Divergent selection as revealed by<i>P</i>_STand QTL‐based<i>F</i>_STin three‐spined stickleback (<i>Gasterosteus aculeatus</i>) populations along a coastal‐inland gradient

Abstract Three measures of divergence, estimated at nine putatively neutral microsatellite markers, 14 quantitative traits, and seven quantitative trait loci (QTL) were compared in eight populations of the three‐spined stickleback ( Gasterosteus aculeatus L.) living in the Scheldt river basin (Belgium). Lowland estuarine and polder populations were polymorphic for the number of lateral plates, whereas upland freshwater populations were low‐plated. The number of short gill rakers and the length of dorsal and pelvic spines gradually declined along a coastal‐inland gradient. Plate number, short gill rakers and spine length showed moderate to strong signals of divergent selection between lowland and upland populations in comparison between P ST (a phenotypic alternative for Q ST ) and neutral F ST . However, such comparisons rely on the unrealistic assumption that phenotypic variance equals additive genetic variance, and that nonadditive genetic effects and environmental effects can be minimized. In order to verify this assumption and to confirm the phenotypic signals of divergence, we tested for divergent selection at the underlying QTL. For plate number, strong genetic evidence for divergent selection between lowland and upland populations was obtained based on an intron marker of the Eda gene, of which the genotype was highly congruent with plate morph. Genetic evidence for divergent selection on short gill rakers was limited to some population pairs where F ST at only one of two QTL was detected as an outlier, although F ST at both loci correlated significantly with P ST . No genetic confirmation was obtained for divergent selection on dorsal spine length, as no outlier F ST s were detected at dorsal spine QTL, and no significant correlations with P ST were observed.