Phylogenomic analyses of Blattodea combining traditional methods, incremental tree-building, and quality-aware support

Despite the many advances of the genomic era, there is a persistent problem in assessing the uncertainty of phylogenomic hypotheses. We see this in the recent history of phylogenetics for cockroaches and termites (Blattodea), where huge advances have been made, but there are still major inconsistencies between studies. To address this, we present a phylogenetic analysis of Blattodea that emphasizes identification and quantification of uncertainty. We analyze 1183 gene domains using three methods (multi-species coalescent inference, concatenation, and a supermatrix-supertree hybrid approach) and assess support for controversial relationships while considering data quality. The hybrid approach—here dubbed “tiered phylogenetic inference”—incorporates information about data quality into an incremental tree building framework. Leveraging this method, we are able to identify cases of low or misleading support that would not be possible otherwise, and explore them more thoroughly with follow-u..., , , # Phylogenomic analyses of Blattodea combining traditional methods, incremental tree-building, and quality-aware support

###### Dominic A. Evangelista, Dvorah Nelson, Zuzana Kotyková Varadínová, Michael Kotyk, Nicolas Rousseaux, Tristan Shanahan, Phillippe Grandcolas, Frédéric Legendre

##### For questions regarding the nature of our data please contact Dominic Evangelista ([[e-mail]](mailto:[e-mail]))

### Supplementary files and descriptions provided via the Digital Repository Dryad

## Worksheets

#### Worksheet1.TaxonList.xlsx

List of all specimens included, with accession numbers of newly sequenced taxa.

#### Worksheet2.AllAUTestResults.xlsx

Results of Approximately Unbiased topological tests.

#### Worksheet3.AllFCLMResults.xlsx

Four-cluster likelihood mapping results. Sheet 1: Results of tests utilizing control (randomized) datasets. Sheet 2: results specifically testing relationships among Ectobiinae and Anaplectoidea. Sheet 3: results specifically tes...,