We study Yukawa Renormalization Group (RG) running effects in the context of the Standard Model Effective Theory (SMEFT).The Yukawa running being flavour dependent leads to RG-induced off-diagonal entries, so that initially diagonal Yukawa matrices at the high scale have to be rediagonalized at the electroweak (EW) scale. Performing such flavour rotations can lead to flavour violating operators which differ from the ones obtained through SMEFT RG evolution. We show, that these flavour rotations can have a large impact on low-energy phenomenology. In order to demonstrate this effect, we compare the two sources of flavour violation numerically as well as analytically and study their influence on several examples of down-type flavour transitions. For this purpose we consider $B_s-bar B_s$ mixing, $bto sgamma$, $bto s ell ell$ as well as electroweak precision observables. We show that the rotation effect can be comparable or even larger than the contribution from pure RGE evolution of the Wilson coefficients.
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