Supporting data for "Simultaneous radiation of bird and mammal lice following the K-Pg boundary"

This zip file contains the supporting alignments and trees for the publication "Simultaneous radiation of bird and mammal lice following the K-Pg boundary" by Johnson, Kevin, Nguyen, Nam-phuong, Sweet, Andrew, Boyd, Bret, Warnow, Tandy, Allen, Julie. The files are: initial.fasta - The concatenated alignment of the 1st and 2nd codon positions of 1,107 single copy genes, grouped by the partitions from the GTR+alpha rate parameters. initial.partition - The partitions of the initial.fasta alignment. RAxML_bipartitions.RAXML.BOOTSTRAP - The RAxML tree estimated from the partitioned concatenated alignment, with bootstrap support. genes.zip - An archive containing the individual gene alignments used to create the concatenated alignment, where each folder is a gene, and the contents are: FNA2AA.fasta - The UPP alignment after translating AA coding sequences into nucleotides FNA2AA.no3rd.fasta - The UPP alignment after removing 3rd codon positions. astral/astral.tree - The ASTRAL tree estimated from the RAxML gene trees astral/raxml.ml.trees - The RAxML trees estimated from the individual gene alignment

Physconelloides gene alignments

Sequence alignments of nuclear exons from ground-dove body lice

Physconelloides voucher photographs

Voucher photographs (TIFFs) of ground-dove body lice specimens used for Illumina full genome sequencing

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 ASTRAL phylogeny

Tree file of ground-dove body louse phylogeny estimated with ASTRAL

Physconelloides ASTRID phylogeny

Tree file of ground-dove body louse phylogeny estimated with ASTRID

Physconelloides mt concatenated alignment

Concatenated alignment of mitochondrial sequence data from ground-dove body lice

Physconelloides association matrix

Association matrix for ground-doves and their body lice. Used as input for cophylogenetic analyses in ParaFit and PACo

Physconelloides mt phylogeny

Tree file of ground-dove body louse phylogeny estimated from mitochondrial sequence data in RAxML

Physconelloides gene trees

Gene trees from nuclear exons of ground-dove body lice. All trees were estimated in RAxML