Supp_File_8

SUPPLEMENTARY FILE 8. Estimates of theta for various datasets and priors. Each of 6 datasets was subjected to a set of alpha and beta parameters allowing for different current and ancestral population sizes: (1) a gamma (2,2000) prior (with`q = 0.001) for small population sizes, and (2) a gamma (1,10) prior (with`q = 0.1) for large population sizes. Three datasets (called ‘allLoci’; n = 954 SNPs) include all SNPs called across all individuals (see Methods), while the three remaining datasets (n = 947) have constant heterozygotes removed; in each of these two groups of datasets, the first dataset includes all lineages, while the other two datasets have one lineage (‘southern’ Z. viridiflavus or ‘intermediate’ mosaic birds) removed. Each theta stands for one of the nodes in the tree. Note how thetas are heavily influenced by the prior

Sequence data for Mixornis gularis

Illumina MiSeq Fastq files, including index read sequence

Supp_File_1

SUPPLEMENTARY FILE 1. Custom script (‘tetracolor’) by Rafael Maia in

Supp_File_10

SUPPLEMENTARY FILE 10. Excel file with six sheets showing associations between ABBA and BABA-like sites with gene ontology (GO) terms from the zebra finch genome. The first three sheets refer to ABBA-like sites; the last three sheets refer to BABA-like sites. Sheets 1 and 4 give associations with GO terms related to cellular components (“cc”), sheets 2 and 5 refer to GO terms related to biological processes (“bp”), and sheets 3 and 6 refer to GO terms related to molecular function (“mf”). In each sheet, GO terms are accompanied by the number of zebra finch genes they are annotated to (“annotated”), followed by the number of ABBA or BABA-linked genes they are annotated to (“significant”), followed by the number of ABBA or BABA-linked genes they would be expected to be annotated to by chance (“expected”), followed by the corrected p value for their over-representation in the ABBA or BABA-linked gene set (“corrected”). The only gene set showing significant (p < 0.05) over-representation of any GO term is the ABBA set for cellular components (sheet 1)

Fig_S2

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

Supp_File_4

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

yeast.tar

Yeast alignment file

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)

Fig_S6

FIGURE S6. (a) Number of contigs mapped against zebra finch chromosomes plotted versus chromosome length; fewer contigs mapped against the Z chromosome (blue) than expected by chromosome length. (b) Number of contigs that contain a SNP with an ABBA or BABA pattern mapped against zebra finch chromosomes versus chromosome length; far fewer ABBA-BABA contigs mapped against the Z chromosome (blue) than expected by chromosome length. (c) Number of contigs that contain an ABBA or BABA pattern versus number of total contigs for each zebra finch chromosome they mapped against; fewer ABBA-BABA contigs mapped to the Z chromosome (blue) than expected. (d) Frequency plot giving the number of ABBA-BABA contigs mapped against each zebra finch chromosome per contigs mapped

sample_1_to_12_mpileup

This is the pileup file (see VarScan application)