DOI: 10.5068/d1rt1j
title: Extended Lissamphibia: A tale of character non-independence, analytical parameters, and islands of trees

description: 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 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.
description: # Extended Lissamphibia: A tale of character non-independence, analytical
 parameters, and islands of trees --- 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 * parsimonyTrees folder contains tree files used for and the output for the leaf stability and RBIC analyses for all most parsimonious trees inferred from the Pardo et al.'s (2017) data matrix and the tree islands identified in Serra Silva and Wilkinson (2021) * all subfolders have the following organisation * *.newick is the input file to RogueNaRok and contains the set of most parsimonious trees to be tested * LeafStabilityIndices_*.txt is the output of the leaf stability analyses run in RogueNaRok * RogueNaRok_droppedRogues_*.txt is the output of the RBIC analyses if the dropset was non-empty * phylogeneticNetworks.zip contains the eps and nex output files from the consensus and reticulation network analyses run in SplitsTree, the input for these analyses was the instabilityTests.zip/parsimonyTrees/AllTrees/mytrees.newick file. For details on the analyses see the main text. * phylogeneticReanylises.zip contains the input matrices, scripts and output for all phylogenetic analyses * phylogeneticReanylises.zip/Pardo folder * Morphy folder contains the input and output of the morphy analyses and the set of x-RF islands identified from the set of inferred trees * MrBayes_Partitioned folder contains the input, settings and output of an explicitlyt partitioned MrBayes analysis, details in the MS * PAUP folder contains a set of subfolders each for a different parsimony analysis, all subfolders contain the input, script (PAUP_morphoblock.nex) and output for each analysis (GapAsFifthState, GapAsFifthState+polymorphism, plolymorphism, bootstrap, postInferenceJackknife, matrix jackknifing (delete-half and Farris), and first-order taxon jackknifing on *Chinlestegophis*, *Eocaecilia* and *Rileymillerus*), details given in the MS and Paup_morphoblock.nex file in each folder * phylogeneticReanylises.zip/Schoch folder * PardoChars folder contains the input, script and output for a reanalysis of Schoch et al.'s 2021 matrix with only the characters shared with Pardo et al. 2019 * Schoch_fullmatrix contains a set of subfolders each for a different parsimony analysis, all subfolders contain input, script and output files * nonIndependentCharRecoding * recoding.r script to inspect and recode the non-independent characters in the Pardo and Schoch matrices * *Characters.nex are the original matrices * *Recoded.nex are the recoded matrices * subfolders contain the input, script and output files for various parsimony analyses ## Sharing/Access information Data also available in a Figshare repository (link in Related Works). If you use the original data matrices or island sets please cite: Pardo, J.D., Small, B.J. and Huttenlocker, A.K., 2017. Stem caecilian from the Triassic of Colorado sheds light on the origins of Lissamphibia. *Proceedings of the National Academy of Sciences*, 114(27), pp.E5389-E5395. Schoch, R.R., Werneburg, R. and Voigt, S., 2020. A Triassic stem-salamander from Kyrgyzstan and the origin of salamanders. *Proceedings of the National Academy of Sciences*, 117(21), pp.11584-11588. Silva, A.S. and Wilkinson, M., 2021. On defining and finding islands of trees and mitigating large island bias. *Systematic Biology*, 70(6), pp.1282-1294.