Reevaluation of the largest published morphological data matrix for phylogenetic analysis of Paleozoic limbed vertebrates
- Published
- Accepted
- Subject Areas
- Biodiversity, Ecology, Evolutionary Studies, Paleontology
- Keywords
- phylogenetics, data matrix, morphology, Lissamphibia, Amphibia, Temnospondyli, Lepospondyli, Anthracosauria, reversal, middle ear
- Copyright
- © 2015 Marjanović et al.
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ PrePrints) and either DOI or URL of the article must be cited.
- Cite this article
- 2015. Reevaluation of the largest published morphological data matrix for phylogenetic analysis of Paleozoic limbed vertebrates. PeerJ PrePrints 3:e1596v1 https://doi.org/10.7287/peerj.preprints.1596v1
Abstract
The largest data matrix for phylogeny of early limbed vertebrates (Ruta M, Coates MI. 2007. J. Syst. Palaeont. 5:69–122) has supported controversial hypotheses; e.g., it has recovered Seymouriamorpha, Diadectomorpha and (in some trees) Caudata as paraphyletic and found the “temnospondyl hypothesis” on the origin of Lissamphibia (TH) to be one step more parsimonious than the “lepospondyl hypothesis” (LH). Scrutiny of the matrix reveals thousands of suboptimal scores (many clearly due to typographic and similar errors) as well as logically linked (redundant) characters, characters with only one described state, and even cases where taxa were scored after presumed relatives. Moreover, all characters – even obviously continuous ones – were unordered, effects of ontogeny were not sufficiently taken into account, and the authors mostly excluded data published after 2001, even their own. Our revised version – we document and justify all changes – yields much longer trees with a different topology, e.g. monophyletic Caudata, Diadectomorpha and (sometimes) Seymouriamorpha, Ichthyostega more rootward than Acanthostega, Anthracosauria more rootward than Temnospondyli, and the LH, which is 10 steps more parsimonious than the TH and 15 more than the “polyphyly hypothesis” (PH). Bootstrap values, though, are low, and few of the topologies are statistically distinguishable. For another set of analyses, we added 48 OTUs to the original 102. This destabilizes parts of the tree, e.g. the relationships of Anthracosauria and Temnospondyli. However, many of the added taxa have a fully resolved position or nearly so; this concerns the well-known Chroniosaurus (sister to a clade containing Solenodonsaurus, Seymouriamorpha, Diadectomorpha, Amniota and Amphibia), but also isolated lower-jaw material from the Devonian and Carboniferous. Despite the addition of Gerobatrachus, Micropholis and Tungussogyrinus and the extremely peramorphic salamander Chelotriton, the difference between LH and TH only shrinks to 9 steps, that between LH and PH to 13 steps. The “lepospondyl” Brachydectes is neither found as sister to Lissamphibia nor in the “microsaur” grade. Bootstrap values plummet, though, and all three hypotheses become statistically indistinguishable at p = 0.05. We then duplicated all analyses after coding all losses of bones as irreversible. Anthracosauria is then consistently placed more rootward than Temnospondyli; given the original taxon sample, the LH is 12 steps shorter than the “temnospondyl hypothesis” and 17 steps shorter than the PH, while the expanded taxon sample makes the LH 10 steps shorter than the TH and only 12 steps shorter than the PH. More robust results could likely be obtained by adding the many characters used in other analyses or discussed in the literature. We discuss phylogeny, approaches to coding, and certain character complexes, in particular the supposed middle ear of temnospondyls.
Author Comment
This is a manuscript that will be submitted to PeerJ for peer review within the next few days. We nevertheless encourage comments; the more people scrutinize this long manuscript and large dataset, the better.We apologize for the compressed abstract (the web form has a limit of 3000 characters). A long article needs a long abstract; please find the originally intended abstract in the body of the file.
Supplemental Information
NEXUS file (plain text) containing our revised data matrix, one MPT from each of Analyses R1–R6, B1 and B2, an additional MPT from Analysis R4, and the settings used for these 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, B1 and B2, an additional MPT from Analysis R4 (with a sufficiently different topology that several characters optimize differently), 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 Data S1, but with one MPT from each of Analyses R7–R12, B3 and B4, and with the settings for these analyses
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 presumably original data matrix of RC07 (see text for discussion), 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 (averaged if necessary) and the caudal end of the skull table in the midline. In salientians, the caudal margin of the orbit (or 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.
