1,721,580 research outputs found
Missing the third dimension in geometric morphometrics: how to assess if 2D images really are a good proxy for 3D structures?
Full text linkProcrustean geometric morphometrics has made large use of 2D images for studying three-dimensional structures such as mammalian bones or arthropod exoskeleta. This type of use of 2D data is still widespread today and will likely remain common for several years due to its simplicity, efficiency and low cost. However, using 2D pictures to measure morphological variation in a 3D object is an approximation that inevitably implies measurement error. Despite this being an obvious problem, which was emphasized since the early days of the first applications of geometric morphometrics to biology, whether 2D is a good proxy for 3D has been a rather neglected topic in the literature until very recently. In this paper, using marmot mandibles and crania as an example, I show how to assess the potentially crucial impact of 'missing the third dimension' in 2D landmarks and suggest a new method to test the accuracy of these data: the method is simple and can be easily performed in a user-friendly free software such as MorphoJ. This test is complimentary to other more exploratory analyses, that can also be performed using free programs and might offer a routine protocol to estimate the goodness of the 2D to 3D approximation in geometric morphometrics. Example data and a fully worked out MorphoJ project are provided for readers to learn how to replicate the analysis
A practical, step-by-step, guide to taxonomic comparisons using Procrustes geometric morphometrics and user-friendly software (part A): introduction and preliminary analyses
No full textIn this second part of the study, using a ‘clean’ dataset without very low precision landmarks and outliers, I describe how to compare mandibular size and shape using Procrustes methods in adult North American marmots. After demonstrating that sex differences are negligible, females and males are pooled together with specimens of unknown sex and species are compared using a battery of tests, that estimate both statistical significance and effect size. The importance of allometric variation and its potential effect on shape differences is also explored. Finally, to provide potential clues on founder effects, I compare the magnitude of variance in mandibular size and shape between the Vancouver Island marmot (VAN) and the hoary marmot, its sister species on the mainland. In almost all main analyses, I explore the sensitivity of results to heterogeneous sample size and small samples using subsamples and randomized selection experiments. For both size and shape, I find a degree of overlap among species variation but, with very few exceptions, mean interspecific differences are well supported in all analyses. Shape, in particular, is an accurate predictor of taxonomic affiliation. Allometry in adults, however, explains a modest amount of within-species shape change. Yet, there is a degree of divergence in allometric trajectories that seems consistent with subgeneric separation. VAN is the most distinctive species for mandibular shape and mandibular morphology suggests a long history of reduced variation in this insular population. Geometric morphometrics (GMM) is a powerful tool to aid taxonomic research. Regardless of the effectiveness of this family of methods and the apparent robustness of results obtained with GMM, however, large samples and careful measurements remain essential for accuracy. Even with excellent data, morphometrics is important, but its findings must be corroborated with an integrative approach that combines multiple lines of evidence to taxonomic assessment. The analytical protocol I suggest is described in detail, with a summary checklist, in the Appendix, not to miss important steps. All the analyses can be replicated using the entire dataset, which is freely available online. Beginners may follow all the steps, whereas more experienced researchers can focus on one specific aspect and read only the relevant chapter. There are limitations, but the protocol is flexible and easy to improve or implement using a programming language such as R
A practical, step-by-step, guide to taxonomic comparisons using Procrustes geometric morphometrics and user-friendly software (part B): group comparisons
No full textIn this second part of the study, using a ‘clean’ dataset without very low precision landmarks and outliers, I describe how to compare mandibular size and shape using Procrustes methods in adult North American marmots. After demonstrating that sex differences are negligible, females and males are pooled together with specimens of unknown sex and species are compared using a battery of tests, that estimate both statistical significance and effect size. The importance of allometric variation and its potential effect on shape differences is also explored. Finally, to provide potential clues on founder effects, I compare the magnitude of variance in mandibular size and shape between the Vancouver Island marmot (VAN) and the hoary marmot, its sister species on the mainland. In almost all main analyses, I explore the sensitivity of results to heterogeneous