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Fig. 1 in A practical, step-by-step, guide to taxonomic comparisons using Procrustes geometric morphometrics and user-friendly software (part B): group comparisons

Fig. 1. Box and jitter-plots of CS, for each species. a. Separate plots for females, males and unknown individuals. b. Plots with pooled sexes. As in part A, as well as shown in Table 1, species names in all figures are abbreviated using the first three letters of the scientific name (e.g., caligata = cal) and F for female, M for male, and U for individuals of unknown sex.

Fig. 2 in A practical, step-by-step, guide to taxonomic comparisons using Procrustes geometric morphometrics and user-friendly software (part B): group comparisons

Fig. 2. Visualization of shape SDM in relation to interspecific differences using a bgPCA. In this, and other Figures, percentages of variance in the scatterplots of multivariate shape are shown in parentheses, below the label for the corresponding axis. On bgPC1–2, which together account for almost all between group variance (94%), there is a large overlap between females and males within each species, whereas, between species, the separation is clear.

Fig. 7 in A practical, step-by-step, guide to taxonomic comparisons using Procrustes geometric morphometrics and user-friendly software (part A): introduction and preliminary analyses

Fig. 7. Example of search for shape outliers (emphasized in red) in yellow-bellied marmots: (a) phenogram of shape; (b1-2) scatterplots of PC1 vs PC3 and PC4 vs PC9 (percentages of variance accounted for by each PC shown in parentheses); (c-d) visualization of individual 193 using displacement vectors for this specimen relative to the sample mean shape (c), as well as its original photograph (d).

Fig. 4 in A practical, step-by-step, guide to taxonomic comparisons using Procrustes geometric morphometrics and user-friendly software (part A): introduction and preliminary analyses

Fig. 4. Graphical examination of replicability in shape using the reduced 12 landmarks configuration. a. PCA scatterplot (in parentheses the variance accounted for by each PC) with convex hulls for the first (grey) and second (red) duplicate. b. Example of phenogram used to count 'sister duplicates' in the whole sample (the inset zooms in the phenogram to exemplify how duplicates 1 and 2 of each individual, e.g., number 97, a female, or number 81, a male, etc., should cluster in pairs, if ME is smaller than inter-individual differences).

Fig. 1 in A practical, step-by-step, guide to taxonomic comparisons using Procrustes geometric morphometrics and user-friendly software (part A): introduction and preliminary analyses

Fig. 1. Study flowchart for both preliminary (A) and main (B) analyses. The flowchart can be used as a reminder for the main analytical steps in a taxonomic study using GMM. To the same aim, at the end of part B, I added a checklist (Appendix B). In the flowchart, I have included the power analysis and few other analyses, which are optional (dotted lines). The power analysis is shown here connected to both the preliminary steps and the group comparisons, because it can be either prospective or retrospective. The sensitivity of results to the inclusion or exclusion of the smallest samples is also connected to both preliminary and main analyses, because it can be used at any step in the analysis. Sometimes (e.g., in the discriminant analysis (DA) of shape), if p is large relative to N and dimensionality reduction is needed, one could also assess the sensitivity of results to the inclusions of different number of PCs. I stress that, as discussed in the main text of both parts A and B, if a taxon is known to have a large SDM, which may vary in pattern depending on the species or subspecies, even preliminary analyses (such as those for ME or outlier detection) should probably be run with separate sexes.

Fig. 3. a in A practical, step-by-step, guide to taxonomic comparisons using Procrustes geometric morphometrics and user-friendly software (part A): introduction and preliminary analyses

Fig. 3. a. Final configuration, reduced to 12 landmarks after excluding low precision landmarks. b. Graphical examination of size replicability (12 landmarks configuration) using a plot of CS in the second duplicate against CS in the first duplicate.

Fig. 2. Initial configuration with 15 in A practical, step-by-step, guide to taxonomic comparisons using Procrustes geometric morphometrics and user-friendly software (part A): introduction and preliminary analyses

Fig. 2. Initial configuration with 15 landmarks (a) and analysis of absolute per-landmark imprecision (b, c). Figure 2b shows the profile plot for the summary statistics of per-landmark variance in the two digitizations. Figure 2c shows the scatter of landmarks purely due to digitization error (red landmarks mark the mean form, to which the differences between the first and second digitization were added).

