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Nucleation of GaN nanowires grown by plasma-assisted molecular beam epitaxy is studied through a combination of two in situ tools: grazing incidence x-ray diffraction and reflection high energy electron diffraction. Growth on bare Si(111) and on AlN/Si(111) is compared. A significantly larger delay at nucleation is observed for nanowires grown on bare Si(111). The difference in the nucleation delay is correlated to a dissimilarity of chemical reactivity between Al and Ga with nitrided Si(111).