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tl;dr Darwin didn't know the sea level goes up and down due to glaciers forming/melting
The article doesn't directly address it, but I wonder if there's any evidence for volcanoes contributing to atolls even if they aren't the primary driving force.
I was wondering the same. Evidence for this would be atolls having formed around volcanoes prior to the rapid fluctuations in sea level, but according to this article, at that time corals formed flat-topped reefs.

Decades ago, Hans Hass noticed that some atolls did not fit Darwin's model, and proposed that these formed because of better nutrient flow around the edges, but the prevalence of these flat-topped reefs suggests that is not the main story, either.

That's really fascinating, I wonder if it's even more complicated than even sea level changes and nutrient availability would suggest.
The original piece does address this. The gist is that the volcanic plateau underlying the carbonate platform influenced the early morphology of the platform (duh) but that its influence became "muted" once the plateau was entirely underwater. Volcanic activity is unlikely to be related beyond that initial effect.
This article would benefit tremendously from illustrations.
The paper The Origin of Modern Atolls: Challenging Darwin's Deeply Ingrained Theory [1]:

> In 1842, Darwin identified three types of reefs: fringing reefs, which are directly attached to volcanic islands; barrier reefs, which are separated from volcanic islands by lagoons; and ring reefs, which enclose only a lagoon and are defined as atolls. Moreover, he linked these reef types through an evolutionary model in which an atoll is the logical end point of a subsiding volcanic edifice, as he was unaware of Quaternary glaciations.

> Here, a comprehensive new model is proposed... During the multiple glacial sea-level lowstands that intensified throughout the Quaternary, the tops of these banks were karstified; then, during each of the five mid-to-late Brunhes deglaciations, coral reoccupied their raised margins and grew vertically, keeping up with sea-level rise and creating the modern atolls.

All coral atolls, therefore, were formed in the last 500,000 years with 100 ky glacial cycles and their associated 120m sea level change. Very cool.

Blue Holes like the one in Belize [2] are collapsed sinkholes created by the same mechanism.

[1] https://www.annualreviews.org/doi/10.1146/annurev-marine-122...

[2] https://en.wikipedia.org/wiki/Great_Blue_Hole

The way things are going, coral atolls will also become something from the past, albeit with photographs of their form and amazing biodiversity.