sample size and small samples using subsamples and randomized selection experiments. For both size and shape, I find a degree of overlap among species variation but, with very few exceptions, mean interspecific differences are well supported in all analyses. Shape, in particular, is an accurate predictor of taxonomic affiliation. Allometry in adults, however, explains a modest amount of within-species shape change. Yet, there is a degree of divergence in allometric trajectories that seems consistent with subgeneric separation. VAN is the most distinctive species for mandibular shape and mandibular morphology suggests a long history of reduced variation in this insular population. Geometric morphometrics (GMM) is a powerful tool to aid taxonomic research. Regardless of the effectiveness of this family of methods and the apparent robustness of results obtained with GMM, however, large samples and careful measurements remain essential for accuracy. Even with excellent data, morphometrics is important, but its findings must be corroborated with an integrative approach that combines multiple lines of evidence to taxonomic assessment. The analytical protocol I suggest is described in detail, with a summary checklist, in the Appendix, not to miss important steps. All the analyses can be replicated using the entire dataset, which is freely available online. Beginners may follow all the steps, whereas more experienced researchers can focus on one specific aspect and read only the relevant chapter. There are limitations, but the protocol is flexible and easy to improve or implement using a programming language such as R
Integration and Modularity in Procrustes Shape Data: Is There a Risk of Spurious Results?
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Crescita e forma in Marmota (Rodentia, Sciuridae): la morfometria geometrica della mandibola nell'indagine ontogenetica e filogenetica.
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Lost in the Other Half: Improving Accuracy in Geometric Morphometric Analyses of One Side of Bilaterally Symmetric Structures
Full text linkSystematists and evolutionary biologists have widely adopted Procrustes-based geometric morphometrics for measuring size and shape in biology. Many structures, and in fact most animals, are bilaterally symmetric with an internal plane of symmetry (also called object symmetry). Often, when quantifying asymmetric variation is not an aim, only one or the other side is measured and analyzed. This approach has been used in hundreds of studies. Its implicit assumption is that the information on the other side is redundant and a single side will, therefore, produce results mirroring those one would have obtained from the analysis of the entire structure with all its left and right landmarks. However, the extent to which this assumption is met has, to my knowledge, never been explored. Using two example data sets, I will show that congruence may be high in analyses at a macroevolutionary level but much lower at a microevolutionary one, and inaccuracies might especially affect shape. I will discuss some of the other factors that may influence results and will suggest a simple expedient that can improve both the visualization and accuracy of shape analyses in one-side-only studies
Left, right or both? Estimating and improving accuracy of one-side-only geometric morphometric analyses of cranial variation
No full textProcrustes-based geometric morphometric analyses of bilaterally symmetric structures are often performed using only one side. This is particularly common in studies of cranial variation in mammals and other vertebrates. When one is not interested in quantifying asymmetry, landmarking one side, instead of both, reduces the number of variables as well as the time and costs of data collection. It is assumed that the loss of information in the other half, on which landmarks are not digitized, is negligible, but this has seldom been tested. Using 10 samples of mammalian crania and a total of more than 500 specimens, and five different landmark configurations, I demonstrate that this assumption is indeed easily met for size. For shape, in contrast, one-side landmarking has potentially more severe consequences on the estimates of similarity relationships in a sample. In this respect, microevolutionary analyses of small differences are particularly affected, whereas macroevolutionary studies are fairly robust. In almost all instances, however, a simple preliminary operation improves accuracy by making one-side-only shape data more similar to those obtained by landmarking both sides. The same operation also makes estimates of allometry more accurate and improves the visualization. This operation consists in estimating the missing side by a mirror reflection of bilateral landmarks. In the Supporting Information, I exemplify how this can be easily done using free user-friendly software. I also provide an example data set for readers to repeat and learn the steps of this simple procedure
How flat can a horse be? Exploring 2D approximations of 3D crania in equids
No full texthttps://www.sciencedirect.com/science/article/pii/S094420062030005
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