Reproducibility in phylogenetics: reevaluation of the largest published morphological data matrix for phylogenetic analysis of Paleozoic limbed vertebrates
Authors: Marjanović David , Laurin Michel 
Published: January 2018

The largest published phylogenetic analysis of early limbed vertebrates (Ruta M, Coates MI. 2007. Journal of Systematic Palaeontology 5:69–122) recovered e.g. 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 misscored cells, most of them due to typographic and similar accidental errors. Further, some characters are duplicated; some have only one described state; for some, 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 added, we find (Analysis R1) much longer trees with e.g. monophyletic Caudata, Diadectomorpha and (in some trees) Seymouriamorpha; Ichthyostega either crownward or rootward of Acanthostega; Anthracosauria either crownward or rootward of Temnospondyli; the LH is 9 steps shorter than the TH (R2; constrained) and 12 steps shorter the “polyphyly hypothesis” (PH – R3; constrained). Brachydectes (Lysorophia) is not found next to Lissamphibia; instead, the sister-group of Lissamphibia is a large clade that includes adelogyrinids, urocordylid “nectrideans” and aïstopods.
Adding 56 OTUs to the original 102 increases the resolution. The added taxa range in completeness from complete articulated skeletons to an incomplete lower jaw. Even though the lissamphibian-like temnospondyls Gerobatrachus, Micropholis and Tungussogyrinus and the extremely peramorphic salamander Chelotriton are added, the difference between LH (R4) and TH (R5) rises to 10 steps, that between LH and PH (R6) to 15; the TH also requires several more regains of lost bones than the LH.
Most bootstrap values are low, and plummet when taxa are added. Statistically, the TH (R2, R5) is not distinguishable from the LH or the PH; the LH (R1) and the PH (R3) may be distinguishable from each other under the original taxon sample at p ≥ 0.04. A test for the upper bound of the p value is not available.
Bayesian inference (Analysis EB, same settings as R4) mostly agrees with R4. High posterior probabilities are found for Lissamphibia (1.00) and for the LH (0.92); however, many branches remain weakly supported, and most are short, as expected from the small character sample.
We discuss phylogeny, approaches to coding, methods of phylogenetics (Bayesian inference vs. equally weighted vs. reweighted parsimony), some character complexes, and prospects for further improvement of this matrix. In its present state, even after our changes, the matrix cannot provide a robust assessment of the phylogeny of early limbed vertebrates; sufficient improvement, however, will be laborious but not difficult.