DOI: 10.5061/dryad.hhmgqnkpc
title: Biogeographic history of pigeons and doves drives the origin and diversification of their parasitic body lice

description: Despite their extensive diversity and ecological importance, the history
 of diversification for most groups of parasitic organisms remains
 relatively understudied. Elucidating broad macroevolutionary patterns of
 parasites is challenging, often limited by the availability of samples,
 genetic resources, and knowledge about ecological relationships with their
 hosts. In this study, we explore the macroevolutionary history of
 parasites by focusing on parasitic body lice from doves. Building on
 extensive knowledge of ecological relationships and previous phylogenomic
 studies of their avian hosts, we tested specific questions about the
 evolutionary origins of the body lice of doves, leveraging whole genome
 data sets for phylogenomics. Specifically, we sequenced whole genomes from
 68 samples of dove body lice, including representatives of all body louse
 genera from 51 host taxa. From these data, we assembled &gt;2,300
 nuclear genes to estimate dated phylogenetic relationships among body lice
 and several outgroup taxa. The resulting phylogeny of body lice was well
 supported, although some branches had conflicting signal across the
 genome. We then reconstructed ancestral biogeographic ranges of body lice
 and compared the body louse phylogeny to phylogeny of doves, and also to a
 previously published phylogeny of the wing lice of doves. Divergence
 estimates placed the origin of body lice in the late Oligocene. Body lice
 likely originated in Australasia and dispersed with their hosts during the
 early Miocene, with subsequent codivergence and host switching throughout
 the world. Notably, this evolutionary history is very similar to that of
 dove wing lice, despite the stronger dispersal capabilities of wing lice
 compared to body lice. Our results highlight the central role of the
 biogeographic history of host organisms in driving the evolutionary
 history of their parasites across time and geographic space.
description: These data are associated with a phylogenomic analysis of
 individual samples of lice sequenced with whole genome sequencing. The
 data include voucher photographs of the individual specimens, resulting
 phylogenetic trees from nuclear and mitochondrial sequences, and relevant
 input and output files from downstream analyses (historical biogeography,
 cophylogenetic analysis). 
description: # Biogeographic history of pigeons and doves drives the origin and
 diversification of their parasitic body lice ## Description of the data
 and file structure \|-- `Biogeography.zip` # Input data and results files
 from biogeographic analyses of dove body lice in BioGeoBEARS \| |--
 `body_lice_biogeo.txt` # matrix of biogeographic regions formatted for
 input in BioGeoBEARS \| |-- `body_lice_mcmctree_og_trimmed.tre` #
 phylogeny used as input into BioGeoBEARS \| |--
 `restable_AICc_rellike_formatted.txt` # output of biogeographic model
 assessment from BioGeoBEARS \|-- `Cophylogeny.zip` \| |--
 `body_lice_jane_input` # Input file for Jane \| |-- `bodyliceGeo.mow` #
 Tree and biogeographic information of body lice for MOWGLI \| |--
 `cospeciation_Ratio_cumulative.csv` # Ratio of host switches and
 cospeciation events to total cumulative speciation events of dove body
 lice \| |-- `dovesGeo.mow` # Dated tree and biogeographic information of
 doves for MOWGLI \| |-- `mowgli_results.out` # Output of MOWGLI \|--
 `Trees.zip` # Phylogenetic trees of dove body lice and outgroup taxa \|
 |-- `body_lice_trim40_concat.tre` # concatenated tree from 40% complete
 alignment, all codon positions \| |-- `bodylice_trim40_astral.tre` #
 ASTRAL tree from 40% complete alignment, all codon positions \| |--
 `body_lice_trim40_12.concat.tre` # concatenated tree from 40% complete
 alignment, first and second codon positions \| |--
 `body_lice_trim40_12_astral.tre` # ASTRAL tree from 40% complete
