3.5.2 Genetic diversity and Hardy Weinberg equilibrium
Hybridization and introgression resulted in an increase of genetic diversity (π, A, Ar, Ho and HE) in the hybrid regions, which was estimated with the whole set of 5,702 SNPs (Figure 4 and Supplementary Tables S7- S9). When the genetic diversity parameters were compared between I. elegans from allopatry and I. elegansfrom sympatry in each of the hybrid regions excluding F1and F2 hybrid individuals, significant differences in all five estimates (π, Na, Ar, Ho and HE) were detected for the north-west hybrid region (all estimates were higher in the north-west hybrid region; Figure 4 and Supplementary Tables S7- S9). We also found significantly higher Ar, Ho and HE in the north-west hybrid region compared to the north-central hybrid region (Figure 4 and Supplementary Tables S7-S9). Similarly, when comparingI. elegans from allopatry and I. elegans from sympatry in each of the hybrid regions not excluding F1 and F2 hybrids, all estimates of genetic diversity (π, A, Ar, Ho and HE) were significantly higher for the north-west hybrid region than for I. elegans from sympatry and than for I. elegans from the north-central hybrid region (Figure 4 and Supplementary Tables S7- S9). No significant differences between regions were detected in the ratio of SNPs at HW disequilibrium per population (p<0.05; see Supplementary Tables S8-S9).
3.5.3 Genetic differentiation between and within species in allopatry and sympatry
Consistent with the finding that hybridization, admixture and introgression results in reduced interspecific differentiation in sympatry, we found that the overall genetic differentiation betweenI. elegans and I. graellsii was lower in the sympatric (excluding F1 and F2 hybrids) (FST=0.691) than in the allopatric distribution (FST=0.725).
Pairwise intraspecific population differentiation in I. elegans from allopatry ranged from FST=0.002-0.245 (8 out of the 10 pairwise FST values were significant at thep <0.05/10), from the north-west hybrid region (excluding F1 and F2 hybrids) ranged from FST=0.012-0.100 (3 out of the 3 pairwise FST values were significant at thep <0.05/3), from the north-central hybrid region (excluding F1 and F2 hybrids) ranged from FST=0.004-0.013 (1 out of the 10 pairwise FST values was significant at thep <0.05/10) (Supplementary Table S10). Pairwise intraspecific population differentiation in I. graellsii from allopatry ranged from FST=0.008-0.068 (2 out of the 3 pairwise FST values were significant at thep <0.05/3), from the north-west hybrid region FST=0.042 (1 out of the 1 pairwise FSTvalues was significant at the p <0.05), and from the north-central hybrid region ranged from FST=0-0.014 (0 out of the 15 pairwise FST values was significant at thep <0.05/15) (Supplementary Table S11).
Some populations were highly genetically distinct from many populations. Specifically, the I. elegans Doniños population from the north-west hybrid region showed comparatively large and statistically significant genetic differences with several other populations (Supplementary Tables S10-S11). Similarly, the I. elegans Leuven population and the I. graellsii Seyhouse population from the allopatric distributions showed comparatively large and statistically significant genetic differences with several other populations (Supplementary Tables S10-S11).