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 phylogeny
Tree file of small New World ground-doves used in cophylogenetic analysis with their parasitic body lice.
ground_doves.tre
Physconelloides ASTRAL phylogeny
Tree file of ground-dove body louse phylogeny estimated with ASTRAL.
physconelloides_astral.tre
Physconelloides ASTRID phylogeny
Tree file of ground-dove body louse phylogeny estimated with ASTRID.
physconelloides_astrid.tre
Physconelloides concatenated phylogeny
Tree file of ground-dove body louse phylogeny estimated from a partitioned concatenated alignment in RAxML.
physconelloides_concatenated_raxml.tre
Physconelloides mt phylogeny
Tree file of ground-dove body louse phylogeny estimated from mitochondrial sequence data in RAxML.
physconelloides_mt.tre
Physconelloides mt phylogeny BEAST
Tree file of ground-dove louse phylogeny estimated from mitochondrial sequence data in BEAST.
physconelloides_mt_beast.tre
Physconelloides mt BEAST XML
XML file of ground-dove lice used as input for BEAST2 analysis of mitochondrial sequence data.
physconelloides_mt_beast.xml
Physconelloides semistrict consensus phylogeny
Tree 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.tre
Physconelloides gene trees
Gene trees from nuclear exons of ground-dove body lice. All trees were estimated in RAxML.
physconelloides_gene_trees.trees
Physconelloides concatenated alignment
Concatenated sequence alignment of nuclear exons from ground-dove body lice and the outgroup.
physconelloides_concatenated_alignment.phy
Physconelloides partitions
Partitions file for the concatenated nuclear exon alignment of ground-dove body lice. The file is an output file from PartitionFinder2.
physconelloides_concatenated_partitions.txt
Physconelloides mt concatenated alignment
Concatenated alignment of mitochondrial sequence data from ground-dove body lice.
physconelloides_mt_concatenated_alignment.phy
Physconelloides gene alignments
Sequence alignments of nuclear exons from ground-dove body lice.
physconelloides_gene_alignments.zip
Physconelloides Jane input
Input file used for the Jane4 cophylogenetic analysis of ground-doves and their body lice.
physconelloides_jane_input.tree
Physconelloides association matrix
Association matrix for ground-doves and their body lice. Used as input for cophylogenetic analyses in ParaFit and PACo.
Physcon_cophy_matrix.txt
Physconelloides voucher photographs
Voucher photographs (TIFFs) of ground-dove body lice specimens used for Illumina full genome sequencing.
physconelloides_voucher_photographs.zip