Global selection at candidate loci
To assess whether candidate loci were under divergent selection across
the six populations, we compared global estimates of Hedrick’sG′ST (Hedrick, 2005), calculated using the
‘diveRsity’ package (Keenan et al., 2013) in R, between neutral
microsatellite and functional SNP markers. Hedrick’sG′ST is suitable for comparing genetic divergence
measures among different marker types since it standardizes for
heterozygosity (Hedrick, 2005). To assess an overall signature of
selection at SNP loci relative to microsatellite markers across all
populations, we first developed a ‘neutral range’ meanG′ST with 99% confidence intervals (CI) for the
microsatellite marker G′ST values using the
‘diffCalc’ function of the R package ‘diveRsity’. Specifically, we used
bias-corrected bootstrapping across microsatellite loci to estimate the
neutral CI range, representing neutrality expectation (presumably due to
genetic drift) based on the G′ST distribution of
microsatellite markers. Next, we determined whether theG′ST values for individual SNP loci fell outside
of the neutral ranges, as such loci are likely to be under selection.
Since the calculated neutral range for G’ST did
not include zero, we were able to identify SNP genes under stabilizing
(lower than neutral expected) and divergent (higher than neutral
expected) selection.