Fig. S1 Contribution of each dataset-contig combination to the total SNP set. The size of each slice corresponds to the number of SNPs identified from that specific read-contig combination (out of the total 95,345 SNPs detected from UK and NL datasets). Slices that represent UK SNPs are shaded.

Table S1 Differences in the methods used for NL and UK datasets.

Table S2 Candidate gene SNPs.

Table S3 Classification of the 9193 genotyped SNPs.

Table S4 Distribution of SNPs across the zebra finch chromosomes and linkage groups.

Table S5 Expected coverage of each chromosome by the SNPs on the chip.

Table S6 GO terms overrepresented in genes located near the 1109 loci with a significant FST value.

Table S7 Regions with multiple SNPs of very high (top 1%) FST values.

Table S8 GO terms overrepresented in the genes in the 11 regions containing multiple SNPs with the most significant FST values.

Data S1 Calculation of binomial probabilities.

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