Fig. A1 in A practical, step-by-step, guide to taxonomic comparisons using Procrustes geometric morphometrics and user-friendly software (part A): introduction and preliminary analyses

Fig. A1. Box and jitter plot of shape SDM estimated using randomized subsampling experiments in yellow-bellied marmots (whiskers in this figure mark the range from minimum to maximum, with no assessment of outliers, which are irrelevant in the context of this didactic example). The total female sample (F) is split in progressively smaller, mutually exclusive, random subsamples and the same is done for males (M). The first subsample of 70 individuals per sex is almost the same of the total samples; the second consists of two female and two male subsamples with 35 individuals each; the third set of subsamples is made of 17–18 individuals per sex and the fourth and fifth include only 10 or 5 individuals respectively. The vertical axis shows the Procrustes distance between means of females and means of males of each set of subsamples. The red circles show the observed mean female to male Procrustes distance in VIM, Alaskan (bro) and Olympic marmots (oly); they are added to the box and jitter plots of yellow-bellied marmot subsamples whose N is closer to the observed N is these three species.

Fig. 5 in A practical, step-by-step, guide to taxonomic comparisons using Procrustes geometric morphometrics and user-friendly software (part A): introduction and preliminary analyses

Fig. 5 (next page). Examples of ME. a. Suspected bias due to a time lag in the data collection. The scatterplots (a2-a3) are ordinations of 3D cranial shapes in a large sample of African adult men; above the ordinations (a1), the mean shape differences between green (first round of data collection, N = 377) and blue (second round, N = 161) groups are shown (magnified five times) in dorsal, side and frontal views. In the PCA (a2) there is a small amount of separation between 'green' and 'blue' on PC2 (variance explained in parentheses). In the DA (a3), the 'green-blue' separation on the horizontal axis (DF1, with, in parentheses, the between group variance explained) is almost perfect despite the fact that groups, whose differences are being maximized in this plot, are in fact the real 32 geographic populations (shown using convex hulls - see main text). b. PC1-2 scatterplots of adult 3D craniofacial shapes in a European sample of adult women (N = 351, shown in pink) and men (N = 380, in blue). The configuration is smaller and different from the one in (a). Above the scatterplots, the shape corresponding to the positive extreme of PC1 (variance explained in parentheses) is shown, in dorsal view, using displacement vectors (b1-b2). The scatterplot to the left (b3) is the full landmark configuration, whereas the one to the right (b4) has euryon removed. Euryon dominates PC1 differences (b3) in the full configuration (b1). After removing it (b2), not only there is no landmark that dominates variation on PC1 (b4), but also the separation of females and males disappears and (see main text) the shape variance accounted for by sex drops from 6% to 3%. c. PC1-2 scatterplot (variance explained in parentheses) of marmot mandibular shape using the reduced landmark configuration in real (c1) and simulated (c2) samples of hoary marmots and woodchucks. The simulated data are obtained by adding to the original shape coordinates large random gaussian noise (SD = 0.05) before Procrustes re-superimposing the data. Random noise (c2) completely obliterates the real differences (c1) and brings the F ratio and Rsq from F = 38 and Rsq = 20%, in the real data, to F = 2 and Rsq = 0.8% in the simulated ones. In both datasets, the tangent space approximation (assessed in TPSSmall) in the real data (c1) produces a correlation of one between shape distances; however, whereas the slope of the least square regression (tangent space Euclidean shape distances onto Procrustes shape distances) is one in the real data, it is 0.97 in the simulated ones, which suggests an almost problematically large amount of shape variance in this second dataset.

Fig. 4 in Determination Of Sexual Dimorphism And Morphological Variation Of Pool Barb, Puntius Sophore (Cypriniformes, Cyprinidae), Using Landmark Based Geometric Morphometric Analysis

Fig. 4. Change of body shape along principal component axis (PC 1 = 43.827 %, and PC 2 = 20.578 %). Left side is the lollipop plots. Right side is the transformation grids of shape change.

Fig. 3, a in Determination Of Sexual Dimorphism And Morphological Variation Of Pool Barb, Puntius Sophore (Cypriniformes, Cyprinidae), Using Landmark Based Geometric Morphometric Analysis

Fig. 3, a — eigenvalues plot of the proportion of variance described by each PC, b — scatter plot showing scores on the first two PCs for the sample of non-breeding season and breeding season fish population (female in red, male in blue and non-breeding season population in green).

