Code and data associated with Adkins et al.

Code:

phylogeny.R: script to generate phylogeny figures

Data

Cc_Cm_CV_FL_HI_allele_counts_by_species_locality_zeroes_ones.csv: dataframe of alleles and what population or location they are in, by species; for input to phylogeny_CV_FL_HI.R

Files

classI_Hawaiian_Cm_trimmedoutgroup.fasta: edited Clustal Omega alignment of MHC alleles

classI_Hawaiian_Cm_trimmedoutgroup.nex: input nexus file for MrBayes

infile.nex.con.tre: MrBayes output consensus tree and input for phylogeny_CV_FL_HI.R

classI_Hawaiian_Cm_159bp.fasta: Clustal omega alignment in correct open reading frame and shortened to 159bp, for HyPhy analyses; direct input for GARD analysis

classI_Hawaiian_Cm_159bp.nex: input nexus file for MrBayes, for HyPhy analyses

infile.nex.con_159bp.tre: output consensus tree of MrBayes, for HyPhy analyses

Cm_Hawaii_HyPhy_Bayesiantree.fasta: input to HyPhy tests

Cm_Hawaii_IQTree.nwk: output tree of IQTree run