Reevaluation of the Largest Published Morphological Data Matrix
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A peer-reviewed version of this preprint was published in PeerJ on 4 January 2019. View the peer-reviewed version (peerj.com/articles/5565), which is the preferred citable publication unless you specifically need to cite this preprint. Marjanović D, Laurin M. 2019. Phylogeny of Paleozoic limbed vertebrates reassessed through revision and expansion of the largest published relevant data matrix. PeerJ 6:e5565 https://doi.org/10.7717/peerj.5565 1 1 Reproducibility in phylogenetics: reevaluation of the 2 largest published morphological data matrix for 3 phylogenetic analysis of Paleozoic limbed vertebrates 4 5 David Marjanović1, Michel Laurin2 6 7 1 Science Programme “Evolution and Geoprocesses”, Museum für Naturkunde (Leibniz 8 Institute for Evolutionary and Biodiversity Research), Berlin, Germany; ORCID: 0000-0001- 9 9720-7726 10 2 Centre de Recherches sur la Paléobiologie et les Paléoenvironnements (CR2P), Centre 11 national de la Recherche scientifique (CNRS)/Muséum national d’Histoire naturelle 12 (MNHN)/Université Pierre et Marie Curie (UPMC; Sorbonne Universités), Paris, France; 13 ORCID: 0000-0003-2974-9835 14 15 Corresponding author: 16 David Marjanović1 17 Museum für Naturkunde, Invalidenstraße 43, D-10115 Berlin, Germany 18 E-mail address: [email protected] 1 PeerJ Preprints | https://doi.org/10.7287/peerj.preprints.1596v3 | CC BY 4.0 Open Access | rec: 15 Jan 2018, publ: 15 Jan 2018 2 19 Abstract 20 21 The largest published phylogenetic analysis of early limbed vertebrates (Ruta M, Coates MI. 22 2007. Journal of Systematic Palaeontology 5:69–122) recovered e.g. Seymouriamorpha, 23 Diadectomorpha and (in some trees) Caudata as paraphyletic and found the “temnospondyl 24 hypothesis” on the origin of Lissamphibia (TH) to be more parsimonious than the 25 “lepospondyl hypothesis” (LH) – though only, as we show, by one step. 26 We report thousands of misscored cells, most of them due to typographic and similar 27 accidental errors. Further, some characters are duplicated; some have only one described 28 state; for some, most taxa were scored after presumed relatives. Even continuous characters 29 were unordered, the effects of ontogeny were not sufficiently taken into account, and data 30 published after 2001 were mostly excluded. 31 After these issues are improved – we document and justify all changes to the matrix –, 32 but no characters are added, we find (Analysis R1) much longer trees with e.g. monophyletic 33 Caudata, Diadectomorpha and (in some trees) Seymouriamorpha; Ichthyostega either 34 crownward or rootward of Acanthostega; Anthracosauria either crownward or rootward of 35 Temnospondyli; the LH is 9 steps shorter than the TH (R2; constrained) and 12 steps shorter 36 the “polyphyly hypothesis” (PH – R3; constrained). Brachydectes (Lysorophia) is not found 37 next to Lissamphibia; instead, the sister-group of Lissamphibia is a large clade that includes 38 adelogyrinids, urocordylid “nectrideans” and aïstopods. 39 Adding 56 OTUs to the original 102 increases the resolution. The added taxa range in 40 completeness from complete articulated skeletons to an incomplete lower jaw. Even though 41 the lissamphibian-like temnospondyls Gerobatrachus, Micropholis and Tungussogyrinus and 42 the extremely peramorphic salamander Chelotriton are added, the difference between LH 43 (R4) and TH (R5) rises to 10 steps, that between LH and PH (R6) to 15; the TH also requires 44 several more regains of lost bones than the LH. 45 Most bootstrap values are low, and plummet when taxa are added. Statistically, the TH 46 (R2, R5) is not distinguishable from the LH or the PH; the LH (R1) and the PH (R3) may be 47 distinguishable from each other under the original taxon sample at p ≥ 0.04. A test for the 48 upper bound of the p value is not available. 49 Bayesian inference (Analysis EB, same settings as R4) mostly agrees with R4. High 50 posterior probabilities are found for Lissamphibia (1.00) and for the LH (0.92); however, 51 many branches remain weakly supported, and most are short, as expected from the small 52 character sample. 53 We discuss phylogeny, approaches to coding, methods of phylogenetics (Bayesian 54 inference vs. equally weighted vs. reweighted parsimony), some character complexes, and 55 prospects for further improvement of this matrix. In its present state, even after our changes, 56 the matrix cannot provide a robust assessment of the phylogeny of early limbed vertebrates; 57 sufficient improvement, however, will be laborious but not difficult. 