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

Abstract

The age, content and inter-order 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 a 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 in 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 are not robust to changes in analytical parameters and that great care should be taken when analysing fossil amphibian datasets. With the set of most parsimonious trees inferred from the unrevised matrix used to propose the extended Lissamphibia hypothesis, I also demonstrate that the phenomenon of large island bias extends to phylogenetic networks, but not to topology-based tests of taxonomic instability that do not rely on split-frequencies.

Keywords:

• Lissamphibia
• taxonomic instability
• large island bias
• phylogenetic networks
• character non-independence
• inapplicable data

Acknowledgements

I would like to thank Mark Wilkinson, Mike Benton and Davide Pisani for their supervision, and, alongside Marc Jones, for their critical commentary of earlier versions of this work. I would further like to thank Mark Wilkinson for enlightening conversations on the large island bias phenomenon, and, along with Marc Jones, for fruitful discussions on amphibian taxonomy and character coding. I would like to thank the Associate Editor, an anonymous reviewer and Bryan Gee for constructive and detailed criticism of the submitted manuscript. This work was supported by the Natural Environment Research Council [NE/L002434/1].

Disclosure statement

No potential conflict of interest was reported by the author(s).

Supplemental material

Supplemental material for this article can be accessed here: https://doi.org/10.1080/14772019.2024.2321620. Data is also available from the Dryad Digital Repository: https://doi.org/10.5068/D1RT1J.

Associate Editor: Jennifer Olori

Additional information

Funding

I would like to thank Mark Wilkinson, Mike Benton and Davide Pisani for their supervision, and, alongside Marc Jones, for their critical commentary of earlier versions of this work. I would further like to thank Mark Wilkinson for enlightening conversations on the large island bias phenomenon, and, along with Marc Jones, for fruitful discussions on amphibian taxonomy and character coding. I would like to thank the Associate Editor, an anonymous reviewer and Bryan Gee for constructive and detailed criticism of the submitted manuscript. This work was supported by the Natural Environment Research Council [NE/L002434/1].