DOI: 10.5061/dryad.qfttdz0ds
title: Data from: Lousy grouse: comparing evolutionary patterns in Alaska galliform lice to understand host evolution and host-parasite interactions

description: 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.
description: 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.
description: 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.