Table S6: Patterns of synonymous and nonsynonymous substitutions

We compared the frequencies of non-synonymous, synonymous and non-protein coding SNPs in the House Finch and poultry populations by comparing three groups of SNPs. The first type were polymorphisms that likely arose in the House Finch MG lineage, as they are fixed in the poultry MG strains but are polymorphic amongst the House Finch ones. The second group are those SNPs that likely arose in the poultry MG population, as they show the opposite pattern and are fixed in the House Finch strains. We also examined SNPs that represented fixed differences between the two populations and likely arose on the lineage separating the poultry and House Finch MG populations. 35 SNPs were excluded from categorization because they were polymorphic in both the poultry and House Finch populations. Finally, we obtained expected numbers of the three types of mutations by simulating mutations in the genome using the maximum a posteriori parameters for the HKY substitution model inferred from our earlier BEAST analysis (Text S2).