DOI: 10.5061/dryad.0cfxpnw8n
title: Data from: Concatenation fails to describe the anomalous radiation of giant cockroaches (Blattodea: Blaberidae) despite moderate to low discordance

description: 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 concatenation
 topology. In follow-up tests we see that the best candidate gene set
 yielded a coalescent species tree that was less discordant with gene
 trees. We conclude from these tests that, although discordance is
 generally rare, it still must be accounted for in order to achieve a
 biologically realistic outcome. The results suggest a few key improvements
 to the Blaberidae phylogeny, including identification of an anomaly zone
 that potentially spans eight or more backbone nodes. These results allow
 us to support other relationships among blaberid cockroaches that were
 previously in flux as they now demonstrate molecular and morphological
 congruence.
description: # 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 the likely name of the protein and gene, and the hypothesized molecular functions. `GTDiscordances.xlsx` #Discordances between estimated gene trees and the concatenation topology. Pairwise distances between the trees (e.g., concat-GTR, concat-codon) are given, Robinson-Foulds (RF) and Path distances are the basis for the comparisons. `Alignments.zip/` \|- Alignments/ \| |- 40AlignmentSet/ #fasta fomatted individual gene alignments for the 40 loci used in the main experiment \| |- AllAlignments/ #fasta fomatted individual gene alignments for the all loci used in tests `GeneTrees.zip/` \|- GeneTrees/ \| |- 40GeneTreeSet/ #multi-tree files for Est.GT.1 topologies and Est.GT.2 topologies \| |- AllGeneTrees/ #individual gene tree hypotheses for all 100 genes across 4 methods ( concatenation, GTRG model estimated, GTRG median model estimated, ECM optimized model estimated ) \| |- 26untestedFMUTSELGeneTrees.tre #gene trees for 26 loci chosen by FMutSel0, but not used in the main experiment \| |- 27untestedSELACGeneTrees.tre #gene trees for 27 loci chosen by SelAC, but not used in the main experiment \| |- 40FMutSel0_trees.trees #gene trees chosen by FMutSel0 from main experiment \| |- 40SelacGTS.trees #gene trees chosen by SelAC from main experiment \| |- 60untestedCODONGeneTrees.tre #gene trees estimated from the optimized empirical codon model, but not used in the main experiment \| |- 60untestedGTRGeneTrees.tre #gene trees estimated from GTRG, but not used in the main experiment \| |- congruenceTree_trees.trees #40 gene tree from the main experiment that exhibited the least discordance with the concatenation topology \| |- IncongruenceTree_trees.trees #40 gene tree from the main experiment that exhibited the most discordance with the concatenation topology `SelACSoftwareInput.zip/` \|- SelACSoftwareInput #Example R scripts to initiate choice of gene trees in the SelAC software package. One example is given for each locus in the main experiment. SpeciesTrees.zip/ `Species trees/` \| |- raw #7 species trees used in the final suite of tests. Each one has tip names matching the organism, not the original sample names. Tree 1 is the concatenation topology with UF bootstrap values, Trees 2-5 were estimated species trees using topologies chosen by different models, Tree 6 and 7 are control trees. Trees 2-7 were inferred using ASTRAL-III and have local posterior probabilities. \| |- treesWithModifiedSupportValues #species tree topologies from "raw" folder with node support values added. All "NullValidation" files are species tree topologies with node support values representing the frequency of splits occuring in 120 gene trees. The "concord.gcf" file is the SelAC species tree with gene concordance factors from 40 gene trees. "AnomalyFinder" files are species tree topologies with node annotations from AnomalyFinder. ## Sharing/Access information Data was derived from the following sources: * [https://www.ncbi.nlm.nih.gov/bioproject/PRJNA482916](https://www.ncbi.nlm.nih.gov/bioproject/PRJNA482916) * [https://resjournals.onlinelibrary.wiley.com/doi/10.1111/syen.12454](https://resjournals.onlinelibrary.wiley.com/doi/10.1111/syen.12454)