopheles sinensis, the primary vectors in the ROK, were used as outgroups for comparison. All three taxa within the Culex pipiens subgroup could be identified with an 82.4%–97.0% accuracy using GM. However, a comparison of the COI regions of the Culex pipiens subgroup revealed no clear differences between the taxa. These data can be used for accurate identification, contributing to effective mosquito control, in addition to providing a foundation for evolutionary and ecological studies on wing shape differences.

opencc-by-4.0Nov 2021View details →

Supplementary data to "Geometric morphometrics of bilateral asymmetry in Eunotia bilunaris (Eunotiales, Bacillariophyceae) as a tool for the quantitative assessment of teratogenic deviations in frustule shapes"

The supplementary data consist of the files "data.txt" and "R_script.odt" including the landmark coordinates and the R script used for the analyses described in the paper submitted to Symmetry.

opencc-by-4.0Mar 2022View details →

Research compendium for 'Practical and technical aspects for the 3D scanning of lithic artefacts using micro-computed tomography techniques and laser light scanners for subsequent geometric morphometric analysis. Introducing the StyroStone protocol'

Abstract: Here, we present a new method to scan a large number of lithic artefacts using three-dimensional (3D) scanning technology. Despite the rising use of high-resolution 3D surface scanners in archaeological sciences, no virtual studies have focused on the 3D digitization and analysis of small lithic implements such as bladelets, microblades, and microflakes. This is mostly due to difficulties in creating reliable 3D meshes of these artefacts resulting from several inherent features (i.e., size, translucency, and acute edge angles), which compromise the efficiency of structured light or laser scanners and photogrammetry. Our new protocol StyroStone addresses this problem by proposing a step-by-step procedure relying on the use of micro-computed tomographic technology, which is able to capture the 3D shape of small lithic implements in high detail. We tested a system that enables us to scan hundreds of artefacts together at once within a single scanning session lasting a few hours. As also bigger lithic artefacts (i.e., blades) are present in our sample, this protocol is complemented by a short guide on how to effectively scan such artefacts using a structured light scanner (Artec Space Spider). Furthermore, we estimate the accuracy of our scanning protocol using principal component analysis of 3D Procrustes shape coordinates on a sample of meshes of bladelets obtained with both micro-computed tomography and another scanning device (i.e., Artec Micro). A comprehensive review on the use of 3D geometric morphometrics in lithic analysis and other computer-based approaches is provided in the introductory chapter to show the advantages of improving 3D scanning protocols and increasing the digitization of our prehistoric human heritage. Content List: <ul> <li>S1. Step-by-step protocol entitled ‘StyroStone: A protocol for scanning and extracting three-dimensional meshes of stone artefacts using Micro-CT scanners’. Also available on protocols.io (dx.doi.org/10.17504/protocols.io.bzbfp2jn);</li> <li>S2. Dataset with all raw semilandmark coordinate data (in .xlsx format) used in the validation study;</li> <li>S3. AGMT3D project. The file “Validation Protocol-MorphoProject.mat” can be used to open the project in the software AGMT3D;</li> <li>S4. Dataset in .csv format of the principal component score data of the validation study;</li> <li>S5. R script used to create Figure 2 using the R package ggplot2;</li> <li>S6. 3D models of the experimental bladelets obtained with the Micro-CT scanner used in the validation study. Both .ply and .wrl formats are provided;</li> <li>S7. 3D models of the experimental bladelets obtained with the Artec Micro scanner used in the validation study. Both .ply and .wrl formats are provided.</li> </ul>