Data from: Integrating phylogenomic and population genomic patterns in avian lice provides a more complete picture of parasite evolution

Parasite diversity accounts for most of the biodiversity on earth, and is
shaped by many processes (e.g. cospeciation, host-switching). To identify
the effects of the processes that shape parasite diversity, it is ideal to
incorporate both deep (phylogenetic) and shallow (population)
perspectives. To this end, we developed a novel workflow to obtain
phylogenetic and population genetic data from whole genome sequences of
body lice parasitizing New World ground-doves. Phylogenies from these data
showed consistent, highly resolved species-level relationships for the
lice. By comparing the louse and ground-dove phylogenies, we found that
over long-term evolutionary scales their phylogenies were largely
congruent. Many louse lineages (both species and populations) also
demonstrated high host-specificity, suggesting ground-dove divergence is a
primary driver of their parasites’ diversity. However, the few louse taxa
that are generalists are structured according to biogeography at the
population level. This suggests dispersal among sympatric hosts has some
effect on body louse diversity, but over deeper time scales the parasites
eventually sort according to host species. Overall, our results
demonstrate that multiple factors explain the patterns of diversity in
this group of parasites, and that the effects of these factors can vary
over different evolutionary scales. The integrative approach we employed
was crucial for uncovering these patterns, and should be broadly
applicable to other studies.