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.