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-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.