Extended Lissamphibia: A tale of character non-independence, analytical parameters, and islands of trees

The age, content, and interorder relationships of crown Lissamphibia remain a debated topic in vertebrate systematics. Recent phylogenetic analyses of fossil amphibians were used to propose an extended Lissamphibia, with Anura and Caudata nested in Dissorophoidea and with Gymnophiona nested in Stereospondyli, but this hypothesis was not supported by subsequent studies on updated matrices. In the parsimony context, the extended Lissamphibia hypothesis was shown to result from the effects of large island bias on the majority-rule consensus, which masked the presence of topologies supporting the restricted Lissamphibia hypothesis, with all extant orders nested in Dissorophoidea or Stereospondyli. Re-analysing this dataset taking into account the presence of inapplicable and polymorphic character states, and revising the scores for logically non-independent characters, shows that the phylogenies inferred from the morphological data matrix used to propose the extended Lissamphibia hypothesis..., , , # Extended Lissamphibia: A tale of character non-independence, analytical parameters, and islands of trees

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Supplementary data for:

Serra Silva, A. (2024). Extended Lissamphibia: A tale of character non-independence, analytical parameters, and islands of trees. *Journal of Systematic Palaeontology*, *22*(1). [https://doi.org/10.1080/14772019.2024.2321620](https://doi.org/10.1080/14772019.2024.2321620).

## Contents of each folder

* instabilityTests.zip: contains tree files used for the leaf stability and RBIC analyses and their output
* bayesianTrees folder
* PardoCharacters.nex.trprobs is the Bayesian tree distribution from an analysis of Pardo et al.'s (2017) data matrix and was re-used from Serra Silva and Wilkinson (2021)
* RnR-lsi_leafStabilityIndices_allTrees.txt is the output of the leaf stability analyses run in RogueNaRok
* RogueNaRok_droppedRogues_*_allTrees.txt is the output of the RBIC analyses run in RogueNaRok
* parsimonyT...