A new Lower Permian ray-finned fish (Actinopterygii) from South Dakota and the use of tree space to find rogue taxa in phylogenetic analysis of morphological data

The divergence of extant lineages from the “palaeoniscoids”, a grade of Paleozoic and early Mesozoic Era species, remains unresolved in analyses of morphological data despite more than four decades of phylogenetic research. We describe a new ray-finned fish, Tenupiscis dakotaensis gen et. sp. nov., from the Lower Permian (Kungurian) of South Dakota to strengthen the phylogenetic framework of Mississippian–Triassic actinopterygians. Our initial parsimony and Bayesian phylogenetic analyses were unable to resolve the relationships of Mississippian–Triassic “palaeoniscoids”. We analyzed the topological variation among the trees sampled in each phylogenetic search (tree space) to determine if uncertainty was concentrated in a small subset of species with highly uncertain phylogenetic relationships relative to other terminal taxa (rogue taxa) or distributed evenly amongst early actinopterygians. The relationships of fourteen species were unresolved in the parsimony strict consensus due to a s..., The input data in the form of phylogenetic trees were generated in a series of analyses (see \"Parsimony analyses\" and \"Bayesian analyses\" below). The matrices that we ran in the phylogenetics programs to make the trees are also provided (see \"matrix construction\" below). We used R to summarize the results of the Bayesian searches as majority rules consensus trees, visualized the variation in the samples of phylogenetic trees (\"Tree space visualization), and determined if any rogue taxa were present in our dataset (\"Rogue taxon search\").
Summary of experimental efforts underlying this dataset:
This document describes a series of phylogenetic analyses of ray-finned fishes (actinopterygians) on the basis of a dataset of morphological data derived from Stack and Gottfried (2022). A full description of the methods is provided in the draft manuscript and supplementary information documents, but we will provide a summary of relevant information for how the data were generated and all informati..., , # A new Lower Permian ray-finned fish (Actinopterygii) from South Dakota and the use of tree space to find rogue taxa in phylogenetic analysis of morphological data

## GENERAL INFORMATION

Principal Investigator: Jack Stack (Virginia Tech, Blacksburg, VA, USA). Email: [[e-mail]](mailto:[e-mail]) Co-authors: Michael D. Gottfried (Michigan State, East Lansing, MI, USA); Michelle R. Stocker (Virginia Tech, Blacksburg, VA, USA).

Date of project: 2021-2023.

## DATA & FILE OVERVIEW

* StacketalSupplementData.zip

1\. File List:

### File Name: Stacketal_SupplementCode.r

File Description: R script file that provides the full code needed to run the tree space visualizations, rogue taxon search, and annotation of the Bayesian consensus tree in R (R Core Team 2021). These are each of the command line instructions we used, and an explanation of what the instruction is for. We attempt to make every step in our search for rogue taxa clear and repeatable, so Stacketal_SupplementCode.r c...,