The higher-level relationships within the Paraneoptera, in particular the position of Thysanoptera, have been controversial for decades. Currently, the superorder Psocodea (= Phthiraptera + Psocoptera) was recognized as being monophyletic whereas its two orders, Phthiraptera and Psocoptera, are mutually paraphyletic 37. Furthermore, some molecular studies support the close relationship between parasitic lice of the suborder Amblycera and booklice (Liposcelididae) 34, 35, 36. A close relationship between parasitic lice (Phthiraptera) and booklice (Liposcelididae, a family of Psocoptera) was recognized based on morphology 33. The monophyly of Psocoptera and Phthiraptera, however, has been challenged in the past several decades. At the order level, Hemiptera and Thysanoptera have long been recognized as monophyletic groups 31, 32. Although recent phylogenomic studies contradict the widely accepted monophyletic origin of Paraneoptera, but these results are not supported in all statistical tests 28 or affected by misleading data matrix composition 29, 30. The monophyly of Paraneoptera is widely accepted and supported by morphological, paleontological, molecular, as well as combined morphological and molecular studies 23, 24, 25, 26, 27. A large number of paraneopteran insects are agricultural pests, animal parasites and disease vectors 23. Paraneopteran insects (Acercaria or hemipteroid assemblage) have over 120,400 described species 22 and are divided into four orders: Hemiptera (aphids, cicadas, planthoppers, true bugs, etc.), Thysanoptera (thrips), Psocoptera (barklice and booklice) and Phthiraptera (parasitic lice) 23. More sophisticated models (e.g., heterogeneous models that allow for heterogeneity across data) that better reflect the evolutionary process and reduce systematic bias are important to phylogenomic study 16, 18, 19, 20, 21. These features, if shared by taxonomically unrelated species, may be responsible for convergent evolution and weaken the true phylogenetic signal 17. Among-lineage compositional heterogeneity (e.g., A + T content heterogeneity) and saturation due to accelerated substitution rates are two important processes causing homoplasy in genomic data 16, 17. These potential biases limit the applicability of mt genome sequences in the reconstruction of higher-level phylogeny of insects, resulting in incongruence with morphological and nuclear data 3, 13, 15. Insect mt genomes tend to have high percentage of A + T content, lineage-specific compositional heterogeneity and accelerated sequence evolution in some groups such as Thysanoptera, Psocodea, Sternorrhyncha (Hemiptera), Strepsiptera and Hymenoptera 3, 4, 10, 11, 12, 13, 14. Analyses of mt genome sequences have improved our understanding of the intraordinal relationships in several insect groups such as Diptera 6, Orthoptera 7 and Coleoptera 8, 9. Like most other bilateral animals, the mt genomes of insects typically contain 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and a large non-coding region (also referred to as the control region, CR) 4. Similar content being viewed by othersÄNA sequencing and analyses have advanced rapidly in the past decade and the utility of mitochondrial (mt) genomes for phylogenetic inference at various taxonomic levels has been exploited 1, 2, 3, 4, 5. Furthermore, Thysanoptera was recovered as the sister group to Hemiptera. Within Psocodea, Liposcelididae is more closely related to Phthiraptera than to other species of Psocoptera. Bayesian inference with nucleotide sequences and heterogeneous models (CAT and CAT + GTR), however, recovered Psocodea, Thysanoptera and Hemiptera each as a monophyletic group. The phylogenies inferred with concatenated sequences of mt genes using maximum likelihood and Bayesian methods and homogeneous models failed to recover Psocodea and Hemiptera as monophyletic groups but grouped, instead, the taxa that had accelerated substitution rates together, including Sternorrhyncha (a suborder of Hemiptera), Thysanoptera, Phthiraptera and Liposcelididae (a family of Psocoptera). We found substantial heterogeneity in base composition and contrasting rates in nucleotide substitution among these paraneopteran insects, which complicate the inference of higher-level phylogeny. We analyzed the mt genomes of 25 insect species from the four paraneopteran orders, aiming to better understand how accelerated substitution rate and compositional heterogeneity affect the inferences of the higher-level phylogeny of this diverse group of hemimetabolous insects. Mitochondrial (mt) genome data have been proven to be informative for animal phylogenetic studies but may also suffer from systematic errors, due to the effects of accelerated substitution rate and compositional heterogeneity.
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