Concatenation fails to describe the anomalous radiation of giant cockroaches (Blattodea: Blaberidae) despite moderate to low discordance

Patterns of discordance between gene trees and the species trees they reside in are crucial to the coalescent vs. concatenation debate and may be key to resolving rapid radiations. However, errors in estimating gene tree topologies complicate the issue. Gene trees may appear erroneously discordant with the species tree when they have errors. In this study, we evaluate the prevalence of discordance between gene trees and their species tree using an empirical dataset for a clade with a rapid radiation (Blaberidae). One key advance of our study is the use of complex, computationally intensive, selection-based codon models (FMutSel0 and SelAC) to identify the maximum likelihood gene tree. Our main hypothesis predicted that, if there are two competing topologies for a particular gene tree, the one that is less discordant with the species tree will have less error. Our experimental framework failed to show evidence for this, but only when discordance was measured in reference to a concatenati..., , , # Concatenation fails to effectively describe the anomalous giant cockroach (Blattodea: Blaberidae) radiation

[https://doi.org/10.5061/dryad.0cfxpnw8n](https://doi.org/10.5061/dryad.0cfxpnw8n)

## Description of the data and file structure

Supplement - BlaberidaeSelac.vFeb22.2024 #Supplementary material (methods, results, and discussion)

`allLnlsCombined.11222023.csv` #lnL and run information for each individual gene tree optimization in SelAC R package
`bestLNLresults.asof_11202023.csv` #best lnL information for each locus optimized in the SelAC R package
`codonModels.csv` #list of model combinations chosen by IQTREE's partitionfinder when specifying ECMS05
`locusInformation.xlsx` #biological information for all genomic loci in our analysis; Column labelled \"Genome?\" notes if a locus is part of the nuclear (NU) or mitochondrial (MT) genome. \"+\" indicates which loci are confirmed to be protein coding. Remaining information are UniProt protein information for each locus, including th...,