Fig. 1, a in Determination Of Sexual Dimorphism And Morphological Variation Of Pool Barb, Puntius Sophore (Cypriniformes, Cyprinidae), Using Landmark Based Geometric Morphometric Analysis

Fig. 1, a — male individual in breeding season; b — digitized image of P. sophore with the 14 landmarks (red points) used for the geometric morphometric analysis: c — scatter plot of 14 landmarks configurations after Procrustes Superimposition.

Fig. 2 in Determination Of Sexual Dimorphism And Morphological Variation Of Pool Barb, Puntius Sophore (Cypriniformes, Cyprinidae), Using Landmark Based Geometric Morphometric Analysis

Fig. 2. Distribution of non-breeding season population and the breeding season (male and female) population along first and second canonical variate axes (female in red, male in blue and non-breeding season population in green).

FIGURE 9 in Morphological variation during post-embryonic development in the centipede Lithobius melanops: traditional and geometric morphometrics approaches

FIGURE 9 Centroid size differences of (A) The forcipular apparatus; (B) The cephalic capsule; and (C) The ultimate leg among epimorphic groups. The median with the first and third quartiles is shown (in boxes), together with the range of variation and outliers.

FIGURE 8 in Morphological variation during post-embryonic development in the centipede Lithobius melanops: traditional and geometric morphometrics approaches

FIGURE 8 Centroid size differences of (A, B) The forcipular apparatus; (C, D) The cephalic capsule; and (E, F) The ultimate leg among sexes in praematurus (left) and maturus (right) epimorphic groups. The median with the first and third quartiles is shown (in boxes), together with the range of variation and outliers.

FIGURE 7 in Morphological variation during post-embryonic development in the centipede Lithobius melanops: traditional and geometric morphometrics approaches

FIGURE 7 Position of landmarks (open circles) and semilandmarks (full circles) for analyzed structures in L. melanops: (A) The forcipular apparatus (ventral view); (B) The cephalic capsule (dorsal view); and (C) The ultimate leg (medial view). Scale bar: (A) and (C) – 1 mm; (B) – 0.5 mm.

FIGURE 6 in Morphological variation during post-embryonic development in the centipede Lithobius melanops: traditional and geometric morphometrics approaches

FIGURE 6 Development of genital appendages on the postpedal segments in males during epimorphic stages in L. melanops (ventral view). (A) Agenitalis; (B) Immaturus; (C) Praematurus; (D) Pseudomaturus early phase; (E) Pseudomaturus late phase; (F) Maturus. Scale bars: 0.2 mm.

FIGURE 5 in Morphological variation during post-embryonic development in the centipede Lithobius melanops: traditional and geometric morphometrics approaches

FIGURE 5 Development of genital appendages on the postpedal segments in females during epimorphic stages in L. melanops (ventral view). (A) Agenitalis; (B) Immaturus early phase; (C) Immaturus late phase; (D) Praematurus early phase; (E) Praematurus middle phase; (F) Praematurus late phase; (G) Pseudomaturus early phase; (H) Pseudomaturus late phase; (I) Maturus. Scale bars: 0.2 mm.

FIGURE 4 in Morphological variation during post-embryonic development in the centipede Lithobius melanops: traditional and geometric morphometrics approaches

FIGURE 4 Arrangement of ocelli during post-embryonic development in L. melanops (lateral view). (A) Anamorph 0; (B) Anamorph 1; (C) Anamorph 2; (D) Anamorph 3; (E) Anamorph 4; (F) Agenitalis; Downloaded from Brill.com 06/21/2024 07:44:41PM (G) Immaturus; (H) Praematurusvia; (I) OpenMaturus Access.. Scale Thisbar is: an 0.2 open mm. access article distributed under the terms of the CC BY 4.0 license. https://creativecommons.org/licenses/by/4.0/

FIGURE 3 in Morphological variation during post-embryonic development in the centipede Lithobius melanops: traditional and geometric morphometrics approaches

FIGURE 3 Development of the forcipular apparatus in L. melanops (ventral view). (A), (B) Anamorph 0; (C), (D) Anamorph 1; (E) Anamorph 2; (F) Anamorph 3; (G) Anamorph 4; (H) Agenitalis; (I) Immaturus; (J) Pseudomaturus; (K) Maturus. Scale bar: 0.2 mm. Specimens colored with toluidine blue: (B) and (D).