DOI: 10.5061/dryad.02sk7
title: Data from: Integrating phylogenomic and population genomic patterns in avian lice provides a more complete picture of parasite evolution

description: 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.
description: 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.zip