Estimating genomic diversity and population differentiation - an empirical comparison of microsatellite and SNP variation in Arabidopsis halleri.

In fact, θ Watterson estimates inferred from introns and intergenic regions were highly correlated to estimates of exon-based θ Watterson (Pearson’s r = 0.988; p < 0.001; see Additional file 9 : Figure S5). Comparison of genetic differentiation estimates derived from microsatellite versus genome-wide SNP variation Mantel tests revealed highly significant correlations between values of pairwise F ST derived from genome-wide SNP data and microsatellite markers (Fig. 4 ).

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