Is the deuterostome clade an artefact?

There is a long-standing consensus that the animal phyla closest to our own phylum of Chordata are the Echinodermata and Hemichordata. These three phyla constitute the major clade of Deuterostomia. Recent analyses have questioned the support for the monophyly of Deuterostomia, however, showing that the branch leading to deuterostomes is very short and may be influenced by systematic error. Here we use a site-by-site approach to explore possible sources of error. Under conditions that promote long-branch attraction (LBA) – especially branch-length heterogeneity and sites constrained in their amino acid composition – we find that deuterostome monophyly is strongly supported. When we make efforts to mitigate these sources of error, support for Deuterostomia markedly decreases or even disappears. Our results call into question one of the longest established major branches of the animal kingdom. A very short, or non-existent, deuterostome branch has implications for interpretating putative d..., , , # Is the deuterostome clade an artefact?

## Directory list:

`dataProvenance.xlsx`: contains the accession numbers and sources for the proteomic and transcriptomic data used in this study

`rawData.zip`: contains the pre-processed input data

* OrthoFinder_input contains the raw genomes/proteomes/transcriptomes listed in dataProvenance.xlsx
* orthoGroups_raw.zip contains the raw [OrthoFinder output](https://github.com/davidemms/OrthoFinder), excluding the WorkingDirectory and the empty Single_Copy_Orthologue_Sequences
* orthoGroups_paraFilter contains the 183 paralogue filtered orthogroups, see main text for methodology

`scripts.zip`: contains any additional script needed to run/modify analyses or their output that are not already available from GitHub repositories (cited in main text). The scripts are roughly organised by task:

* dataProcessing
* IQTreeOutputProcessing
* IQTreeSearches
* plotting
* renamingScripts
* simulations

From here all subfolders follow these naming conventio...,