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, phylogeny
- Copyright
- © 2016 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
- 2016. Reevaluation of the largest published morphological data matrix for phylogenetic analysis of Paleozoic limbed vertebrates. PeerJ Preprints 4:e1596v2 https://doi.org/10.7287/peerj.preprints.1596v2
Abstract
The largest published data matrix for phylogenetic analysis of Paleozoic limbed vertebrates (Ruta M, Coates MI. 2007. Journal of Systematic Palaeontology 5:69–122) supported variously controversial hypotheses; e.g., it recovered Seymouriamorpha, Diadectomorpha and (in some trees) Caudata as paraphyletic and found the “temnospondyl hypothesis” on the origin of Lissamphibia (TH) to be more parsimonious than the “lepospondyl hypothesis” (LH) – though only, as we show, by one step.
We report thousands of suboptimal scores due to typographic and similar errors and to questionable coding decisions: logically linked (redundant) characters, others with only one described state, even characters for which most taxa were scored after presumed relatives. Even continuous characters were unordered, the effects of ontogeny were not sufficiently taken into account, and data published after 2001 were mostly excluded.
After these issues are improved – we document and justify all changes to the matrix –, but no characters are removed or added, we find (Analysis R1) much longer trees with e.g. monophyletic Caudata, Diadectomorpha and (in some trees) Seymouriamorpha; Ichthyostega rootward of Acanthostega; Anthracosauria rootward of Temnospondyli which includes Caerorhachis; the LH is 9 steps shorter than the TH (R2; constrained) and 12 steps shorter the “polyphyly hypothesis” (PH – R3; constrained).
We then added 48 OTUs to the original 102. This destabilizes some parts of the tree, e.g. the positions of Anthracosauria, Temnospondyli and Caerorhachis. Yet, many added taxa have well-resolved positions, ranging from the well known Chroniosaurus (Chroniosuchia), which lies just crownward of Temnospondyli and Gephyrostegidae, to isolated lower jaws. Even though Gerobatrachus, Micropholis and Tungussogyrinus and the extremely peramorphic salamander Chelotriton are added, the difference between LH (R4) and TH (R5) rises to 12 steps, that between LH and PH (R6) to 17 steps; the TH also requires several more regains of lost bones than the LH. Brachydectes (Lysorophia) is not found next to Lissamphibia.
We duplicated all analyses after coding losses of bones as irreversible. The impact on the results is modest. Anthracosauria is always rootward of Temnospondyli. With 102 OTUs, the LH (R7) is 10 steps shorter than the TH (R8) and 11 steps shorter than the PH (R9); with 150, the LH (R10) is 14 steps shorter than the TH (R12) – and 13 steps shorter than the PH (R11).
Bootstrap values are mostly low, and plummet when taxa are added. Statistically, the TH (R2, R5, R8, R12) is not distinguishable from the LH or the PH, but the LH (R1, R4, R7, 53 R10) and the PH (R3, R6, R9, R11) may be distinguishable from each other under both taxon samples and both reversibility settings. A reliable test is not available.
We discuss the relationships of certain taxa, approaches to coding, some character complexes, and prospects for further improvement of this matrix.
Author Comment
This is the first revision and has been submitted to PeerJ for a second round of review.
New features:
– Color-coded changes in Appendix 2, as recommended by a reviewer.
– We found a bunch of discrepancies between Appendix 1 and the matrix (Data S1, S2). These have been corrected and all analyses repeated (pure calculation time: two months). At this opportunity we updated the scores of several taxa, including but not limited to Triadobatrachus and Brachydectes. Several changes to the trees have resulted, mostly greater resolution and somewhat different topologies, concerning in particular colosteids, dvinosaurs, adelospondyls and diadectomorphs.
– Many new explanatory tree figures, as recommended by a reviewer, to illustrate the current state of various questions.
– New sections on continuous characters and on the reasons for why we haven't used maximum likelihood or Bayesian inference, in reaction to comments from two reviewers.
– The chapter on the middle ear has been taken out for separate publication.
– Scale bars on the photos; better photos of Sauropleura; more visible labels on the photos.
– The statistical tests were inappropriate, as noted by a reviewer and a commenter. Appropriate tests are not available for practical purposes, so we now interpret the results more cautiously.
– The confusion about different versions of the matrix of Ruta & Coates (2007) has evaporated: there is only one version. In one of the files we have of the matrix, some characters are mislabeled, that's all. We have consequently eliminated two chapters.
– Two references were missing from the list; we have filled them in, thanks to a reviewer and a commenter.
Supplemental Information
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.
