DOI: 10.5061/dryad.w0vt4b93r
title: Incorporating continuous characters in joint estimation of dicynodont phylogeny

description: Continuous characters have received comparatively little attention in
 Bayesian phylogenetic estimation. This is predominantly because they
 cannot be modeled by a standard phylogenetic Q-matrix approach due to
 their non-discrete nature. In this manuscript, we explore the use of
 continuous traits under two Brownian Motion models to estimate a
 phylogenetic tree for Dicynodontia, a well-studied group of early
 synapsids (stem mammals) in which continuous characters have been
 extensively used in parsimony-based tree reconstruction. We examine the
 differences in phylogenetic signal between a continuous trait partition, a
 discrete trait partition, and a joint analysis with both types of
 characters. We find that continuous and discrete traits contribute
 substantially different signals to the analysis, even when other parts of
 the model (clock and tree) are held constant. Tree topologies
 resulting from the new analyses differ strongly from the established
 phylogeny for dicynodonts, highlighting continued difficulty in
 incorporating truly continuous data in a Bayesian phylogenetic framework.
description: # Incorporating continuous characters in joint estimation of dicynodont
 phylogeny
 [https://doi.org/10.5061/dryad.w0vt4b93r](https://doi.org/10.5061/dryad.w0vt4b93r) ## Description of the data and file structure This project reuses data from Kammerer et al 2019. New data was not generated. The dataset contains discrete and continuous morphological characters, as well as fossil ages. The character data is stored in Nexus (flat file) format. It can be viewed in a text editor and is meant to be used with phylogenetic software, such as RevBayes (as we did in this manuscript). The fossil ages are a tab-separated file and can be read by a text editor, spreadsheet viewer, or phylogenetic software. Kammerer, C. F., P. A. Viglietti, P. J. Hancox, R. J. Butler, and J. N. Choiniere. 2019. A new Kannemeyeriiform dicynodont (*Ufudocyclops mukanelai*, gen. et sp. nov.) from subzone C of the cynognathus assemblage zone, Triassic of South Africa, with implications for biostratigraphic correlation with other African Triassic faunas. Journal of Vertebrate Paleontology 39:e1596921. ### Files and variables #### File: Continuous.nex **Description:** A nexus file intended to be read with a text editor or phylogenetic software. This file contains the continuous traits used for phylogenetic estimation in this study. #### File: Kammerer2019.nex **Description:** A nexus file intended to be read with a text editor or phylogenetic software. This file contains the discrete traits used for phylogenetic estimation in this study. #### File: Therapsid_Ages_CFK_2023.tsv **Description:** A tab-separated value file containing fossil ages. Can be viewed in a text editor, spreadsheet viewer, or phylogenetic software. ##### Variables * taxon: The species to which the age corresponds * max_age: The oldest the taxon could be. In millions of years. * min_age: The youngest the taxon could be. In millions of years. **Zipped Files:** | Name | Contents | File Type | Used For | Other Accessory Files Needed | 
 
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 :-------------------------- | :------------------------------------ |
 :--------------------------------- | ------ | | treespace.zip | Opens to
 several log files | Tab-separated Files | Used to generate treespace
 figure | Code contained in FiguresUpdated.R | None | | 
 
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 | | TreeLengthsSampledAncestors.zip | Opens to tree length files for
 analyses with sampled ancestors | Comma-separated Value files | Used to
 Generate branch length figure | Code contained in FiguresUpdated.R | 
 
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 | | tree\_lengths.zip | Opens to tree length files for analyses with no
 sampled ancestors | Comma-separated Value files | Used to generate branch
 length figure | Code contained in FiguresUpdated.R | 
 
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 | | **log\_posterior, tree posterior** | Log files generated from
 RevBayes | Tab-separated values | Processed to produce Fig. 2 and 3 | Code
 contained in FiguresUpdated.R | 
 
 | ## Code/software | FBD\_BM\_strict.zip | Code for the strict Brownian
 Motion Analysis with continuous characters |
 [https://github.com/revbayes/revbayes/releases/tag/v1.2.5-beta1](https://github.com/revbayes/revbayes/releases/tag/v1.2.5-beta1) | .Rev Files meant for use with RevBayes | Plain Text | | -------------------------- | ------------------------------------------------------------------------------------------ | -------------------------------------------------------------------------------------------------------------------------------- | -------------------------------------- | ---------- | | FBD\_BM\_relaxed.zip | Code for the Relaxed Brownian Motion Analysis with continuous characters | [https://github.com/revbayes/revbayes/releases/tag/v1.2.5-beta1](https://github.com/revbayes/revbayes/releases/tag/v1.2.5-beta1) | .Rev Files meant for use with RevBayes | Plain Text | | FBD\_Combined\_strict.zip | Code for the strict Brownian Motion Analysis with both continuous and discrete characters | [https://github.com/revbayes/revbayes/releases/tag/v1.2.5-beta1](https://github.com/revbayes/revbayes/releases/tag/v1.2.5-beta1) | .Rev Files meant for use with RevBayes | Plain Text | | FBD\_Combined\_relaxed.zip | Code for the Relaxed Brownian Motion Analysis with both continuous and discrete characters | [https://github.com/revbayes/revbayes/releases/tag/v1.2.5-beta1](https://github.com/revbayes/revbayes/releases/tag/v1.2.5-beta1) | .Rev Files meant for use with RevBayes | Plain Text | | FBD\_Discrete.zip | Code for the FBD Mk analysis with discrete characters | [https://github.com/revbayes/revbayes/releases/tag/v1.2.5-beta1](https://github.com/revbayes/revbayes/releases/tag/v1.2.5-beta1) | .Rev Files meant for use with RevBayes | Plain Text | | Figures\_Updated.R | R Code for figures | [https://cran.r-project.org/bin/windows/base/old/4.4.2](https://cran.r-project.org/bin/windows/base/old/4.4.2) | .R Files meant for use with R/RStudio | Plain Text | ## Access information Data was derived from the following sources: * Kammerer, C. F., P. A. Viglietti, P. J. Hancox, R. J. Butler, and J. N. Choiniere. 2019. A new Kannemeyeriiform dicynodont (*Ufudocyclops mukanelai*, gen. et sp. nov.) from subzone C of the Cynognathus Assemblage Zone, Triassic of South Africa, with implications for biostratigraphic correlation with other African Triassic faunas. Journal of Vertebrate Paleontology 39:e1596921