 alignment, first and second codon positions \| |--
 `body_louse_trim40_genetrees.tre` # gene trees from 40% complete
 alignments, all codon positions \| |--
 `body_louse_trim40_12_genetrees.tre` # gene trees from 40% complete
 alignments, first and second codon positions \| |--
 `body_lice_trim90_12.concat.tre` # concatenated tree from 90% complete
 alignment, first and second codon positions \| |--
 `body_lice_trim90_12_astral.tre` # ASTRAL tree from 0% complete alignment,
 first and second codon positions \| |-- `body_lice_trim90_astral.tre` #
 ASTRAL tree from 90% complete alignment, all codon positions \| |--
 `body_lice_trim90_concat.tre` # concatenated tree from 90% complete
 alignment, all codon positions \| |-- `body_lice_trim90_genetrees.tre` #
 gene trees from 90% complete alignments, all codon positions \| |--
 `body_lice_trim90_12_genetrees.tre` # gene trees from 90% complete
 alignments, first and second codon positions \| |--
 `body_louse_notrim_12_concat.tre` # concatenated tree from untrimmed
 alignment, first and second codon positions \| |--
 `body_louse_notrim_concat.tre` # concatenated tree from untrimmed
 alignment, all codon positions \| |--
 `body_louse_combined_dating_ranges_pairs_max_root_u01.timetree.tre` #
 dated phylogeny with age estimates from the LSD2 method \| |--
 `body_louse_dated_mcmctree_calib_60_run1.tre` # dated phylogeny with age
 estimates from the MCMCtree \| |--
 `body_louse_dated_mcmctree_calib_60_run2.tre` # dated phylogeny with age
 estimates from a second run in MCMCtree \|-- `Voucher_photos.zip` #
 voucher photographs of louse specimens used for extraction of genomic DNA
 \| |-- `AlspHabad.TIF` \| |-- `Auaff.dmap.jpg` \| |-- `AuspDubic.dmap.jpg`
 \| |-- `AuspDupac.dmap.jpg` \| |-- `AuspPtriv.dmap.jpg` \| |--
 `Cabid.dmap.jpg` \| |-- `Cacam5337.dmap.jpg` \| |-- `Cacom1.jpg` \| |--
 `Cadur.dmap.jpg` \| |-- `Caele.dmap.jpg` \| |-- `Cafla.dmap.jpg` \| |--
 `Cafre.dmap.jpeg.jpg` \| |-- `Cahet.dmap.jpg` \| |-- `CaspColcm.dmap.jpg`
 \| |-- `CaspGehum.dmap.jpg` \| |-- `CaspGeplu.dmap.jpg` \| |--
 `CaspGesmi.dmap.jpg` \| |-- `CaspPhhis.dmap.jpg` \| |-- `Cccas.dmap.jpg`
 \| |-- `Ccchi.dmap.jpg` \| |-- `Cccla.jpg` \| |-- `Ccdam.dmap.jpg` \| |--
 `CcdorMaamb.dmap.jpg` \| |-- `CcdorManig.dmap.jpg` \| |-- `Ccfur.dmap.jpg`
 \| |-- `Ccgra.dmap.jpg` \| |-- `Cchil.dmap.jpg` \| |-- `Cclat.dmap.jpg` \|
 |-- `Ccmus.dmap.jpg` \| |-- `Ccset.dmap.jpeg.jpg` \| |--
 `CcspAplar.dmap.jpg` \| |-- `CcspChind.dmap.jpg` \| |--
 `CcspCosjo.PMAX.jpeg.jpg` \| |-- `CcspGecun.dmap.jpg` \| |--
 `CcspGehum.dmap.jpg` \| |-- `CcspGepla.dmap.jpg` \| |-- `CcspGestr.jpg` \|
 |-- `CcspMamac.dmap.jpg` \| |-- `CcspOclop.jpg` \| |--
 `CcspPealb.dmap.jpg` \| |-- `CcspPeruf.dmap.jpg` \| |--
 `CcspPhele.dmap.jpg` \| |-- `CcspStcap.jpg` \| |-- `CcspStlug.jpg` \| |--
 `CcspStpic.dmap.jpg` \| |-- `CcspStsem.dmap.jpg` \| |--
 `CcspTucha.dmap.jpg` \| |-- `CcspTutym.dmap.jpg` \| |-- `Ccste.jpg` \| |--
 `Cctav.dmap.jpg` \| |-- `GDORT_1-4-8_scale.jpg` \| |--
 `Gdass.PMax.jpeg.jpg` \| |-- `Gdast.pmax.tif` \| |-- `Gdbio.Pmax.jpeg.jpg`
 \| |-- `Gdcen.Pmax.jpeg.jpg` \| |-- `Gdmer.Pmax.jpeg.jpg` \| |--
 `GdspCacal.pmax.tif` \| |-- `GdspPhcol.pmax.tif` \| |-- `Gochr.dmap.jpg`
 \| |-- `GospMerei.Pmax.jpeg.jpg` \| |-- `Gotal.pmax.tif` \| |--
 `Kosub.dmap.jpg` \| |-- `MuspNyalb.TIF` \| |-- `Phcer1.dmap.jpg` \| |--
 `Phcer5.dmap.jpg` \| |-- `Phcub.dmap.jpg` \| |--
 `Pheur2.Clpre.5.26.2015.6.jpg` \| |-- `Phper.dmap.jpeg.jpg` \| |--
 `Phrob.Mecec.5.26.2015.7.jpg` \| |-- `PhspPhcha.dmap.jpg` \| |--
 `Phspe1.dmap.jpg` \| |-- `Phwis.dmap.jpg` \| |-- `Phzen.dmap.jpg` \| |--
 `Pnzum.Pmax.jpeg.jpg` \| |-- `Popap.TIF` \| |-- `PpspTymel.TIF` \| |--
 `PyspOdste.dmap.jpg` \| |-- `Tiele.TIF` \-- `cox1.zip` # data associated
 with cox1 for dove body lice and outgroup taxa \| |--
 `COI_alignment_dna_aligned.fasta` # alignment of cox1 sequences \| |--
 `COI_alignment_dna_aligned.tre` # phylogeny from alignment of cox1
 sequences