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Lice are considered a model system for studying the process of cospeciation because they are obligate and permanent parasites and are often highly host‐specific. Among lice, species in the family Echinophthiriidae Enderlein (Anoplura) are unique in that they infest mammalian hosts with an amphibious lifestyle, i.e. pinnipeds and the river otter. There is evidence that the ancestor of this group infested the terrestrial ancestor of pinnipeds, which suggests these parasites coevolved with their hosts during the transition to marine environments. However, there has been no previous study investigating the phylogenetic relationships among sucking lice parasitizing seals and sea lions. To uncover the evolutionary history of these parasites, we obtained genomic data for Antarctophthirus microchir Trouessart and Neumann (from two hosts), Antarctophthirus carlinii Leonardi et al., Antarctophthirus lobodontis Enderlein, Antarctophthirus ogmorhini Enderlein, Lepidophthirus macrorhini Enderlein, and Proechinophthirus fluctus Ferris. From genomic sequence reads, we assembled > 1000 nuclear genes and used these data to infer a phylogenetic tree for these lice. We also used the assembled genes in combination with read‐mapping to estimate heterozygosity and effective population size from individual lice. Our analysis supports the monophyly of lice from pinnipeds and uncovers phylogenetic relationships within the group. Surprisingly, we found that A. carlinii, A. lobodontis, and A. ogmorhini have very little genetic divergence among them, whereas the divergence between different geographic representatives of A. microchir indicate that they are possibly different species. Nevertheless, our phylogeny of Echinophthiriidae suggests that these lice have consistently codiverged with their hosts with minimal host switching. Population genomic metrics indicate that louse effective population size is linked to host demographics, which further highlights the close association between pinnipeds and their lice.

Psocodea (booklice and parasitic lice) is an order of insects containing species with extensive mitochondrial genome rearrangements, particularly within the suborder Troctomorpha, in which some species possess an extremely fragmented mitochondrial genome with several small minichromosomes. In the remaining suborders of Psocodea, there are groups with the ancestral pancrustacean arrangement, quite extensive rearrangements (e.g. Trogiomorpha), or in which the small number of species analysed to date have rearrangements of only a few protein‐coding genes and/or tRNAs (e.g. Psocomorpha). Despite the apparent high rate of rearrangements in the order as a whole, a small number of complete mitochondrial genomes are available, especially for suborder Psocomorpha, the largest free‐living suborder. To understand the evolution of the gene arrangement of the mitochondrial genome within Psocomorpha and its phylogenetic implications, we assembled and analysed the mitochondrial genomes of 33 species of bark lice belonging to nine families in two infraorders. Within the infraorder Homilopsocidea, four families were analysed, mainly from Lachesillidae (which included 22 species of this family). Within the infraorder Caeciliusetae, seven species representing five families were analysed. Mitochondrial gene rearrangements were identified in seven of the nine families. Some of these rearrangements were unique to a single species, while some contained phylogenetic signal, being shared by related species. These rearrangements typically corresponded to transpositions and inversions of tRNAs, possibly caused by tandem duplication–random loss (TDRL) and/or recombination events. Phylogenetic analyses of mitochondrial gene sequences provided phylogenetic resolution for several branches of the tree, including monophyly of Lachesillinae. The genus Hemicaecilius Enderlein was found to be embedded within the genus Lachesilla Westwood, rending the latter paraphyletic. Monophyly was also never recovered for Lachesillidae and Elipsocidae as currently defined. However, instability was observed for some higher level relationships within Psocomorpha, including the relationships among the major clades of Lachesillidae.