Selection signature and variant type
To characterize the role of SNP variant type (i.e., missense, synonymous, downstream or upstream), we determined the proportion of SNPs that showed signatures of neutral processes or selection at the global and pairwise levels (with combined data across all fifteen comparisons) within each variant type. Given our functional SNPs were derived from transcribed sequences, we would expect selection to be more common among missense variants, as they would result in a different amino acid sequence in the protein.
Results
Microsatellite vs. SNP marker characteristics
We developed nine microsatellite markers (Supplementary Material S5) and applied them across all individuals to assess reproductive isolation and establish “neutral” control data for functional SNP locus divergence. We also developed 117 functional SNP loci (Supplementary Material S4) from a de-novo transcriptome for snow buntings which were expected to show local selection effects among breeding populations based on their putative gene function. The microsatellite panel was more polymorphic than the SNP panel: observed heterozygosity for microsatellite markers was higher (0.345-0.708) than for SNP locus markers (0.098-0.111) (Supplementary Material S6). We were able to successfully extract DNA for all 221 samples across six populations for microsatellite and SNP marker genotyping.