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Reproducibility in phylogenetics: reevaluation of the largest published morphological data matrix for phylogenetic analysis of Paleozoic limbed vertebrates

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248 days ago
PJpreprint: Reproducibility in phylogenetics: reevaluation of the largest published morphological data matrix for phylogenetic analysis of Paleozoic limbed vertebrates https://t.co/BQNABITzI1
248 days ago
Reproducibility in phylogenetics: reevaluation of the largest published morphological data matrix for phylogenetic analysis of Paleozoic limbed vertebrates https://t.co/3EJuYKaWBh
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Supplemental Information

Revised data matrix for parsimony analyses

NEXUS file (plain text) containing our revised data matrix (the machine-readable version of Appendix 2), one MPT from each of Analyses R1–R6, the bootstrap trees from B1 and B2, and the settings used for these analyses. Executing the file in PAUP* repeats Analyses R1–R6 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.

DOI: 10.7287/peerj.preprints.1596v3/supp-1

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 distortion) 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 rostral margin of the otic capsule was assumed to lie at the caudal margin of the orbitotemporal fenestra, not at 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 3). 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, *Caseasauria by Eothyris.

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.

DOI: 10.7287/peerj.preprints.1596v3/supp-2

Revised data matrix for Bayesian analysis

NEXUS file (plain text) containing our revised data matrix, a tree from Analysis EB in two formats (one with the posterior probabilities as node labels), and the settings used for this analysis. The stepmatrix characters (32 and 134 in both Appendices and Data S1) are split into two or three characters each, as explained in the text and Appendix 1. Executing the file in MrBayes repeats Analysis EB.

DOI: 10.7287/peerj.preprints.1596v3/supp-3

Original data matrix of RC07. 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.

DOI: 10.7287/peerj.preprints.1596v3/supp-4

Homoplasy per character in our revised matrix given an MPT from Analysis R1 (unconstrained, original taxon sample) and one from R4 (unconstrained, expanded taxon sample)

The line numbers are the numbers of the characters (1–277). Column A shows the minimum of necessary steps per character (its number of states minus one); column B shows the steps actually found in R1 or R4 on the trees included in Data S1; column C is the difference between A and B, sorted from lowest to highest in column E, counted in columns G and H and plotted in the file as well as in Fig. 22. The line between the data points in the plots is meaningless, but makes it easier to compare the distributions to an exponential curve. Compare Goloboff, Torres & Arias (2017: fig. 1(a)).

DOI: 10.7287/peerj.preprints.1596v3/supp-5

Additional Information

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

David Marjanović conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Michel Laurin conceived and designed the experiments, contributed reagents/materials/analysis tools, wrote the paper, reviewed drafts of the paper.

Data Deposition

The following information was supplied regarding data availability:

All data are contained in the Supplementary Information.

Funding

At the beginning of the study period, D. M. was a beneficiary of the university student subsidy office (Studienbeihilfenbehörde) of the Federal Republic of Austria; later he received an unnumbered two-year postdoctoral research grant from the Alexander von Humboldt Foundation. M. L. received no funding for this work. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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