Multispecies coalescent analysis unravels the non-monophyly and controversial relationships of Hexapoda

With the increase in the availability of genomic data, sequences from different loci are usually concatenated in a supermatrix for phylogenetic inference. However, as an alternative to the supermatrix approach, several implementations of the multispecies coalescent (MSC) have been increasingly used in phylogenomic analyses due to their advantages in accommodating gene tree topological heterogeneity by taking account population-level processes. Moreover, the development of faster algorithms under the MSC is enabling the analysis of thousands of loci/taxa. Here, we explored the MSC approach for a phylogenomic dataset of Insecta. Even with the challenges posed by insects, due to large effective population sizes coupled with short deep internal branches, our MSC analysis could recover several orders and evolutionary relationships in agreement with current insect systematics. However, some phylogenetic relationships were not recovered by MSC methods. Most noticeable, a remiped crustacean was positioned within the Insecta. Additionally, the interordinal relationships within Polyneoptera and Neuropteroidea contradicted recent works, by suggesting the non-monophyly of Neuroptera. We notice, however, that these phylogenetic arrangements were also poorly supported by previous analyses and that they were sensitive to gene sampling.