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Dryad

Biogeographic history of pigeons and doves drives the origin and diversification of their parasitic body lice

Cite this dataset

Sweet, Andrew; Doña Reguera, Jorge; Johnson, Kevin (2024). Biogeographic history of pigeons and doves drives the origin and diversification of their parasitic body lice [Dataset]. Dryad. https://doi.org/10.5061/dryad.hhmgqnkpc

Abstract

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 >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.

README: 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

Methods

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). 

Funding

National Science Foundation, Award: 1239788, DEB

National Science Foundation, Award: 1342604, DEB

National Science Foundation, Award: 1925487, DEB

National Science Foundation, Award: 1926919, DEB

European Commission, Award: H2020-MSCA-IF-201

Arkansas Biosciences Institute

Arkansas State University