Phylogenomics of Parasitic and Nonparasitic Lice (Insecta: Psocodea): Combining Sequence Data and Exploring Compositional Bias Solutions in Next Generation Data Sets

Abstract

The insect order Psocodea is a diverse lineage comprising both parasitic (Phthiraptera) and non-parasitic members (Psocoptera). The extreme age and ecological diversity of the group may be associated with major genomic changes, such as base compositional biases expected to affect phylogenetic inference. Divergent morphology between parasitic and non-parasitic members has also obscured the origins of parasitism within the order. We conducted a phylogenomic analysis on the order Psocodea utilizing both transcriptome and genome sequencing to obtain a data set of 2,370 orthologous genes. All phylogenomic analyses, including both concatenated and coalescent methods suggest a single origin of parasitism within the order Psocodea, resolving conflicting results from previous studies. This phylogeny allows us to propose a stable ordinal level classification scheme that retains significant taxonomic names present in historical scientific literature and reflects the evolution of the group as a whole. A dating analysis, with internal nodes calibrated by fossil evidence, suggests an origin of parasitism that predates the K-Pg boundary. Nucleotide compositional biases are detected in third and first codon positions and result in the anomalous placement of the Amphientometae as sister to Psocomorpha when all nucleotide sites are analyzed. Likelihood-mapping and quartet sampling methods demonstrate that base compositional biases can also have an effect on quartet-based methods.

Highly rearranged mitochondrial genome in Falcolipeurus lice (Phthiraptera: Philopteridae) from endangered eagles

“…However, Johnson et al analyzed 1107 single-copy orthologous genes of 46 species and showed that the Philopteridae was monophyletic [ 45 ]. De Moya et al analyzed 2370 orthologous genes and also showed that Philopteridae was monophyletic [ 46 ].…”

The Acari Hypothesis, II: Interspecies Operability of Pattern Recognition Receptors

“…Accordingly, any ectoparasite with PRRs similar to those of man might influence human immunity by the mechanism proposed here. Review of phylogenic emergence estimates of human ectoparasites [ 52 , 53 , 54 , 55 , 56 , 57 , 58 ] and of IgE [ 59 ], however, indicates most ectoparasites could not have supplied the evolutionary pressure leading to the formation of IgE, Figure 4 . The Acari, on the other hand, predate emergence of IgE [ 58 ].…”

Highly Rearranged Mitochondrial Genome in Falcolipeurus lice (Phthiraptera: Philopteridae) from Endangered Eagles

“…Mt genome sequences are effective molecular markers to study the phylogenetic and systematic relationships at various taxonomic ranks across the phylum Arthropoda, including ectoparasites [41][42][43][44][45][46]. DNA sequencing provides the opportunity to further evaluate the phylogenetic relationships of the Philopteridae.…”

“…However, Johnson et al analyzed 1107 single-copy orthologous genes of 46 species and showed that the Philopteridae to be monophyletic [43]. de Moya et al, analyzed 2,370 orthologous genes and showed that the Philopteridae to be monophyletic [44]. To date, the phylogenetic position of the Philopteridae in deep-level relationships within the order Phthiraptera could not be con dently determined.…”