DOI: 10.5061/dryad.wstqjq2rw
title: Phylogenomic analyses of Blattodea combining traditional methods, incremental tree-building, and quality-aware support

description: 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-up tests. In particular, quality annotations
 pointed towards nodes with high bootstrap support that later turned out to
 have large ambiguities, sometimes resulting from low-quality data. We also
 clarify issues related to some recalcitrant nodes: Anaplectidae’s
 placement lacks unbiased signal, Ectobiidae s.s. and Anaplectoideini need
 greater taxon sampling, the deepest relationships among most Blaberidae
 lack signal. As a result, several previous phylogenetic uncertainties are
 now closer to being resolved (e.g., African and Malagasy “Rhabdoblatta”
 spp. are the sister to all other Blaberidae, and Oxyhaloinae is sister to
 the remaining Blaberidae). Overall, we argue for more approaches to
 quantifying support that take data quality into account to uncover the
 nature of recalcitrant nodes.
description: # 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
 ([dominicev@gmail.com](mailto:dominicev@gmail.com)) ### 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 testing
 relationships among Ectobiinae and Anaplectoidea. ####
 Worksheet4.deltaGLSResults.xlsx Results of delta Gene Likelihood Score
 tests. Sheet 1: Detailed results organized by taxon of interest. TTest
 results compare the difference of mean deltaLnL score among alternative
 hypotheses. Results under “Rate het., Seq. dist., # of rogue tips, RCFV,
 and Compositional Bias” give a quantitative interpretation of ANOVA
 results. “No corr” indicates no significant correlation (alpha &gt; 0.001)
 "-" values indicate potentially invalid statistical results due
 to limited sampling (genes and taxa). Sheet 2: Explanation of hypotheses
 tested for each taxon of interest. #### Worksheet5.FullDataSetVsQA.xlsx A
 detailed comparison of traditional node support values and QA node support
 values across 30 nodes. "NA" values mean "not
 applicable". ## Trees All tree files are in the zipped archive
 Trees.zip | # | Name | # of trees | Topology | Support values | Quality
 aware? | Notes | | :- |
 :------------------------------------------------------- | :--------- |
 :------------------------------- | :-------------- | :------------- |
 :-------------------------------------------------------------------------- | | 0 | 0\_1183Loci\_ASTRAL.LBfromRootNNodermvd.unrooted.trimmed | 1 | ASTRAL-III inferred (1183 genes) | ASTRAL support | No | Derived from gene trees after outlier tips were pruned | | 1 | 1\_4tiersCombined.trees | 4 | 4 tier IQTREE2 inferred | UFBootstrap | No | Ordered: Tier 4, Tier 3, Tier2, Tier 1 | | 2 | 2\_RewrittenNodesupportAndStatus.CDDbest.tre | 1 | 4th tier IQTREE2 inferred | UFBootstrap | Yes | Node support annotations correspond to tiers (A=1st, B=2nd, C=3rd, D=4th) | | 3 | 3\_CDD.grafted.bootAwareSupport.tre | 1 | Manually modified from #2 | UFBootstrap | Yes | Grafts correspond to modifications suggested by total support tests | | 4 | 4\_combined.sCF.4Tiers.trees | 4 | 4 tier IQTREE2 inferred | sCF | No | Ordered: Tier 4, Tier 3, Tier2, Tier 1 | | 5 | 5\_CDDGrafted.sCFAwareSupport.tre | 1 | Same as 3 | sCF | Yes | Grafts correspond to modifications suggested by total support tests | | 6 | 6\_CDD.sCFAwareSupport.tre | 1 | 4th tier IQTREE2 inferred | sCF | Yes | Node support annotations correspond to tiers (A=1st, B=2nd, C=3rd, D=4th) | | 7 | 7\_freqFrom219boottrees.ON.rA.raxml.bestTree | 1 | RaXML-NG inferred (1183 genes) | Bootstrap (TBE) | No | 219 bootstrap replicates summarized with the Transfer Bootstrap Expectation | | 8 | 8\_freqFrom219RAXMLboottrees.ON.CDDGrafted.tree | 1 | Same as 3 | Bootstrap (TBE) | No | 219 bootstrap replicates summarized with the Transfer Bootstrap Expectation | | 9 | 9\_1183ASTRAL.bigTree.out.tree | 1 | Same as 0 | None | No | Node annotations are from Anomaly Finder (Linkem, et al. 2016) |