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I like your final suggestion, John - that would make sense, but I seem to recall that Atta feed on the fungi they grow, rather than on prey items - unless the Philygria pupae have just been "tidied up" from upper regions of the nest? Most Philygria are found in drier habitats, away from water, but we do need more observations.
Johan - did you record the species of ant with which your Philygria was associated?