Alcaide_etal_PeerJ_MHC_classI_alignment

This alignment was used in the analysis of the paper in PeerJ by M. Alcaide, M. Liu and S. Edwards entitled "Major Histocompatibility Complex class I evolution in songbirds: universal primers, rapid evolution and base compositional shifts in exon 3". The alignment begins on the first position of the codon and was made according to methods described in the paper. Taxa without Genbank numbers are original data; Genbank nubmers for these sequences can be found on Genbank. Taxa with Genbank numbers were taken from Genbank

sequences of 447 CDS in nexus format

sequences of the 447 genes use in the stud

Fig_S4

FIGURE S4. STRUCTURE plots showing 10 in-group individuals for three replicated runs (‘rep’) in which we excluded SNPs whose coverage amongst called individuals was greater than two standard deviations above the mean (n = 32,103) with K = 2 (upper panel) and K = 3 (lower panel)

all_combined

All sequences in fasta format. The fasta identifier includes the name of the gene and individual IDs for included specimens

Supp_File_3

SUPPLEMENTARY FILE 3. Tabular BLASTN results for the Zimmerius contigs against the zebra finch genome, retaining only hits with e-value ≤ 1e-20

Fig_S1

FIGURE S1. Fraction of missing SNP calls in each individual

Supp_File_4

SUPPLEMENTARY FILE 4. The output from VarScan used as our SNP datafile for downstream analysis

Fig_S2

FIGURE S2. Number of 100-bp Illumina reads per individual. Individual labels refer to those used in Table S4 and Figure 5

zimmerius_prg.fasta

This is the Pseudo-Reference Genome (PRG) assembly file

Supp_File_5.tar

SUPPLEMENTARY FILE 5. Our main analysis script for population genetic and introgression analyses compiled by P.R.W. (requires python 2.6+ and Biopython). Includes all required accompanying data files. Best run interactively