Extended Lissamphibia: A tale of character non-independence, analytical parameters, and islands of trees
Data files
Mar 05, 2024 version files 301.81 MB
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instabilityTests.zip
117.57 KB
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phylogeneticNetworks.zip
3.63 MB
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phylogeneticReanalyses.zip
298.05 MB
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README.md
4.22 KB
Mar 05, 2024 version files 301.81 MB
-
instabilityTests.zip
117.57 KB
-
phylogeneticNetworks.zip
3.63 MB
-
phylogeneticReanalyses.zip
298.05 MB
-
README.md
4.35 KB
Abstract
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.
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.
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
- all subfolders have the following organisation
- bayesianTrees folder
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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
- phylogeneticReanylises.zip/Pardo folder
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.