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Neptune's dark spots are thought to occur in the troposphere at lower altitudes than the brighter cloud features, so they appear as holes in the upper cloud decks. As they are stable features that can persist for several months, they are thought to be vortex structures. Often associated with dark spots are brighter, persistent methane clouds that form around the tropopause layer. The persistence of companion clouds shows that some former dark spots may continue to exist as cyclones even though they are no longer visible as a dark feature. Dark spots may dissipate when they migrate too close to the equator or possibly through some other unknown mechanism.

What do Neptune's dark spots appear as in the cloud decks?
holes