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Table of contents and other important additions

PeerJ has a lot of secret house style that is neither negotiable nor mentioned anywhere in the author guidelines. This fact requires a number of comments.

First of all, our ORCIDs are:

D. M.: 0000-0001-9720-7726

M. L.: 0000-0003-2974-9835

PeerJ does not publish ORCIDs anywhere. I have no clue why. Repeated pleas to let us publish with our scientist numbers have only generated restatements of the fact that the policy exists; it has not occurred to anybody to explain why it was at some point decided upon.

We had to remove the table of contents despite the size of this paper. Here it is. The page numbers refer to the PDF.

Introduction 2

......Aims 4

............Accuracy of analysis procedure 4

............Accuracy of the matrix of RC07 5

............Phylogeny of early limbed vertebrates 8

............The effects of different methods of analysis 9

......Phylogenetic background 10

Nomenclature 13

......Taxonomic nomenclature 13

......Formal and informal phylogenetic nomenclature 14

......Anatomical nomenclature 14

Materials and methods 15

......Treatment of characters 15

............Character interdependence; redundant characters 15

............Ordering of multistate characters 16

............Continuous characters 17

............Inapplicable characters and mergers 17

............“Ontogeny discombobulates phylogeny” (Wiens, Bonett & Chippindale, 2005) 21

............Deleted, recoded and split characters 22

............Blockwise scoring of taxa 23

......Modifications to individual cells 23

............Literature 25

............Specimens 29

............The albanerpetid neck 30

............The skull roof of Brachydectes 32

......Treatment of OTUs 33

............Paleothyris/Protorothyris 33

............Dendrerpetidae 33

............Rhynchonkos 34

............Taxa added as parts of existing OTUs 35

......OTUs added for a separate set of analyses 36

............Further temnospondyls other than stereospondylomorphs 37

............Stereospondylomorphs 39

............Chroniosuchians 41

............“Microsaurs” 42

............Synapsids 46

............Lissamphibians 46

............Seymouriamorph 48

............Undoubted colosteids 48

............Anthracosaurs 49

............Aïstopods 49

............Devonian enigmas 49

............Mississippian enigmas 50

............Pennsylvanian enigma 51

............Taxa that were not added 54

......Phylogenetic analyses 56

............Maximum-parsimony analyses 56

............Robustness analyses 57

............Measure of similarity 58

............Exploratory Bayesian analysis 59

Results 60

......Reanalyses of the matrix of Ruta & Coates (2007) 60

......Amount, distribution and impact of revised scores 64

......Analyses of our revised matrix 67

............Analysis R1 68

............Analysis R2 74

............Analysis R3 77

............Analysis R4 78

............Analysis R5 81

............Analysis R6 83

............Bootstrap analyses B1 and B2 84

............Analysis EB 88

Discussion 91

......Bias in the matrices? 92

............Bias in the scores? 93

............Bias in character selection? 96

......Methods of phylogenetic analysis 96

............Bayesian inference and parsimony in comparison

............Reweighting and equal weighting in comparison

......Phylogenetic relationships 101

............Devonian taxa, Whatcheeriidae and Perittodus 101

............More Mississippian mysteries 103

............Colosteidae 106

............The interrelationships of Anthracosauria, Silvanerpeton, Caerorhachis, Gephyrostegidae, Casineria and Temnospondyli 108

............The “Parrsboro jaw” 112

............Anthracosaurian phylogeny 113

............Temnospondyl large-scale phylogeny 113

............Stereospondylomorpha 120

............Dissorophoidea 121

............Other added temnospondyls 123

............Chroniosuchia 125

............Seymouriamorpha 126

............Amniota and Diadectomorpha 129

............Westlothiana 130

............The lepospondyl problem 130

............The interrelationships of the “microsaurs” 138

............Added “microsaurs” 140

............Lissamphibian origins 141

............Lissamphibian phylogeny 145

......Characters 147

............Continued problems with the character sample 147

............Surprising reversals 148

............Other recently discussed characters that are included in this matrix 153

............Preaxial polarity in limb development

............Other characters that are potentially important for the origin of lissamphibians but not considered in this matrix 156

Conclusions 158

......Matrix accuracy 158

......Phylogeny 158

......Phylogenetics 160

Abbreviations 161

Acknowledgments 162

Additional information and declarations 164

References 165

In the references list, please note that secret house style orders works with several authors before, not after, single-authored works by the same first author, and that Milner AC is ordered before Milner AR even though their single-authored works are cited just as “Milner (year)” in the text because there is no danger of confusion there.

Secret house style further posits that the “final” version of a paper should be cited whenever possible, and defines “final” as possessing the final volume, issue and page numbers – even if the text and the layout have not changed since online publication of the corrected proofs over a year earlier, and even if the journal in question insists that the corrected proofs are the “Version of Record” and does not even correct typos with nomenclatural significance in them. Thus, the following works are cited misleadingly:

Goloboff, Torres & Arias “2018”: “Version of Record online” 4 June 2017, printed 14 months later in August 2018; the issue was published online on 13 July 2018.

Marjanović & Laurin “2014”: published 4 July 2013, printed in early June 2014.

O’Reilly et al. “2018”: published 31 October 2017, printed January 2018.

Pereira Pacheco et al. “2017”: published 11 April 2016, printed March 2017. Importantly, the new species name Konzhukovia sangabrielensis and the new family name Konzhukoviidae are ICZN-valid from 11 April 2016 because the online "Version of Record" published that day already contained a line showing that it was registered in ZooBank.

Schoch & Witzmann “2011”: published 18 June 2010, issue online 9 June 2011, issue printed July 2011.

Simmons “2012”a: published 3 October 2011, issue online 9 March 2012, issue printed April 2012.

Simmons “2012”b: published 21 October 2011 (after Simmons “2012”a), printed January 2012 (before Simmons “2012”a).

Simões et al. “2017”: published on 24 April 2016 (before Simões et al. 2016[b], which was published, online only, in October 2016); printed April 2017.

Spindler et al. 2016: “available online” 30 December 2015, though that was the accepted manuscript without the final layout. The final version dates from around September 2016.

Watanabe “2016”: published 15 July 2015, printed June 2016.

Witzmann “2011”: published 29 July 2010, issue online 9 June 2011, issue printed July 2011.

Witzmann “2016”: published 25 November 2015, printed October 2016.

Errata

Discussion: Phylogenetic relationships: Solenodonsaurus: This headline should not be in italics in the PDF, because third-level headlines are in italics by default. Surprisingly, the HTML version doesn't seem to support italics in headlines at all.

Additional information and declarations: Data availability (p. 164): In the last sentence, “This” refers to the references list. The sentence was moved there from the beginning of the References section, where secret house style does not allow it to be.

Acknowledgements: This spelling must be secret house style. PeerJ otherwise uses American spelling; therefore, the accepted manuscript said "Acknowledgments"...

References: Polley & Reisz (2011) (p. 184): Polley & Reisz capitalized the Lower Permian correctly, and so did we in the accepted manuscript; we must have overlooked this at the proof stage.

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