Mitochondrial DNA phylogeography of a species-specific sucking louse, Johnsonpthirus heliosciuri, act as a proxy to provide insights into the population connectivity of its host, Smith’s bush squirrels, Paraxerus cepapi

Permanent, species-specific lice and their hosts often exhibit congruent phylogenetic or phylogeographic structures due to co-speciation. However, because parasites typically have smaller effective population sizes than their hosts, their phylogeographic structures are often more pronounced. As a result, the phylogeographic structure of a permanent, species-specific louse can serve as a more sensitive indicator of host dispersal. This study investigates the phylogeographic structure of the squirrel Paraxerus cepapi and one of its louse species, Johnsonpthirus heliosciuri , sampled from eight localities in South Africa. Statistical haplotype networks derived from 51 host mitochondrial DNA control region sequences revealed a lack of geographic genetic structure among sampling sites, with most genetic variation found within populations (Φ _ST  = 0.304, P  < 0.05). In stark contrast, analyses of 43 louse mitochondrial COI sequences showed a clear pattern of geographic genetic structure, with most variation occurring between populations (Φ _ST  = 0.797, P  < 0.05). Nuclear Eukaryotic Elongation Factor 1 (EF1) data revealed no geographic structure in either species. The lack of phylogeographic congruence between host and louse, as well as between mitochondrial and nuclear markers, is likely due to stochastic differences in the evolutionary rates of host and parasite DNA. In this study, the species-specific permanent parasite acted as a biological proxy—or a ‘magnifying glass’—for host phylogeography. The mitochondrial DNA data suggest that recent anthropogenic habitat fragmentation may indeed be limiting squirrel movement across the landscape.