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.Ground-dove phylogenyTree file of small New World ground-doves used in cophylogenetic analysis with their parasitic body lice.ground_doves.trePhysconelloides ASTRAL phylogenyTree file of ground-dove body louse phylogeny estimated with ASTRAL.physconelloides_astral.trePhysconelloides ASTRID phylogenyTree file of ground-dove body louse phylogeny estimated with ASTRID.physconelloides_astrid.trePhysconelloides concatenated phylogenyTree file of ground-dove body louse phylogeny estimated from a partitioned concatenated alignment in RAxML.physconelloides_concatenated_raxml.trePhysconelloides mt phylogenyTree file of ground-dove body louse phylogeny estimated from mitochondrial sequence data in RAxML.physconelloides_mt.trePhysconelloides mt phylogeny BEASTTree file of ground-dove louse phylogeny estimated from mitochondrial sequence data in BEAST.physconelloides_mt_beast.trePhysconelloides mt BEAST XMLXML file of ground-dove lice used as input for BEAST2 analysis of mitochondrial sequence data.physconelloides_mt_beast.xmlPhysconelloides semistrict consensus phylogenyTree file of a semistrict consensus phylogeny of ground-dove body lice. The phylogeny is a consensus of the concatenated, ASTRAL, ASTRID, and mitochondrial phylogenies.physconelloides_semistrict_consensus.trePhysconelloides gene treesGene trees from nuclear exons of ground-dove body lice. All trees were estimated in RAxML.physconelloides_gene_trees.treesPhysconelloides concatenated alignmentConcatenated sequence alignment of nuclear exons from ground-dove body lice and the outgroup.physconelloides_concatenated_alignment.phyPhysconelloides partitionsPartitions file for the concatenated nuclear exon alignment of ground-dove body lice. The file is an output file from PartitionFinder2.physconelloides_concatenated_partitions.txtPhysconelloides mt concatenated alignmentConcatenated alignment of mitochondrial sequence data from ground-dove body lice.physconelloides_mt_concatenated_alignment.phyPhysconelloides gene alignmentsSequence alignments of nuclear exons from ground-dove body lice.physconelloides_gene_alignments.zipPhysconelloides Jane inputInput file used for the Jane4 cophylogenetic analysis of ground-doves and their body lice.physconelloides_jane_input.treePhysconelloides association matrixAssociation matrix for ground-doves and their body lice. Used as input for cophylogenetic analyses in ParaFit and PACo.Physcon_cophy_matrix.txtPhysconelloides voucher photographsVoucher photographs (TIFFs) of ground-dove body lice specimens used for Illumina full genome sequencing.physconelloides_voucher_photographs.zipFunding provided by: National Science FoundationCrossref Funder Registry ID: http://dx.doi.org/10.13039/100000001Award Number: DEB-1239788; DEB-134260