Contributions to Zoology, 84 (2) – 2015Valentin Rineau; Anaïs Grand; René Zaragüeta; Michel Laurin: Experimental systematics: sensitivity of cladistic methods to polarization and character ordering schemes

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Online supplementary information

S1. Vba script used to generate the individual Nexus text files from the columns of discretized simulated data in Excel obtained using S2 and 7 and compiled into S4 (the latter is processed using S1 to get individual Nexus text files).

S2. Spreadsheet using the vba script presented in S1 to produce Nexus files for parsimony analysis.

S3. Spreadsheet using the vba script presented in S1 to produce Nexus files for 3ta analysis.

S4. The 1800 PAUP nexus files used in our parsimony analyses. Each sheet presents 100 matrices corresponding to one tree. Each sheet is identified by two numbers; the first number refers to the topology (1, pectinate; 2, symmetrical; 3, equiprobable), and second, branch length (sorted from shortest to longest). Thus, sheet 2.3 presents the matrices obtained from the symmetrical tree (Fig. 5B) with the third set of branch lengths (1). For the third topology, there are 12 branch lengths, corresponding to three branch lengths associated with Fig. 5C, six branch lengths associated with Fig. 5D, and with Fig. 5E-G).

S5. Resolving power and artefactual resolution in trees of various branch lengths.

S6. Frequency distribution of character states, based on 10000 characters in 21 taxa, obtained by discretization of continuous data generated by Brownian motion on the equiprobable tree (Fig. 5C, with outgroup branch length set at full tree depth).

S7. Individual ITRIs of the 1800 matrices (each of which was analysed using the three methods, for 5400 ITRI values for resolving power, and as many for artefactual resolution) used to compute resolving power and artefactual resolutions.

S8. Impact of branch length and topology on resolving power and artefactual resolution. Each cell value represents ITRI means for 100 matrices.