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690 results for “Geometric morphometric”
Cave-adapted evolution in the North American Amblyopsid fishes inferred using phylogenomics and geometric morphometrics
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Geometric morphometrics of endophytic oviposition traces of Odonata (Eocene, Argentina)
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Data from: Wing geometric morphometrics and molecular assessment of members in the Albitarsis Complex from Colombia
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Data from: Biostratigraphy and geometric morphometrics of conchostracans (Crustacea, Branchiopoda) from the Late Triassic fissure deposits of Cromhall Quarry, UK
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Data from: Geometric morphometric character suites as phylogenetic data: extracting phylogenetic signal from gastropod shells
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Data from: Evolution of neck vertebral shape and neck retraction at the transition to modern turtles: an integrated geometric morphometric approach
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Data from: Investigating population differentiation in a major African agricultural pest: evidence from geometric morphometrics and connectivity suggests high invasion potential
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Data from: Geometric morphometric analysis applied to theropod tracks from the lower Cretaceous (Berriasian) of Spain
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A geometric morphometric approach to the study of sexual dimorphism in the modern human frontal bone
<p>Code and data to replicate the results reported in the paper "A geometric morphometric approach to the study of sexual dimorphism in the modern human frontal bone"</p>
Data from: Using three-dimensional geometric morphometric and dental topographic analyses to infer the systematics and paleoecology of fossil treeshrews (Mammalia, Scandentia)
<p>Treeshrews are small, Indomalayan mammals closely related to primates. Previously, three-dimensional geometric morphometric analyses were used to assess patterns of treeshrew lower second molar morphology, which showed that the position of molar landmarks covaries with intraordinal systematics. Another analysis used dental topographic metrics to test patterns of functional dental morphology and found that molar curvature, complexity, and relief were an effective means for examining patterns of variation in treeshrew dietary ecology. Here, we build on these analyses by adding two fossil taxa; <i>Prodendrogale yunnanica</i>, from the Miocene of China and <i>Ptilocercus kylin</i> from the Oligocene of China. Our results show that <i>Pr. yunnanica</i> had a dental bauplan more like that of a tupaiid than that of a ptilocercid, but that the extant tupaiids, including <i>Tupaia</i> and <i>Dendrogale</i>, are more similar to one another in this regard than any are to <i>Prodendrogale. </i>This is contrary to our expectations as <i>Prodendrogale </i>is hypothesized to be most closely related to <i>Dendrogale. Ptilocercus kylin, </i>which has been proposed to be the sister taxon of <i>Pt. lowii,</i> is characterized by dental morphology like that of <i>Pt. lowii </i>in crest and cuspal position but is interpreted to have been more frugivorous. It has been claimed that <i>Ptilocercus </i>has undergone little morphological change through time. Our results suggest that <i>Pt. kylin</i> was more ecologically distinct from <i>Pt. lowii</i> than previously proposed, providing a glimpse into a more complex evolutionary history of that group than had been inferred.</p>
Figure 2 in Traditional and geometric morphometric analyses reveal homogeneity in European Scutacarus acarorum Goeze, 1780 populations (Acari: Scutacaridae: Heterostigmatina)
Figure 2. Landmarks on the posterior sternal plate used for geometric morphometrics. The selected landmarks include the insertions of ventral setae (landmarks 1–6 and 8–13) and the crossing point of particular apodemata (landmark 7).
Figure 4 in Traditional and geometric morphometric analyses reveal homogeneity in European Scutacarus acarorum Goeze, 1780 populations (Acari: Scutacaridae: Heterostigmatina)
Figure 4. Scatter plots from principal component analysis (PCA). (A) Log-transformed raw data; (B) log-transformed size corrected data; (C) shape coordinates (including deformation grids showing the shape deformation explained by PC1 and PC2).
Figure 5 in Traditional and geometric morphometric analyses reveal homogeneity in European Scutacarus acarorum Goeze, 1780 populations (Acari: Scutacaridae: Heterostigmatina)
Figure 5. Plots contrasting the first two canonical variates gained from (A) log-transformed raw data; (B) log-transformed size corrected data; (C) shape coordinates.
Figure 3 in Traditional and geometric morphometric analyses reveal homogeneity in European Scutacarus acarorum Goeze, 1780 populations (Acari: Scutacaridae: Heterostigmatina)
Figure 3. Box-whisker plot showing the interquartile range, median, minimum and maximum of the 'size' (defined as the geometric mean) of Scutacarus acarorum populations.
Figure 1 in Traditional and geometric morphometric analyses reveal homogeneity in European Scutacarus acarorum Goeze, 1780 populations (Acari: Scutacaridae: Heterostigmatina)
Figure 1. Sampling sites of the studied Scutacarus acarorum populations. (1) Thomatal, (2) Southern Styria, (3) Lienz, (4) Erlangen (5) Sandomierz, (6) Poznan, (7) Yalta, (8) Wales, (9) Cheshire and (10) New York.
Figure 6 in Traditional and geometric morphometric analyses reveal homogeneity in European Scutacarus acarorum Goeze, 1780 populations (Acari: Scutacaridae: Heterostigmatina)
Figure 6. Unrooted neighbour-joining (NJ) trees of Scutacarus acarorum populations based on squared Mahalanobis distances obtained from canonical variates analysis (CVA) on canonical variates values of (A) log-transformed raw data; (B) log-transformed size corrected data; (C) shape coordinates.
