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213 results for “Geometric morphometric analysis”
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"
<p>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".</p> <p>Contains the raw data, the Generalised Procrustes Analysis dataset, the Elliptic Fourier Analysis dataset and all the variables tested (on the EFA dataset). </p>
Effects of taphonomic deformation on geometric morphometric analysis of fossils: a case study using the dicynodont Diictodon feliceps (Therapsida, Anomodontia)
<p>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 <i>Diictodon feliceps</i>. Distorted <i>Diictodon </i>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 <i>Diictodon </i>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.</p>
Geometric morphometric wing analysis represents a robust tool to identify female mosquitoes (Diptera: Culicidae) in Germany
<p>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 <i>Aedes</i> species: <i>Aedes annulipes</i> vs. <i>Aedes cantans</i>, <i>Aedes cinereus</i> vs. <i>Aedes rossicus</i> and <i>Aedes communis </i>vs. <i>Aedes punctor.</i> 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 <i>Aedes</i>-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.</p>
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'
<p><strong>Abstract:</strong></p> <p>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 <em>StyroStone</em> 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.</p> <p><strong>Content List:</strong></p> <ul> <li><strong>S1. </strong>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><strong>S2. </strong>Dataset with all raw semilandmark coordinate data (in .xlsx format) used in the validation study;</li> <li><strong>S3. </strong>AGMT3D project. The file “Validation Protocol-MorphoProject.mat” can be used to open the project in the software AGMT3D;</li> <li><strong>S4. </strong>Dataset in .csv format of the principal component score data of the validation study;</li> <li><strong>S5.</strong> R script used to create Figure 2 using the R package ggplot2;</li> <li><strong>S6. </strong>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><strong>S7. </strong>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>
Data from: A 3D geometric morphometric analysis of the bovid distal humerus, with special reference to Rusingoryx atopocranion (Pleistocene, Eastern Africa)
<p>The family Bovidae [Mammalia: Artiodactyla] is speciose and has extant representatives on every continent, forming key components of mammal communities. For these reasons, bovids are ideal candidates for studies of ecomorphology. In particular, the morphology of the bovid humerus has been identified as highly related to functional variables such as body mass and habitat. This study investigates the functional morphology of the bovid distal humerus in isolation due to its increased likelihood of preservation in the fossil record, and the resulting opportunity for better understanding the ecomorphology of extinct bovids. A landmark scheme of 30 landmarks was used to capture the 3D distal humerus morphology in 111 extant bovid specimens. We find that the distal humerus has identifiable morphologies associated with body mass, habitat preference, and tribe affiliation, and that some characteristics are shared between high body mass bovids and those living on hard, flat terrain which is likely due to the high stress on the bone in both cases. We directly apply our findings regarding extant bovids to the extinct alcelaphine bovid, <em>Rusingoryx</em> <em>atopocranion</em> from the mid to late Pleistocene (>33-45 ka) Lake Victoria region of Kenya. This species is known for some peculiar morphologies including a domed cranium with hollow nasal crests, and having small hooves for a bovid of its size. Another interesting aspect of <em>Rusingoryx</em>'s skeletal morphology which has not been addressed is an unusual protrusion on the lateral epicondyle of the distal humerus. Despite considerable individual variation in the <em>Rusingoryx</em> specimens, we find evidence to support its historical assignment to the tribe Alcelaphini, and that it likely preferred open grassland habitats, which is consistent with independent reconstructions of the paleoenvironment. We also provide the most accurate body mass estimate for <em>Rusingoryx</em> to date, based on distal humerus centroid size. Overall, we are able to conclude that the distal humerus in extant bovids is highly informative regarding body mass, habitat preference and tribe, and that this can be applied directly to a fossil taxon with promising results.</p>
Fig. 2. 60 in Identification and Distribution of Wedge Clams (Donacidae: Bivalvia) in Thailand by Geometric Morphometric and Molecular Analysis.
Fig. 2. 60 Outline digitized landmarks along the inner edge of left valve. Scale bar = 5 mm.
Fig. 7. Reconstructed denticles shapes using a in Geometric morphometric on a new species of Trichodinidae. A tool to discriminate trichodinid species combined with traditional morphology and molecular analysis
Fig. 7. Reconstructed denticles shapes using a range of 20 harmonic.
Fig. 6 in Geometric morphometric on a new species of Trichodinidae. A tool to discriminate trichodinid species combined with traditional morphology and molecular analysis
Fig. 6. Fourier harmonic power spectrum based on Elliptical Fourier analysis.
Fig. 6 in Fractal analysis of ostracod shell variability: A comparison with geometric and classic morphometrics
Fig. 6. Location of landmarks chose on Krithe valve for shape analysis.
Figure 1. Landmarks and curves selection. A. Fore wing. B. Hind wing. C in Geometric morphometric analysis of Eysarcoris guttiger, E. annamita and E. ventralis (Hemiptera: Pentatomidae)
Figure 1. Landmarks and curves selection. A. Fore wing. B. Hind wing. C. Pygophore.
Figure 3. PCA analysis. A. Fore wing. B. Hind wing. C in Geometric morphometric analysis of Eysarcoris guttiger, E. annamita and E. ventralis (Hemiptera: Pentatomidae)
Figure 3. PCA analysis. A. Fore wing. B. Hind wing. C. Pygophore.
Figure 4. A in Further geometric morphometric analysis on the genus Eysarcoris (Hemiptera: Pentatomidae) from China
Figure 4. A dendogram showing the relationship of the eight species of Eysarcoris.
