NEXUS file (plain text) containing our revised data matrix (the machine-readable version of Appendix 2), one MPT from each of Analyses R1–R6, B1 and B2, and the settings used for these analyses
Executing the file in PAUP* repeats Analyses R1–R3, B1, R4–R6 and B2 in this order and then performs the statistical comparisons (Kishino-Hasegawa test, Templeton test, winning-sites test) of the trees that are already stored in the file.
NEXUS file (plain text) containing the same matrix as S1, but with one MPT from each of Analyses R7–R12, B3 and B4, and with the settings for these analyses: some characters are coded as irreversible
Data S2: NEXUS file (plain text) containing the same matrix as Data S1, but with one MPT from each of Analyses R7–R12, B3 and B4, and with the settings for these analyses: several characters are coded as irreversible. Executing the file in PAUP* repeats Analyses R7–R9, B3, R10–R12 and B4 in this order and then performs the statistical comparisons of the trees that are already stored in the file.
NEXUS file (plain text) containing the original data matrix of RC07, a tree from Analyses O1 and O2 each, as well as the settings for these analyses
Executing the file in PAUP* repeats these analyses in this order and then performs the statistical comparisons of the trees that are already stored in the file.
Excel file containing our measurements and their ratios relevant to characters PREMAX 7 and SKU TAB 1
On the sheet “Data”, the OTUs are listed such that the line numbers are the same as the numbers the OTUs have in the matrix; OTUs that cannot be measured for any of the parameters are represented by blank lines. Calculations are underlain in yellow or blue. The raw measurements, in cm, will mostly be difficult to reproduce: they were taken from illustrations (we preferred reconstruction drawings to avoid the effects of diagenetic compression) on paper or on a screen, in the latter cases usually but not always at a magnification such as 150%, 200% or 300%. The ratios, however, should be fairly well reproducible. Column B is the distance (at a right angle to the sagittal plane) between the lateral extremities of the premaxillae, measured in ventral view when the premaxillae are insufficiently exposed in dorsal view. Column C is the maximum width of the dermatocranium in dorsal view. Column D is the maximum width of the skull table; when sharp edges between the table and the temporal regions are absent or unknown, this can be measured across the “tabular horns”, across the supratemporals across the rostral ends of the temporal notches, or across the intertemporals, whichever is widest. When possible, we have consulted lateral views to determine where the dorsal and the lateral surfaces of the skull roof meet. Column E cites our sources (all of them are also cited in the main text and/or Appendix 1 and therefore listed in the References section). Column G is the ratio of premaxillary width to skull roof width (B divided by C), which we decided to use as the raw data for PREMAX 7 (Appendix-Table 1). Column H is the ratio of premaxillary width to skull table width (B/D). Column I is the postorbital skull table length, in other words the rostrocaudal distance between the caudal margins of the orbits or orbitotemporal fenestrae (averaged if necessary) and the caudal end of the skull table in the midline. In salientians, the caudal margin of the orbitotemporal fenestra was taken to be the rostral margin of the otic capsule, not that of the lateral process of the parietal which covers only the caudal or caudomedial part of the otic capsule. Column J is the postorbital skull roof length, in other words the rostrocaudal distance between the caudal margins of the orbits (averaged if necessary) and the caudalmost extent of the dermatocranium, which may be the caudal end of the skull table in the midline, the tips of “tabular horns” (averaged if necessary), or the caudal ends of the suspensoria excluding the quadrates (averaged if necessary). Column K is the ratio of skull roof width to postorbital skull roof length (C/J). Column L is the ratio of skull table width to postorbital skull table length (D/I), which we decided to use as the raw data for SKU TAB 1 (Appendix-Table 6). Column M is the ratio of skull roof width to postorbital skull table length (C/I), and column N is the ratio of skull table width to postorbital skull roof length (D/J). OTUs are represented by their most complete and skeletally most mature known members, except that Sauropleura is represented by S. scalaris rather than the morphological outlier S. pectinata (which is measured in line 153); Dendrerpetidae is represented by Dendrysekos, Albanerpetidae by Celtedens.
On all other sheets, OTUs scored 0 by RC07 are underlain in blue (for PREMAX 7 on the sheets “pmx-roof” and “pmx-table”, for SKU TAB 1 on the others), OTUs scored 1 by RC07 are underlain in yellow, and OTUs scored as unknown by RC07 as well as those that we have added retain a white background. On each sheet, the values from one of the calculated columns on “Data” are ordered by size in column B (from highest to lowest for PREMAX 7, from lowest to highest for SKU TAB 1, in agreement with the original state definitions) and plotted; the line between the data points is of course meaningless, but we included it in order to see more easily where morphological gaps would lie. Column C on the sheets “pmx-roof” (for PREMAX 7) and “po table” (for SKU TAB 1) shows the state we have assigned to each OTU. Sheet “pmx-roof” is column G of the sheet “Data”, “pmx-table” is H, “po roof” is K, “po table” is L, “roof width, table length” is M, “table width, roof length” is N.
We updated the measurements of Brachydectes (Pardo & Anderson, 2016) only after our phylogenetic analyses. Therefore, on each sheet, Brachydectes now forms an extra peak (positive or negative) in the line that connects the data points. The score SKU TAB 1(2) remains correct; the score PREMAX 7(1) should have been 0.