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.