Pieris brassicae geometric morphometric data
<p class="CxSpFirst">By adopting a longitudinal study design and through geometric morphometrics methods, we investigated size and shape regulation in the head capsule during the larval development of the cabbage butterfly <i>Pieris brassicae</i> under laboratory conditions. We found evidence of size regulation by compensatory growth, although not equally effective in all larval stages. Size compensation is not attained through the regulation of developmental timing, but rather through the modulation of per-time growth rate. As for the shape, neither the variance of the symmetric component of shape, nor the level of fluctuating asymmetry show any evidence of increase across stages, either at the population or individual level, which is interpreted as a mark of ontogenetic shape regulation. In addition, also the geometry of individual asymmetry is basically conserved across stages. While providing specific documentation on the ontogeny of size and shape variation in this insect, this study may contribute to a more general understanding of developmental regulation and its influence on phenotypic evolution.</p>
Data from: Cryptic species or inadequate taxonomy? implementation of 2D geometric morphometrics based on integumental organs as landmarks for delimitation and description of copepod taxa
Discovery of cryptic species using molecular tools has become common in many animal groups but it is rarely accompanied by morphological revision, creating ongoing problems in taxonomy and conservation. In copepods, cryptic species have been discovered in most groups where fast-evolving molecular markers were employed. In this study at Yeelirrie in Western Australia we investigate a subterranean species complex belonging to the harpacticoid genus Schizopera Sars, 1905, using both the barcoding mitochondrial COI gene and landmark-based two-dimensional geometric morphometrics. Integumental organs (sensilla and pores) are used as landmarks for the first time in any crustacean group. Complete congruence between DNA-based species delimitation and relative position of integumental organs in two independent morphological structures suggests the existence of three distinct evolutionary units. We describe two of them as new species, employing a condensed taxonomic format appropriate for cryptic species. We argue that many supposedly cryptic species might not be cryptic if researchers focus on analyzing morphological structures with multivariate tools that explicitly take into account geometry of the phenotype. A perceived supremacy of molecular methods in detecting cryptic species is in our view a consequence of disparity of investment and unexploited recent advancements in morphometrics among taxonomists. Our study shows that morphometric data alone could be used to find diagnostic morphological traits and gives hope to anyone studying small animals with a hard integument or shell, especially opening the door to assessing fossil diversity and rich museum collections. We expect that simultaneous use of molecular tools with geometry-oriented morphometrics may yield faster formal description of species. Decrypted species in this study are a good example for urgency of formal descriptions, as they display short-range endemism in small groundwater calcrete aquifers in a paleochannel, where their conservation may be threatened by proposed mining.
Data from: Tuning Geometric Morphometrics: an R tool to reduce information loss caused by surface smoothing
The application of Geometric Morphometrics has remarkably increased since 3D imaging techniques have become widespread, such as high-resolution computerised tomography, laser scanning and photogrammetry. Acquisition, 3D rendering and simplification of virtual objects produce faceting and topological artefacts, which can be counteracted by applying decimation and smoothing algorithms. Nevertheless, smoothing algorithms can have detrimental effects. This work aims at developing a method to assess the amount of information loss or recovery after the application of 3D surface smoothing. The method presented here is conceived to optimise the smoothing procedure for 3D surfaces used in Geometric Morphometrics. We implemented the method in a tool running in the r statistical environment. The tool requires one surface, one landmark set and one surface semilandmark set to estimate the best smoothing settings, including algorithm type, iteration and scale factor value. Additional parameters can be tuned by the user. We describe the method in detail, reporting the tool usage, including its main settable parameters. One example is provided as a further explanation of the method. Our method reduces the chances of losing information in Geometric Morphometrics applications and is a unique attempt of standardising a widespread, potentially damaging procedure. The tool represents an advance in the application of Geometric Morphometrics.
Data from: The utility of cranial ontogeny for phylogenetic inference: a case study in crocodylians using geometric morphometrics
The degree to which the ontogeny of organisms could facilitate our understanding of phylogenetic relationships has long been a subject of contention in evolutionary biology. The famed notion that 'ontogeny recapitulates phylogeny' has been largely discredited, but there remains an expectation that closely related organisms undergo similar morphological transformations throughout ontogeny. To test this assumption, we used three-dimensional geometric morphometric methods to characterize the cranial morphology of 10 extant crocodylian species and construct allometric trajectories that model the post-natal ontogenetic shape changes. Using time-calibrated molecular and morphological trees, we employed a suite of comparative phylogenetic methods to assess the extent of phylogenetic signal in these trajectories. All analyses largely demonstrated a lack of significant phylogenetic signal, indicating that ontogenetic shape changes contain little phylogenetic information. Notably, some Mantel tests yielded marginally significant results when analysed with the morphological tree, which suggest that the underlying signal in these trajectories is correlated with similarities in the adult cranial morphology. However, despite these instances, all other analyses, including more powerful tests for phylogenetic signal, recovered statistical and visual evidence against the assumption that similarities in ontogenetic shape changes are commensurate with phylogenetic relatedness and thus bring into question the efficacy of using allometric trajectories for phylogenetic inference.
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.