The oculomotor capture triggered by a peripheral onset is subject to habituation, a basic form of learning consisting in a response decrement toward a repeatedly presented stimulus. However, it is unclear whether habituation of reflexive saccades takes place at the saccadic programming or execution stage (or both). To address this issue, we exploited the fact that during fixation the programming of a reflexive saccade exerts a robust but short-lasting phasic inhibition in the absolute microsaccadic frequency. Hence, if habituation of reflexive saccades occurs at the programming stage, then this should also affect the microsaccadic frequency, with a progressive reduction of the inhibitory phase. Conversely, if habituation occurs only at the later stage of saccade execution, the no change in the microsaccadic pattern is expected. Participants were repeatedly exposed to a peripheral onset distractor, and when eye movements were allowed, we replicated the oculomotor capture habituation. Crucially, however, when fixation was maintained the microsaccadic response did not change as exposure to the onset progressed, suggesting that habituation of reflexive saccades does not take place at the programming stage in the superior colliculus (SC), but at the later stage of saccade execution in the brainstem, where the competition between different saccades might be resolved. This scenario challenges one of the main assumptions of the competitive integration model for oculomotor control, which assumes that competition between exogenous and endogenous saccade programs occurs in the (SC). Our results and interpretation are instead in agreement with neurophysiological studies in non-human primates showing that saccadic adaption, another form of oculomotor plasticity, takes place downstream from the SC.

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