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Abstract Genetic analyses of host‐specific parasites can elucidate the evolutionary histories and biological features of their hosts. Here, we used population‐genomic analyses of ectoparasitic seal lice (Echinophthirius horridus) to shed light on the postglacial history of seals in the Arctic Ocean and the Baltic Sea region. One key question was the enigmatic origin of relict landlocked ringed seal populations in lakes Saimaa and Ladoga in northern Europe. We found that that lice of four postglacially diverged subspecies of the ringed seal (Pusa hispida) and Baltic gray seal (Halichoerus grypus), like their hosts, form genetically differentiated entities. Using coalescent‐based demographic inference, we show that the sequence of divergences of the louse populations is consistent with the geological history of lake formation. In addition, local effective population sizes of the lice are generally proportional to the census sizes of their respective seal host populations. Genome‐based reconstructions of long‐term effective population sizes revealed clear differences among louse populations associated with gray versus ringed seals, with apparent links to Pleistocene and Holocene climatic variation as well as to the isolation histories of ringed seal subspecies. Interestingly, our analyses also revealed ancient gene flow between the lice of Baltic gray and ringed seals, suggesting that the distributions of Baltic seals overlapped to a greater extent in the past than is the case today. Taken together, our results demonstrate how genomic information from specialized parasites with higher mutation and substitution rates than their hosts can potentially illuminate finer scale population genetic patterns than similar data from their hosts. 

Abstract Lachesillidae is one of the largest families of bark lice and includes more than 420 described species, in 26 genera and three subfamilies. This family belongs in the suborder Psocomorpha, infraorder Homilopsocidea. The classification of Lachesillidae is based on male and female genital morphologies, but questions remain regarding the monophyly of the family and some of its genera. Here, we used whole genome and transcriptome data to generate a 2060 orthologous gene data matrix of 2,438,763 aligned bp and used these data to reconstruct the phylogenetic relationships of species of Lachesillidae and relatives. Taxon sampling included 24 species from Lachesillidae and 23 additional species belonging to related families from the infraorders Homilopsocidea and Caeciliusetae. Phylogenetic relationships reconstructed with maximum likelihood and coalescent‐based analyses indicated paraphyly of Lachesillidae, and monophyly of the tribe Graphocaeciliini and the genusLachesillawere also never recovered. Instability was observed in the position ofEolachesilla chilensis, which was recovered either as sister to Elipsocidae or to Mesopsocidae species, so we cannot conclusively determine the position of this genus within the Homilopsocidea. Given our results, a reclassification is necessary, but more taxon sampling of other species in Mesopsocidae and Peripsocidae would be useful to add to a tree in future before proposing a new classification.