Understanding both sides of host-parasite relationships can provide more complete insights into host and parasite biology in natural systems. For example, phylogenetic and population genetic comparisons between a group of hosts and their closely associated parasites can reveal patterns of host dispersal, interspecies interactions, and population structure that might not be evident from host data alone. These comparisons are also useful for understanding factors that drive host-parasite coevolutionary patterns (e.g., codivergence or host switching) over different periods of time. However, few studies have compared the evolutionary histories between multiple groups of parasites from the same groups of hosts at a regional geographic scale. Here, we used genomic data to compare phylogenomic and population genomic patterns of Alaska ptarmigan and grouse species (Aves: Tetraoninae) and two genera of their associated feather lice: Lagopoecus and Goniodes. We used whole-genome sequencing to obtain hundreds of genes and thousands of single nucleotide polymorphisms (SNPs) for the lice and double digest restriction associated DNA sequences to obtain SNPs from Alaska populations of two species of ptarmigan. We found that both genera of lice have some codivergence with their galliform hosts, but these relationships are primarily characterized by host switching and phylogenetic incongruence. Population structure was also uncorrelated between the hosts and lice. These patterns suggest that grouse, and ptarmigan in particular, share habitats and have likely had historical and ongoing dispersal within Alaska. However, the two genera of lice also have sufficient dissimilarities in the relationships with their hosts to suggest there are other factors, such as differences in louse dispersal ability, that shape the evolutionary patterns with their hosts.

Louse specimens were collected from their ptarmigan and grouse hosts using fumigation or visual inspection, and then photographed before extracting DNA for sequencing. Nuclear gene alignments (exons) of the lice were generated from sequences assembled from 150bp paired-end shotgun Illumina read libraries. Mitochondrial sequences were obtained with Sanger sequencing or by assembling mitochondrial reads from Illumina libraries. Additional nuclear and mitochondrial sequences were obtained from GenBank and included as outgroups. SNPs were called by mapping reads to sets of nuclear exons from closely related references. Phylogenies were estimated from both nuclear and mitochondrial multiple sequence alignments. Two types of phylogenetic analyses were carried out using the nuclear data: 1) a partitioned analysis from the concatenated alignment and 2) a coalescent analysis from separate gene trees. The resulting phylogenies were used in cophylogenetic analyses to compare with previously published host phylogenies.

Names of individual lice in the alignment, phylogeny, and SNP files refer to the "Extract Names" column in Table S1. Tip names in the phylogenies used in cophylogenetic analyses are representatives from separate OTUs.