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The number of population-specific outlier loci differed between species, likely owing to differential selective pressures within the intertidal environment. We found relatively low numbers of outlier SNPs within each species, and identified outlier genes associated with different selective pressures than those previously identified in studies conducted over larger environmental gradients. Using pooled restriction site associated DNA (RAD) sequencing, we described patterns of genomic variation and identified outlier loci in both species. To assess adaptive signals between microhabitats within the rocky shore, we compared genomic variation between the Cape urchin ( Parechinus angulosus), which is a low to mid-shore species, and the Granular limpet ( Scutellastra granularis), a high shore specialist. Therefore, the focus of this study is to characterize genomic variation and selective signals over short geographic areas within a largely homogeneous region. However, most studies are carried out in regions with distinct environmental gradients or across large geographical areas, in which local adaptation is expected to occur. Genomic tools are increasingly being used on non-model organisms to provide insights into population structure and variability, including signals of selection.