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

Evangelista, Dominic1; Gilchrist, Michael2; Legendre, Frédéric3; O'Meara, Brian2

Published Jul 25, 2025 on Dryad. https://doi.org/10.5061/dryad.0cfxpnw8n

Data files

Jul 25, 2025 version files 1.94 MB

Abstract

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.