Hemipteroid insects (Paraneoptera), with over 10% of all known insect diversity, are a major component of terrestrial and aquatic ecosystems. Previous phylogenetic analyses have not consistently resolved the relationships among major hemipteroid lineages. We provide maximum likelihood-based phylogenomic analyses of a taxonomically comprehensive dataset comprising sequences of 2,395 single-copy, protein-coding genes for 193 samples of hemipteroid insects and outgroups. These analyses yield a well-supported phylogeny for hemipteroid insects. Monophyly of each of the three hemipteroid orders (Psocodea, Thysanoptera, and Hemiptera) is strongly supported, as are most relationships among suborders and families. Thysanoptera (thrips) is strongly supported as sister to Hemiptera. However, as in a recent large-scale analysis sampling all insect orders, trees from our data matrices support Psocodea (bark lice and parasitic lice) as the sister group to the holometabolous insects (those with complete metamorphosis). In contrast, four-cluster likelihood mapping of these data does not support this result. A molecular dating analysis using 23 fossil calibration points suggests hemipteroid insects began diversifying before the Carboniferous, over 365 million years ago. We also explore implications for understanding the timing of diversification, the evolution of morphological traits, and the evolution of mitochondrial genome organization. These results provide a phylogenetic framework for future studies of the group.

The gene composition, gene order and structure of the mitochondrial genome are remarkably stable across bilaterian animals. Lice (Insecta: Phthiraptera) are a major exception to this genomic stability in that the canonical single chromosome with 37 genes found in almost all other bilaterians has been lost in multiple lineages in favour of multiple, minicircular chromosomes with less than 37 genes on each chromosome.

The taxonomy, fossil record, phylogeny, and systematic placement of the booklouse family Liposcelididae (Insecta: Psocodea: ‘Psocoptera’) were reviewed. An apterous specimen from lower Eocene, erroneously identified as Embidopsocus eocenicus Nel et al., 2004 in the literature, is recognized here as an unidentified species of Liposcelis Motschulsky, 1852. It represents the oldest fossil of the genus. Phylogenetic relationships within the family presented in the recent literature were re-analyzed, based on a revised data matrix. The resulting tree was generally in agreement with that originally published, but the most basal dichotomy between the fossil taxon Cretoscelis Grimaldi & Engel, 2006 and the rest of the Liposcelididae was not supported. Monophyly of Liposcelis with respect to Troglotroctes Lienhard, 1996 is highly questionable, but the latter genus is retained because of lack of conclusive evidence. Paraphyly of Psocoptera (i.e., closer relationship between Liposcelididae and parasitic lice) is now well established, based on both morphological and molecular data. Monophyly of Phthiraptera is questionable, but support for the ‘Polyphyly of Lice Hypothesis’ is still not definitive. A checklist of valid names of all presently recognized Liposcelididae taxa (10 genera, 200 species) is also included with information on their geographical distribution. Because monophyly of the subfamily Embidopsocinae is highly questionable, we list the genera alphabetically without adopting the usual subdivision into two subfamies.