Ribosomal protein genes of holometabolan insects reject the Halteria, instead revealing a close affinity of Strepsiptera with Coleoptera

The phylogenetic relationships among holometabolan insect orders remain poorly known, despite a wealth of previous studies. In particular, past attempts to clarify the sister-group of the enigmatic order Strepsiptera with rRNA genes have led to intense debate about long-branch attraction (the ‘Strepsiptera problem’), without resolving the taxonomic question at hand. Here, we appealed to alternative nuclear sequences of 27 ribosomal proteins (RPs) to generate a data matrix of 10,731 nucleotides for 22 holometabolan taxa, including two strepsipteran species. Phylogenetic relationships among holometabolan insects were analyzed under several nucleotide-coding schemes to explore differences in signal and systematic biases. Saturation and compositional bias particularly affected third positions, which greatly differed in AT content (18–72%). Such confounding factors were best reduced by R-Y coding and removal of third codon positions, resulting in more strongly supported topologies, whereas amino acid coding gave poor resolution. The placement of Strepsiptera with Coleoptera (the Coleopterida) was recovered under most coding schemes and analytical methods, if often with modest support and ambiguity. In contrast, an alternative sister-group with Diptera (the Halteria) was only found in one analysis using parsimony, and weakly supported. The topologies here generally support a Coleoptera + Strepsiptera as sister-group to Mecopterida (Siphonaptera + Mecoptera + Diptera + Lepidoptera + Trichoptera), while Hymenoptera were always recovered as sister-group to the remaining Holometabola.