Effects of taphonomic deformation on geometric morphometric analysis of fossils: a case study using the dicynodont Diictodon feliceps (Therapsida, Anomodontia)
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Data from: A 3D geometric morphometric analysis of the bovid distal humerus, with special reference to Rusingoryx atopocranion (Pleistocene, Eastern Africa)
Open the record for dataset details and reuse information.
Geometric morphometric wing analysis represents a robust tool to identify female mosquitoes (Diptera: Culicidae) in Germany
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Geometric morphometric analysis of Protoconites minor from the Cambrian (Terreneuvian) Yanjiahe Formation in Three Gorges, South China
<p>The Ediacaran to Cambrian transition is a critical interval of time during which major evolutionary changes occurred. Recently, abundant <em>Protoconites minor</em> have been recovered from the silty shales of the lower Cambrian Yanjiahe Formation (Terreneuvian, Fortunian – Stage 2) in the Three Gorges area of South China. These fossils represent an important ecological diversification of macroscopic organisms at the onset of the Cambrian. <em>Protoconites minor</em> is a probable cnidarian-grade organism preserved by carbon compression. Herein, geometric morphometric analyses are applied to crack out specimens of <em>P. minor</em> to reveal any cryptic morphological details that may have implications for their morphological diversity, ontogenetic processes, and taxonomic identification. These statistical analyses reveal a strong relationship between size and shape, which indicates that the overall shape of <em>P. minor</em> was mainly controlled by allometric growth. The smaller specimens are generally wider at the anterior, and more commonly have straight-sides. Larger individuals tend to be narrower at the anterior, with bending more common. Our analyses demonstrate that there are transitional forms between larger, strongly bent specimens and smaller, straight specimens, suggesting that the assemblage likely consists of a single species.</p>
Data from: Geometric morphometric analysis applied to theropod tracks from the lower Cretaceous (Berriasian) of Spain
Geometric morphometric methods applied to theropod tracks from the Huérteles Formation (Berriasian, Spain) are here shown to be invaluable for drawing comparisons between theropod tracks with different preservation modes (true tracks, shallow undertracks and natural casts) or differing in the preservation of anatomical features (e.g. digital pads). Principal components analysis and thin-plate spline methods can quantitatively distinguish between the broad groups of tracks in a sample and establish the main differences between them. These methods offer a promising approach for estimating ichnodiversity, achieved by evaluating just the morphology of the tracks independent of other factors such as size. The theropod tracks of the Huérteles Formation can be classified into two broad groups: minute-to-medium-sized gracile theropod tracks (Kalohipus bretunensis) and medium-to-large-sized robust theropod tracks (Iberosauripus). The presence of a third group of more gracile medium-to-large-sized theropod tracks (Megalosauripus) cannot be proven with certainty on the basis of the current data. These results indicate that the theropod ichnodiversity of the Huérteles Formation is probably lower than that estimated by means of conventional methods alone (e.g. qualitative description of the tracks) and that many of the described theropod morphotypes may represent extramorphological or ontogenetic variations of other morphotypes.
Data from: Taxonomic and evolutionary pattern revisions resulting from geometric morphometric analysis of Pennsylvanian Neognathodus conodonts, Illinois Basin
Conodont fossils are highly valuable for Paleozoic biostratigraphy and for interpreting evolutionary change, but identifying and describing conodont morphologies, and characterizing gradual shape variation remain challenging. We used geometric morphometrics (GM) to conduct the first landmark-based morphometric analysis of the biostratigraphically useful conodont genus Neognathodus. Our objective is to assess whether previously defined morphotype groups are reliably distinct from one another. As such, we reevaluate patterns of morphologic change in Neognathodus P1elements, perform maximum likelihood tests of evolutionary modes, and construct novel, GM-based biozonations through a Desmoinesian (Middle Pennsylvanian) section in the Illinois Basin. Our GM results record the entire spectrum of shape variability among Neognathodus morphotypes thus alleviating the problem of documenting and classifying gradual morphologic transitions between morphotypes. Statistically distinct GM groups support previously established classifications of N. bassleri, N. bothrops, and N. roundyi. Statistically indistinct pairs of GM groups do not support literature designations of N. medadultimus and N. medexultimus, and N. dilatus and N. metanodosus, and we synonymize each pair. Maximum likelihood tests of evolutionary modes provide the first statistical assessment of Neognathodus evolutionary models in the Desmoinesian. The most likely evolutionary models are an unbiased random walk or a general random walk. We name four distinct biozones through the Desmoinesian using GM results and these align with previous biozonation structure based on the Neognathodus Index (NI) illustrating that Neognathodus-based biostratigraphic correlations would not change between GM or NI methods. The structural similarity between both biozonations showcases that determining GM-based biozones is not redundant, as this comparison validates using landmark-based GM work to construct viable biozonations for subsequent stratigraphic correlations. Although this study is limited to the Illinois Basin, our quantitative methodology can be broadly applied to additional genera to test taxonomic designations, interpret statistically-robust evolutionary patterns, and construct valid biozones for this significant chordate group.
Fig. 4 in Functional morphology of the cave bear (Ursus spelaeus) mandible: a 3D geometric morphometric analysis
Fig. 4 PCAs on the regression residuals of all extant Ursidae and U. spelaeus after a regression analysis of the Procrustes coordinates onto log centroid size pooled per species (a, b) and on the regression residuals of the regression taking phylogeny into account (c, d). The colors indicate the
Fig. 6 in Functional morphology of the cave bear (Ursus spelaeus) mandible: a 3D geometric morphometric analysis
Fig. 6 Scatterplot of the PC1 scores versus the logarithm of the percentage of foliage in the diet. Linear regression lines were fitted with the 95 % confidence interval of the group mean and the mean scores of U. spelaeus (vertical line)
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