Outlier analyses
The 21 loci under selection used in this study were detected by two different outlier search analyses conducted in a previous study (Llanos-Garrido et al. 2019), one of them independent of population coancestry (an extension of the Lewontin–Krakauer test; Bonhomme et al. 2010) and the other one not (Bayescan v.2.1; Foll and Gaggiotti 2008).
The outlier analysis performed with Bayescan detected 12 outlier loci with α > 0 (0.97 < α < 1.35) and q < 0.05, while the FLK analysis identified nine additional loci with p < 0.001, none of which was previously detected by Bayescan. An MDS analysis performed elsewhere with these 21 SNPs putatively under selection, placed sampled populations along a first major axis that recovered the same pattern of differentiation observed for mtDNA and for some relevant phenotypic traits (Llanos-Garrido et al., 2019). Moreover, these phenotypes were interpreted as adaptive after a process of ecologically-driven divergence in a much wider sample (Díaz et al., 2017). Thus, despite the fact that these outliers could not be the genetic basis of adaptive phenotypes, they showed a genetic differentiation that mirrors local adaptation to the environmental conditions at sampled populations.