58 2 3 59 Table of contents 60 61 Introduction 5 62 Aims 6 63 Accuracy of analysis procedure 6 64 Accuracy of the matrix of RC07 8 65 The effects of different methods of analysis 10 66 Phylogeny of early limbed vertebrates 11 67 Phylogenetic background 12 68 Abbreviations 15 69 Nomenclature 16 70 Taxonomic nomenclature 16 71 Phylogenetic nomenclature 17 72 Anatomical nomenclature 18 73 Material and methods 18 74 Treatment of characters 18 75 Character interdependence; redundant characters 18 76 Ordering of multistate characters 19 77 Continuous characters 19 78 Inapplicable characters and mergers 20 79 “Ontogeny discombobulates phylogeny” (Wiens, Bonett & 80 Chippindale, 2005) 22 81 Deleted, recoded and split characters 23 82 Modifications to individual cells 25 83 The albanerpetid neck 29 84 Treatment of OTUs 30 85 Paleothyris/Protorothyris 30 86 Dendrerpetidae 30 87 Rhynchonkos 31 88 The skull roof of Brachydectes 32 89 Taxa added as parts of existing OTUs 32 90 Taxa added as new OTUs for a separate set of analyses 33 91 Taxa that were not added 49 92 Phylogenetic analyses 51 93 Maximum-parsimony analyses 51 94 Robustness analyses 52 95 Exploratory Bayesian analysis 53 96 Results 54 97 Reanalysis of the matrix of Maddin, Jenkins & Anderson (2012) 54 98 Reanalysis of the matrix of Pardo, Small & Huttenlocker (2017) 57 99 Reanalyses of the matrix of Ruta & Coates (2007) 58 100 Analyses of our revised matrix 63 101 Analysis R1 63 102 Analysis R2 65 103 Analysis R3 67 104 Analysis R4 69 105 Analysis R5 72 106 Analysis R6 72 107 Bootstrap analyses B1 and B2 75 108 Analysis EB 79 3 4 109 Discussion 81 110 Bayesian inference and parsimony in comparison 82 111 Reweighting and equal weighting in comparison 84 112 Persisting problems with the character sample 85 113 Phylogenetic relationships 87 114 Devonian taxa and Whatcheeriidae 88 115 More Mississippian mysteries 89 116 Colosteidae 92 117 The interrelationships of Anthracosauria, Silvanerpeton, 118 Caerorhachis, Gephyrostegidae, Casineria and 119 Temnospondyli 93 120 The “Parrsboro jaw” 97 121 Anthracosaurian phylogeny 98 122 Temnospondyl large-scale phylogeny 98 123 Stereospondylomorpha 105 124 Dissorophoidea 105 125 Other added temnospondyls 107 126 Chroniosuchia 109 127 Solenodonsaurus 111 128 Seymouriamorpha 111 129 Amniota and Diadectomorpha 112 130 Westlothiana 113 131 The lepospondyl problem 113 132 The interrelationships of the “microsaurs” 120 133 Added “microsaurs” 122 134 Lissamphibian origins 123 135 Lissamphibian phylogeny 127 136 Characters 128 137 Surprising reversals 128 138 Other recently discussed characters that are included in this 139 matrix 132 140 Preaxial polarity in limb development 133 141 Other characters that are potentially important for the origin of 142 lissamphibians but not considered in this matrix 135 143 Conclusions 138 144 Phylogeny 136 145 Phylogenetics 138 146 Errata in some of our previous publications 139 147 Errata caused by the lack of page proofs at PLOS ONE 140 148 Acknowledgments 140 149 References 142 150 Supplementary Information 173 151 Appendix 1: Changes to the matrix of RC07 175 152 Appendix 2: Revised matrix 336 153 154 4 5 155 Introduction 156 157 This ancient inhabitant of the coal swamps of Nova Scotia, was, in short, as we often find to be 158 the case with the earliest forms of life, the possessor of powers and structures not usually, in the 159 modern world, combined in a single species. It was certainly not a fish, yet its bony scales, and 160 the form of its vertebræ, and of its teeth, might, in the absence of other evidence, cause it to be 161 mistaken for one. We call it a batrachian, yet its dentition, the sculpturing of the bones of its 162 skull, which were certainly no more external plates than the similar bones of a crocodile, its ribs, 163 and the structure of its limbs, remind us of the higher reptiles; and we do not know that it ever 164 possessed gills, or passed through a larval or fish-like condition. Still, in a great many important 165 characters, its structures are undoubtedly batrachian. It stands, in short, in the same position with 166 the Lepidodendra and Sigillariæ under whose shade it crept, which though placed by palæo- 167 botanists in alliance with certain modern groups of plants, manifestly differed from these in 168 many of their characters, and occupied a different position in nature. In the coal period, the 169 distinctions of physical and vital conditions were not well defined—dry land and water, 170 terrestrial and aquatic plants and animals, and lower and higher forms of animal and vegetable 171 life, are consequently not easily separated from each other. 172 – Dawson (1863: 23–24) about Dendrerpeton acadianum 173 174 Homoplasy Is even More Common than I, or perhaps Anyone, Has ever Imagined 175 – section headline in Wake (2009: 343) 176 177 What is required is a more complete discussion of the character coding of previous data matrices, 178 and a thorough reanalysis based on those matrices. This would enable a well-founded discussion 179 of lissamphibian origins in light of a supermatrix based on all the current and pertinent data. 180 – Sigurdsen & Green (2011: 459) 181 182 Giant morphological data matrices are increasingly common in cladistic analyses of vertebrate 183 phylogeny, reporting numbers of characters never seen or expected before. However, the concern 184 for size is usually not followed by an equivalent, if any, concern for character 185 construction/selection criteria.